bluuebunny/crossref_metadata_2025 huggingface dataset:
Flexible analysis of RNA-seq data using mixed effects models
Authors: Turro Ernest , Astle William J. , Tavaré Simon
Published: November 2013

Motivation: Most methods for estimating differential expression from RNA-seq are based on statistics that compare normalized read counts between treatment classes. Unfortunately, reads are in general too short to be mapped unambiguously to features of interest, such as genes, isoforms or haplotype-specific isoforms. There are methods for estimating expression levels that account for this source of ambiguity. However, the uncertainty is not generally accounted for in downstream analysis of gene expression experiments. Moreover, at the individual transcript level, it can sometimes be too large to allow useful comparisons between treatment groups.

Results: In this article we make two proposals that improve the power, specificity and versatility of expression analysis using RNA-seq data. First, we present a Bayesian method for model selection that accounts for read mapping ambiguities using random effects. This polytomous model selection approach can be used to identify many interesting patterns of gene expression and is not confined to detecting differential expression between two groups. For illustration, we use our method to detect imprinting, different types of regulatory divergence in cis and in trans and differential isoform usage, but many other applications are possible. Second, we present a novel collapsing algorithm for grouping transcripts into inferential units that exploits the posterior correlation between transcript expression levels. The aggregate expression levels of these units can be estimated with useful levels of uncertainty. Our algorithm can improve the precision of expression estimates when uncertainty is large with only a small reduction in biological resolution.

Availability and implementation: We have implemented our software in the mmdiff and mmcollapse multithreaded C++ programs as part of the open-source MMSEQ package, available on https://github.com/eturro/mmseq.

Contact: et341@cam.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
mCSM: predicting the effects of mutations in proteins using graph-based signatures
Authors: Pires Douglas E. V. , Ascher David B. , Blundell Tom L.
Published: November 2013

Motivation: Mutations play fundamental roles in evolution by introducing diversity into genomes. Missense mutations in structural genes may become either selectively advantageous or disadvantageous to the organism by affecting protein stability and/or interfering with interactions between partners. Thus, the ability to predict the impact of mutations on protein stability and interactions is of significant value, particularly in understanding the effects of Mendelian and somatic mutations on the progression of disease. Here, we propose a novel approach to the study of missense mutations, called mCSM, which relies on graph-based signatures. These encode distance patterns between atoms and are used to represent the protein residue environment and to train predictive models. To understand the roles of mutations in disease, we have evaluated their impacts not only on protein stability but also on protein–protein and protein–nucleic acid interactions.

Results: We show that mCSM performs as well as or better than other methods that are used widely. The mCSM signatures were successfully used in different tasks demonstrating that the impact of a mutation can be correlated with the atomic-distance patterns surrounding an amino acid residue. We showed that mCSM can predict stability changes of a wide range of mutations occurring in the tumour suppressor protein p53, demonstrating the applicability of the proposed method in a challenging disease scenario.

Availability and implementation: A web server is available at http://structure.bioc.cam.ac.uk/mcsm.

Contact:  dpires@dcc.ufmg.br; tom@cryst.bioc.cam.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Revisiting amino acid substitution matrices for identifying distantly related proteins
Authors: Yamada Kazunori , Tomii Kentaro
Published: November 2013

Motivation: Although many amino acid substitution matrices have been developed, it has not been well understood which is the best for similarity searches, especially for remote homology detection. Therefore, we collected information related to existing matrices, condensed it and derived a novel matrix that can detect more remote homology than ever.

Results: Using principal component analysis with existing matrices and benchmarks, we developed a novel matrix, which we designate as MIQS. The detection performance of MIQS is validated and compared with that of existing general purpose matrices using SSEARCH with optimized gap penalties for each matrix. Results show that MIQS is able to detect more remote homology than the existing matrices on an independent dataset. In addition, the performance of our developed matrix was superior to that of CS-BLAST, which was a novel similarity search method with no amino acid matrix. We also evaluated the alignment quality of matrices and methods, which revealed that MIQS shows higher alignment sensitivity than that with the existing matrix series and CS-BLAST. Fundamentally, these results are expected to constitute good proof of the availability and/or importance of amino acid matrices in sequence analysis. Moreover, with our developed matrix, sophisticated similarity search methods such as sequence–profile and profile–profile comparison methods can be improved further.

Availability and implementation: Newly developed matrices and datasets used for this study are available at http://csas.cbrc.jp/Ssearch/.

Contact:  k-tomii@aist.go.jp

Supplementary information:  Supplementary data are available at Bioinformatics online
Aroma Stability of Millet Powder During Storage and Effects of Cooking Methods and Antioxidant Treatment
Authors: Wang Ruican , Chen Yijing , Ren Jianhua , Guo Shuntang
Published: November 2013

Foxtail millet is a cereal crop that contains high levels of unsaturated fatty acids, so that processed food such as instant millet powder is susceptible to lipid oxidation, which gradually leads to deteriorated flavor and quality. In this work, volatiles of millet powder samples with or without storage at room temperature for 12 months were extracted and analyzed by gas chromatography–olfactometry/mass spectrometry. In fresh steamed millet powder, hexanal, 2‐pentylfuran, and 3‐octen‐2‐one might be dominant odorants, whereas in deteriorated steamed millet powder, volatiles such as 1‐octen‐3‐ol, (E)‐2‐octen‐1‐ol, (E)‐2‐octenal, 3‐nonen‐2‐one, (E)‐2‐nonenal, decanal, 2‐undecanone, and 2‐methylnaphthalene emerged or increased over time, among which 1‐octen‐3‐ol and (E)‐2‐nonenal were highly responsible for its rancid flavor. We also compared millet powder prepared with two different processing methods, steaming and extrusion. Compared with steaming, extrusion was a cooking method of millet that helped slow the generation of oxidized flavor to some extent. When 0.04 g/kg (w/w millet) of ascorbyl palmitate was added as an antioxidant before drying, the production of unpleasant odorants was significantly inhibited, so that the quality of final products was improved. Analysis of odorants can be an alternative method for evaluating the storage stability of processed food.
Management ofMeloidogyne incognitawith Jesup (Max-Q) Tall Fescue Grass Prior to Peach Orchard Establishment
Authors: Nyczepir A. P. , Brannen P. M. , Cook J. , Meyer S. L. F.
Published: November 2013

The effects of two preplant Jesup (Max-Q) tall fescue (Schedonorus arundinaceus) ground cover treatments as alternatives to chemical control of Meloidogyne incognita were investigated from 2006 to 2013. The experiment was initiated in 2006 in a site known to be infested with M. incognita. Treatments included (i) 1 year of peach followed by 1 year of Jesup (Max-Q), (ii) 2 years of continuous Jesup (Max-Q), (iii) 2 years of continuous peach, and (iv) 2 years of continuous peach followed by fumigation with 1,3-dichloropropene (1,3-D). Both Jesup (Max-Q) treatments suppressed (P ≤ 0.05) population densities of M. incognita second-stage juveniles (J2) compared with the 2-year continuous peach treatments (prior to fumigation); no J2 were detected in soil samples taken from 2-year continuous Jesup (Max-Q) plots. Evaluation of the effects of the Jesup (Max-Q) treatments on subsequent peach tree planting was initiated in 2008, when herbicide was applied to the tall fescue treatment plots and half the continuous peach plots were fumigated with 1,3-D (nematicide treatment control). Peach trees were planted into all plots in 2009. By the end of the experiment (48 months after orchard establishment), trunk diameter was greater (P ≤ 0.01) in both of the Jesup (Max-Q) treatments and in the 1,3-D-fumigated treatment than in the nonfumigated treatment. Moreover, trunk diameter did not differ among the Jesup (Max-Q) and the fumigated treatments. Preplant Jesup (Max-Q) tall fescue was as effective as 1,3-D fumigation in increasing tree growth in an M. incognita-infested site.
First Report of Moroccan watermelon mosaic virus in Zucchini Crops in Greece
Authors: Malandraki I. , Vassilakos N. , Xanthis C. , Kontosfiris G. , Katis N. I. , Varveri C.
Published: November 2013

In the summer of 2012, zucchini (Cucurbita pepo L.) plants of F1 hybrid Rigas showing very severe malformation and blisters in leaves and fruit were observed in the prefectures of Ilia and Messinia, Peloponnese, southwestern Greece. Over 100 samples were collected and only a few were found by double antibody sandwich (DAS)-ELISA to be singly or mixed infected with the commonly encountered Cucumber mosaic virus (CMV, genus Cucumovirus), Zucchini yellow mosaic virus (ZYMV, genus Potyvirus), and Watermelon mosaic virus (WMV, genus Potyvirus), to which Rigas is known to be tolerant. All affected plants were also tested by DAS-ELISA and RT-PCR (2) for the presence of Moroccan watermelon mosaic virus (MWMV; genus Potyvirus), a virus not previously reported in Greece, and were consistently found positive by both methods. Sap from plants in which MWMV was solely detected was used to mechanically inoculate Chenopodium quinoa Willd. and cucurbit species (zucchini, cucumber, melon, and watermelon). C. quinoa produced chlorotic local lesions, while cucurbits showed very severe mosaic and malformation of leaves. Zucchini plants of F1 hybrids Rigas, Golden (tolerant to WMV and ZYMV), and Elion (not exhibiting any tolerance) grown in a screenhouse produced equivalent severe symptoms on leaves and fruits. Furthermore, transmission experiments in a non-persistent manner using a clone of Myzus persicae Sulz. and zucchini plants of F1 hybrid Boreas as donor and test plants were carried out. Ten plants were used in each experiment (one aphid/plant) and this was repeated five times (50 plants in total). The transmission rate was high ranging from 75 to 90%. RT-PCR obtained amplicons of 627 bp were subjected to direct sequencing (GenBank Accession No KF772944), which revealed 99% sequence identity to the corresponding region of a MWMV Tunisian isolate (EF579955). In 2013, in addition to zucchini plants found MWMV positive, watermelon (Citrullus lanatus Thunb.) plants from the same region of Peloponnese showing leaf malformation and mosaic symptoms were found MWMV positive (4/30) by DAS-ELISA and RT-PCR, revealing the virus establishment and further spread. In the Mediterranean basin, the virus has already been reported in Morocco, Italy, France, Spain, Tunisia, and Algeria, where it has emerged recently from a common source, has quickly become established through rapid dissemination and is considered as an important emerging threat (4). Isolates from these countries, including the present one from Greece, are very closely molecularly related to each other, contrary to isolates from sub-Saharan Africa (South Africa, Sudan, Congo, Zimbabwe, Niger, Cameroon, Nigeria) that are much more divergent (1,3). To our knowledge, this is the first report of MWMV in Greece.

References: (1) H. Lecoq et al. Plant Dis. 85:547, 2001. (2) H. Lecoq et al. New Dis. Rep. 16:19, 2007. (3) A. T. Owolabi et al. Int. J. Virol. 8:258, 2012. (4) S. Yakoubi et al. Arch. Virol. 153:775, 2008.
A century-long genetic record reveals that protist effective population sizes are comparable to those of macroscopic species
Authors: Watts Phillip C. , Lundholm Nina , Ribeiro Sofia , Ellegaard Marianne
Published: November 2013

Effective population size (Ne) determines the rate of genetic drift and the relative influence of selection over random genetic changes. While free-living protist populations characteristically consist of huge numbers of cells (N), the absence of any estimates of contemporaryNeraises the question whether protist effective population sizes are comparably large. Using microsatellite genotype data of strains derived from revived cysts of the marine dinoflagellatePentapharsodinium daleifrom sections of a sediment record that spanned some 100 years, we present the first estimates of contemporaryNefor a local population in a free-living protist. The estimates ofNeare relatively small, of the order of a few 100 individuals, and thus are similar in magnitude to values ofNereported for multicellular animals: the implications are thatNeofP. daleiis of many orders of magnitude lower than the number of cells present (Ne/N∼ 10−12) and that stochastic genetic processes may be more prevalent in protist populations than previously anticipated.
Proton transfer reactions and hydrogen-bond networks in protein environments
Authors: Ishikita Hiroshi , Saito Keisuke
Published: November 2013

In protein environments, proton transfer reactions occur along polar or charged residues and isolated water molecules. These species consist of H-bond networks that serve as proton transfer pathways; therefore, thorough understanding of H-bond energetics is essential when investigating proton transfer reactions in protein environments. When the pKavalues (or proton affinity) of the H-bond donor and acceptor moieties are equal, significantly short, symmetric H-bonds can be formed between the two, and proton transfer reactions can occur in an efficient manner. However, such short, symmetric H-bonds are not necessarily stable when they are situated near the protein bulk surface, because the condition of matching pKavalues is opposite to that required for the formation of strong salt bridges, which play a key role in protein–protein interactions. To satisfy the pKamatching condition and allow for proton transfer reactions, proteins often adjust the pKavia electron transfer reactions or H-bond pattern changes. In particular, when a symmetric H-bond is formed near the protein bulk surface as a result of one of these phenomena, its instability often results in breakage, leading to large changes in protein conformation.
Wavelet analysis in ecology and epidemiology: impact of statistical tests
Authors: Cazelles Bernard , Cazelles Kévin , Chavez Mario
Published: November 2013

Wavelet analysis is now frequently used to extract information from ecological and epidemiological time series. Statistical hypothesis tests are conducted on associated wavelet quantities to assess the likelihood that they are due to a random process. Such random processes represent null models and are generally based on synthetic data that share some statistical characteristics with the original time series. This allows the comparison of null statistics with those obtained from original time series. When creating synthetic datasets, different techniques of resampling result in different characteristics shared by the synthetic time series. Therefore, it becomes crucial to consider the impact of the resampling method on the results. We have addressed this point by comparing seven different statistical testing methods applied with different real and simulated data. Our results show that statistical assessment of periodic patterns is strongly affected by the choice of the resampling method, so two different resampling techniques could lead to two different conclusions about the same time series. Moreover, our results clearly show the inadequacy of resampling series generated by white noise and red noise that are nevertheless the methods currently used in the wide majority of wavelets applications. Our results highlight that the characteristics of a time series, namely its Fourier spectrum and autocorrelation, are important to consider when choosing the resampling technique. Results suggest that data-driven resampling methods should be used such as the hidden Markov model algorithm and the ‘beta-surrogate’ method.
Fish responses to flow velocity and turbulence in relation to size, sex and parasite load
Authors: Hockley F. A. , Wilson C. A. M. E. , Brew A. , Cable J.
Published: November 2013

Riverine fish are subjected to heterogeneous flow velocities and turbulence and may use this to their advantage by selecting regions that balance energy expenditure for station holding while maximizing energy gain through feeding opportunities. This study investigated microhabitat selection by guppiesPoecilia reticulatain terms of flow characteristics generated by hemisphere boulders in an open channel flume. Velocity and turbulence influenced the variation in swimming behaviour with respect to size, sex and parasite intensity. With increasing body length, fish swam further and more frequently between boulder regions. Larger guppies spent more time in the areas of high-velocity and low-turbulence regions beside the boulders, whereas smaller guppies frequented the low-velocity and high-turbulence regions directly behind the boulders. Male guppies selected the regions of low velocity, indicating possible reduced swimming ability owing to hydrodynamic drag imposed by their fins. With increasingGyrodactylus turnbulliburden, fish spent more time in regions with moderate velocity and lowest turbulent kinetic energy which were the most spatially and temporally homogeneous in terms of velocity and turbulence. These findings highlight the importance of heterogeneous flow conditions in river channel design owing to the behavioural variability within a species in response to velocity and turbulence.
Optimal indolence: a normative microscopic approach to work and leisure
Authors: Niyogi Ritwik K. , Breton Yannick-Andre , Solomon Rebecca B. , Conover Kent , Shizgal Peter , Dayan Peter
Published: November 2013

Dividing limited time between work and leisure when both have their attractions is a common everyday decision. We provide a normative control-theoretic treatment of this decision that bridges economic and psychological accounts. We show how our framework applies to free-operant behavioural experiments in which subjects are required to work (depressing a lever) for sufficient total time (called the price) to receive a reward. When the microscopic benefit-of-leisure increases nonlinearly with duration, the model generates behaviour that qualitatively matches various microfeatures of subjects’ choices, including the distribution of leisure bout durations as a function of the pay-off. We relate our model to traditional accounts by deriving macroscopic, molar, quantities from microscopic choices.
From Down House to Avebury: John Lubbock, prehistory and human evolution through the eyes of his collection
Authors: Owen Janet
Published: November 2013

When Sir John Lubbock died in May 1913, his estate included a seemingly eclectic assortment of prehistoric stone tools and ethnographic artefacts displayed on the walls of his home at High Elms and hidden away in storage. However, detailed analysis of the history of this collection reveals a fascinating story of a man inspired by Darwin and like-minded evolutionary thinkers, who became one of the most important intellectuals in Victorian Britain to examine the controversial subject of human evolution. Six acquisitions are used in this article to explore how Lubbock began as Darwin's friend and scientific apprentice and became an international champion for the study of prehistory and the protection of prehistoric ancient monuments.
Experimental evidence for friction-enhancing integumentary modifications of chameleons and associated functional and evolutionary implications
Authors: Khannoon Eraqi R. , Endlein Thomas , Russell Anthony P. , Autumn Kellar
Published: November 2013

The striking morphological convergence of hair-like integumentary derivatives of lizards and arthropods (spiders and insects) demonstrates the importance of such features for enhancing purchase on the locomotor substrate. These pilose structures are responsible for the unique tractive abilities of these groups of animals, enabling them to move with seeming ease on overhanging and inverted surfaces, and to traverse inclined smooth substrates. Three groups of lizards are well known for bearing adhesion-promoting setae on their digits: geckos, anoles and skinks. Similar features are also found on the ventral subdigital and distal caudal skin of chameleons. These have only recently been described in any detail, and structurally and functionally are much less well understood than are the setae of geckos and anoles. The seta-like structures of chameleons are not branched (a characteristic of many geckos), nor do they terminate in spatulate tips (which is characteristic of geckos, anoles and skinks). They are densely packed and have attenuated blunt, globose tips or broad, blade-like shafts that are flattened for much of their length. Using a force transducer, we tested the hypothesis that these structures enhance friction and demonstrate that the pilose skin has a greater frictional coefficient than does the smooth skin of these animals. Our results are consistent with friction being generated as a result of side contact of the integumentary filaments. We discuss the evolutionary and functional implications of these seta-like structures in comparison with those typical of other lizard groups and with the properties of seta-mimicking synthetic structures.
Increased brain size in mammals is associated with size variations in gene families with cell signalling, chemotaxis and immune-related functions
Authors: Castillo-Morales Atahualpa , Monzón-Sandoval Jimena , Urrutia Araxi O. , Gutiérrez Humberto
Published: November 2013

Genomic determinants underlying increased encephalization across mammalian lineages are unknown. Whole genome comparisons have revealed large and frequent changes in the size of gene families, and it has been proposed that these variations could play a major role in shaping morphological and physiological differences among species. Using a genome-wide comparative approach, we examined changes in gene family size (GFS) and degree of encephalization in 39 fully sequenced mammalian species and found a significant over-representation of GFS variations in line with increased encephalization in mammals. We found that this relationship is not accounted for by known correlates of brain size such as maximum lifespan or body size and is not explained by phylogenetic relatedness. Genes involved in chemotaxis, immune regulation and cell signalling-related functions are significantly over-represented among those gene families most highly correlated with encephalization. Genes within these families are prominently expressed in the human brain, particularly the cortex, and organized in co-expression modules that display distinct temporal patterns of expression in the developing cortex. Our results suggest that changes in GFS associated with encephalization represent an evolutionary response to the specific functional requirements underlying increased brain size in mammals.
Endoplasmic Reticulum Glucosidases and Protein Quality Control Factors Cooperate to Establish Biotrophy inUstilago maydis
Authors: Fernández-Álvarez Alfonso , Elías-Villalobos Alberto , Jiménez-Martín Alberto , Marín-Menguiano Miriam , Ibeas José I.
Published: November 2013

Secreted fungal effectors mediate plant–fungus pathogenic interactions. These proteins are typically N-glycosylated, a common posttranslational modification affecting their location and function. N-glycosylation consists of the addition, and subsequent maturation, of an oligosaccharide core in the endoplasmic reticulum (ER) and Golgi apparatus. In this article, we show that two enzymes catalyzing specific stages of this pathway in maize smut (Ustilago maydis), glucosidase I (Gls1) and glucosidase II β-subunit (Gas2), are essential for its pathogenic interaction with maize (Zea mays). Gls1 is required for the initial stages of infection following appressorium penetration, and Gas2 is required for efficient fungal spreading inside infected tissues. While U. maydis Δgls1 cells induce strong plant defense responses, Δgas2 hyphae are able to repress them, showing that slight differences in the N-glycoprotein processing can determine the extent of plant–fungus interactions. Interestingly, the calnexin protein, a central element of the ER quality control system for N-glycoproteins in eukaryotic cells, is essential for avoiding plant defense responses in cells with defective N-glycoproteins processing. Thus, N-glycoprotein maturation and this conserved checkpoint appear to play an important role in the establishment of an initial biotrophic state with the plant, which allows subsequent colonization.
Scanning transmission X-ray microscopy probe forin situmechanism study of graphene-oxide-based resistive random access memory
Authors: Nho Hyun Woo , Kim Jong Yun , Wang Jian , Shin Hyun-Joon , Choi Sung-Yool , Yoon Tae Hyun
Published: November 2013

Here, anin situprobe for scanning transmission X-ray microscopy (STXM) has been developed and applied to the study of the bipolar resistive switching (BRS) mechanism in an Al/graphene oxide (GO)/Al resistive random access memory (RRAM) device. To performin situSTXM studies at the CK- and OK-edges, both the RRAM junctions and theI0junction were fabricated on a single Si3N4membrane to obtain local XANES spectra at these absorption edges with more delicateI0normalization. Using this probe combined with the synchrotron-based STXM technique, it was possible to observe unique chemical changes involved in the BRS process of the Al/GO/Al RRAM device. Reversible oxidation and reduction of GO induced by the externally applied bias voltages were observed at the OK-edge XANES feature located at 538.2 eV, which strongly supported the oxygen ion drift model that was recently proposed fromex situtransmission electron microscope studies.
RNA interference‐mediated silencing of a Halloween gene spookier affects nymph performance in the small brown planthopper Laodelphax striatellus
Authors: Jia Shuang , Wan Pin‐Jun , Zhou Li‐Tao , Mu Li‐Li , Li Guo‐Qing
Published: November 2013

Post‐embryonic development of insects is highly dependent on ecdysteroid hormone 20‐hydroxyecdysone. Halloween gene spookier (spok, cyp307a2) has been documented to be involved in ecdysteroidogenesis in Drosophila melanogaster and Bombyx mori. We describe here the cloning and characterization of Halloween gene spookier (Lsspok, Lscyp307a2) in the small brown planthopper Laodelphax striatellus, a hemipteran insect species. LsSPOK has three insect‐conserved P450 motifs, that is, Helix‐K, PERF motif and heme‐binding domain. Temporal and spatial expression patterns of Lsspok were evaluated by quantitative polymerase chain reaction. Through the fouth‐instar and the early fifth‐instar stages, Lsspok showed two expression peaks in the second‐ and fifth‐day fourth‐instar nymphs, and two troughs in the first‐day fourth and fifth instars. On day 5 of the fourth‐instar nymphs, Lsspok clearly had a high transcript level in the thorax where prothoracic glands were located. Dietary introduction of double‐stranded RNA of Lsspok in the nymph stage successfully knocked down the target gene, decreased expression level of ecdysone receptor (LsEcR) gene, caused nymphal lethality and delayed development. Ingestion of 20‐hydroxyecdysone in Lsspok‐dsRNA‐exposed nymphs did not increase Lsspok expression level, but almost completely rescued the LsEcR mRNA level and relieved the negative effects on survival and development. Thus, our data suggest that the ecdysteroidogenic pathway is conserved in insects and LsSPOK is responsible for specific steps in ecdysteroidogenesis in L. striatellus.
Apple, Carrot, and Hibiscus Edible Films Containing the Plant Antimicrobials Carvacrol and Cinnamaldehyde Inactivate Salmonella Newport on Organic Leafy Greens in Sealed Plastic Bags
Authors: Zhu Libin , Olsen Carl , McHugh Tara , Friedman Mendel , Jaroni Divya , Ravishankar Sadhana
Published: November 2013

The objective of this study was to investigate the antimicrobial effects of carvacrol and cinnamaldehyde incorporated into apple, carrot, and hibiscus‐based edible films against Salmonella Newport in bagged organic leafy greens. The leafy greens tested included organic Romaine and Iceberg lettuce, and mature and baby spinach. Each leafy green sample was washed, dip inoculated with S. Newport (107 CFU/mL), and dried. Each sample was put into a Ziploc® bag. Edible films pieces were put into the Ziploc bag and mixed well. The bags were sealed and stored at 4 °C. Samples were taken at days 0, 3, and 7 for enumeration of survivors. On all leafy greens, 3% carvacrol films showed the best bactericidal effects against Salmonella. All 3 types of 3% carvacrol films reduced the Salmonella population by 5 log10 CFU/g at day 0 and 1.5% carvacrol films reduced Salmonella by 1 to 4 log10 CFU/g at day 7. The films with 3% cinnamaldehyde showed 0.5 to 3 log reductions on different leafy greens at day 7. The films with 0.5% and 1.5% cinnamaldehyde and 0.5% carvacrol also showed varied reductions on different types of leafy greens. Edible films were the most effective against Salmonella on Iceberg lettuce. This study demonstrates the potential of edible films incorporated with carvacrol and cinnamaldehyde to inactivate S. Newport on organic leafy greens.
Spore formation inBacillus subtilis
Authors: Tan Irene S. , Ramamurthi Kumaran S.
Published: November 2013

Although prokaryotes ordinarily undergo binary fission to produce two identical daughter cells, some are able to undergo alternative developmental pathways that produce daughter cells of distinct cell morphology and fate. One such example is a developmental programme called sporulation in the bacteriumBacillus subtilis, which occurs under conditions of environmental stress. Sporulation has long been used as a model system to help elucidate basic processes of developmental biology including transcription regulation, intercellular signalling, membrane remodelling, protein localization and cell fate determination. This review highlights some of the recent work that has been done to further understand prokaryotic cell differentiation during sporulation and its potential applications.
Harms to ‘others’ from alcohol consumption in the minimum unit pricing policy debate: a qualitative content analysis of UK newspapers (2005–12)
Authors: Wood Karen , Patterson Chris , Katikireddi Srinivasa Vittal , Hilton Shona
Published: November 2013

Background and aims

Minimum unit pricing is a fiscal intervention intended to tackle the social and health harms from alcohol to individual drinkers and wider society. This paper presents the first large‐scale qualitative examination of how newsprint media framed the debate around the harms of alcohol consumption to ‘others’ during the development and passing of minimum unit pricing legislation in Scotland.

Methods

Qualitative content analysis was conducted on seven UK and three Scottish national newspapers between 1 January 2005 and 30 June 2012. Relevant articles were identified using the electronic databases Nexis UK and Newsbank. A total of 403 articles focused on the harms of alcohol consumption to ‘others’ and were eligible for detailed coding and analysis.

Results

Alcohol harms to wider society and communities were identified as being a worsening issue increasingly affecting everyone through shared economic costs, social disorder, crime and violence. The availability of cheap alcohol was blamed, alongside a minority of ‘problem’ youth binge drinkers. The harm caused to families was less widely reported.

Conclusions

If news reporting encourages the public to perceive the harms caused by alcohol to wider society as having reached crisis point, a population‐based intervention may be deemed necessary and acceptable. However, the current focus in news reports on youth binge drinkers may be masking the wider issue of overconsumption across the broader population.
The association of childhood physical abuse with the onset and extent of drug use among regular injecting drug users
Authors: Darke Shane , Torok Michelle
Published: November 2013

Aims

To determine whether childhood physical abuse (CPA) histories were associated with age of onset of psychoactive substance use and injecting, and the extent of polydrug use among injecting drug users (IDU).

Design

Cross‐sectional.

Setting

Sydney, Australia.

Participants and measurements

A total of 300 IDU were administered a structured interview examining the prevalence and severity of CPA and drug use histories.

Findings

Of the participants, 40.3% had experienced severe abuse (SA), 34.0% mild–moderate abuse (MMA) and 25.7% no abuse history (NA). After controlling for other variables, a history of severe CPA was a significant independent correlate of an earlier age at first alcohol intoxication compared to both the NA (β = −0.23, P < 0.01) and MMA (β = 0.20, P < 0.01) groups. Severe CPA was also a significant independent correlate of an earlier age at first illicit drug use compared to both the NA (β = −0.16, P < 0.05) and MMA (β = −0.15, P < 0.05) groups. In contrast, CPA histories were not independently associated with the onset of injecting drug use. After controlling for potential confounders, both the MMA (β = 0.28, P < 0.001) and SA (β = 0.27, P < 0.001) groups were associated with more extensive life‐time polydrug use, but did not differ from each other (P = 0.82). After controlling for potential confounders, both MMA (β = 0.20, P < 0.01) and SA (β = 0.33, P < 0.001) group membership were associated with more extensive recent polydrug use but, again, did not differ significantly from each other (P = 0.08).

Conclusions

Severe childhood physical abuse severity is associated with an earlier initiation into drug use. Any level of abuse is associated with more extensive life‐time and recent polydrug use.
Review article: management of chronic hepatitis C in patients with contraindications to anti‐viral therapy
Authors: Carreño V.
Published: November 2013

Background

There are patients with chronic hepatitis C who are not eligible for the current interferon‐based therapies or refuse to be treated due to secondary effects.

Aim

To provide information on alternative treatments for the management of these patients.

Methods

A PubMed search was performed to identify relevant literature. Search terms included hepatitis C virus, anti‐inflammatory treatment, antioxidant, natural products and alternative treatment, alone or in combination. Additional publications were identified using the references cited by primary and review articles.

Results

Several approaches, such as iron depletion (phlebotomy), treatment with ursodeoxycholic acid or glycyrrhizin, have anti‐inflammatory and/or anti‐fibrotic effects. Life interventions like weight loss, exercise and coffee consumption are associated with a biochemical improvement. Other alternatives (ribavirin monotherapy, amantadine, silibinin, vitamin supplementation, etc.) do not have any beneficial effect or need to be tested in larger clinical studies.

Conclusion

There are therapeutic strategies and lifestyle interventions that can be used to improve liver damage in patients with chronic hepatitis C who cannot receive or refuse interferon‐based treatments.
The impact of being newly diagnosed with a bipolar disorder and the short‐term outcome of disorder‐specific management
Authors: Parker Gordon B , Graham Rebecca K , Fletcher Kathryn , Futeran Shulamit M , Friend Paul
Published: November 2013

Objectives

The aim of the study was to determine the impact of a first‐time diagnosis of bipolar disorder in patients previously generally managed as having a unipolar disorder, and to quantify the impact of disorder‐specific management strategies for such newly diagnosed patients over the following three months.

Methods

A total of 157 patients receiving a diagnosis of bipolar disorder for the first time by a psychiatrist at a specialist depression clinic completed a research interview and questionnaires, with 106 (68%) also completing 12‐week quantitative and qualitative evaluations. Assessing psychiatrists undertook baseline and follow‐up assessments recording management changes, reactions to the diagnosis and global changes in functioning over time.

Results

The majority of patients had a positive response to receiving a diagnosis of bipolar disorder, and most implemented a number of clinician‐suggested bipolar management strategies. Patients showed improvement on five of the six self‐report measures over the three‐month study period. Multivariate analyses quantified lamotrigine as making the most distinctive contribution to ‘improver’ status, particularly for the bipolar II disorder subset.

Conclusions

Results are encouraging in identifying a generally positive acceptance of a diagnosis of bipolar disorder, improved outcome following the introduction of diagnostic‐specific management components, and a distinctive contribution of lamotrigine to improved three‐month outcome.
MicroRNA‐148a is downregulated in gastric cancer, targets MMP7, and indicates tumor invasiveness and poor prognosis
Authors: Sakamoto Naoya , Naito Yutaka , Oue Naohide , Sentani Kazuhiro , Uraoka Naohiro , Oo Htoo Zarni , Yanagihara Kazuyoshi , Aoyagi Kazuhiko , Sasaki Hiroki , Yasui Wataru
Published: November 2013

Gastric cancer (GC) develops through deregulation of gene expression and accumulation of epigenetic abnormalities, leading to tumor cell acquisition of malignant features. MicroRNAs (miRNAs) play a critical role in cancer development where they can act as oncogenes or oncosuppressors. To identify miRNAs that are associated with some clinicopathologic features of GC and/or participate in tumor progression, miRNA expression in 20 GC tissues and five corresponding non‐neoplastic gastric mucosa was examined by miRNA microarray. Oligonucleotide array analysis was carried out for miRNA target prediction. The functions of candidate miRNAs and their target genes were also analyzed by quantitative RT‐PCR, Western blotting, reporter gene assay, and cell invasion assay. Comparison of miRNA expression profiles revealed that downregulation of miR‐148a was identified in most of the GC tissues. Downregulation of miR‐148a was significantly correlated with an advanced clinical stage, lymph node metastasis, and poor clinical outcome. Custom oligonucleotide array analysis revealed that MMP7 expression was markedly downregulated in miR‐148a‐overexpressing GC cells; MMP7 was found to be a direct and functional target of miR‐148a, participating in cell invasion. These results suggest that miR‐148a contributes to the maintenance of homeostasis in normal stomach tissue and plays an important role in GC invasion by regulating MMP7 expression.
Zebrafish: A model vertebrate suitable for the analysis of human genetic disorders
Authors: Ota Satoshi , Kawahara Atsuo
Published: November 2013

Zebrafish is a popular model vertebrate because of its conservation of a significant number of morphological and physiological processes in vertebrate organogenesis. A number of zebrafish mutants isolated from chemical mutagenesis screens exhibit characterized morphological defects that often resemble the symptoms of human genetic disorders. Recent innovations in genome‐editing technologies, such as transcription activator‐like effector nucleases (TALEN) and the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, enable us to investigate the loss‐of‐function phenotypes of developmentally regulated genes in zebrafish. This review highlights recent advances in reverse genetic technologies for zebrafish and presents possible applications of zebrafish for the study of human genetic disorders.
The effect of rehabilitation on health‐care utilisation in COPD patients in Copenhagen
Authors: Jacobsen Ramune , Rusch Ea , Andersen Per Kragh , Adams John , Jensen Cecilia Ravn , Frølich Anne
Published: November 2013

Introduction

The Integrated Rehabilitation Programme for Chronic Conditions project (SIKS) implemented rehabilitation programmes for people with four chronic conditions in the local area within the Municipality of Copenhagen.

Objectives

The objective of this study was to evaluate the impact of rehabilitation on health‐care utilisation in chronic obstructive pulmonary disease (COPD) patients as a subgroup of SIKS.

Methods

For the analyses, data from Danish National Registers' were obtained. The following outcomes were analysed: (i) COPD hospital admissions, (ii) COPD bed days, (iii) COPD outpatient visits, (iv) COPD emergency room visits, (v) general practitioner visits, (vi) specialist visits, and (vii) COPD specific medication. The rehabilitation group consisted of 118 patients who completed the programme. The control group consisted of 236 COPD patients in Copenhagen who did not undergo rehabilitation and were matched with the intervention group according to propensity score calculated on the basis of patient socio‐demographic characteristics and health‐care utilisation pattern in 2 years prior to the rehabilitation programme. The effect was assessed by applying the principle of difference‐in‐difference analysis.

Results

Compared with their matched controls, the patients participating in the rehabilitation programme showed a statistically significantly smaller increase in hospital admissions, bed days and outpatient visits.

Conclusions

The study provides the policy decision makers in the Municipality of Copenhagen with an assessment of the effect of a real‐life intervention. It shows that the pulmonary rehabilitation programme introduced had the anticipated effects on health‐care utilisation. The study also suggests that the methods used for evaluation were appropriate.
Yellow nail syndrome presenting with postpartum massive pleural effusion
Authors: Günbatar Hülya , Sertogullarindan Bunyamin , Ekin Selami , Arisoy Ahmet , Özkol Hatice Uce
Published: November 2013

Yellow nail syndrome (YNS) is an uncommon clinical syndrome characterized by yellow‐green discoloration of nails and recurrent respiratory tract lesions, pleural effusions and lymphedema.

A 38‐year‐old woman was referred to the emergency complaining of chronic cough and increasing dyspnea within last 2 weeks. She had given birth 1 month ago. On examination, the patient exhibited dystrophic yellowish nails and mild peripheral lymphedema. A chest roentgenogram revealed a large right pleural effusion and a small left pleural effusion.

YNS is a rare clinical entity but should be taken into consideration in patients with massive pleural effusions and persistent lymphedemas on the postpartum period.
Gender differences revealed by the Brief Illness Perception Questionnaire in allergic rhinitis
Authors: Pesut Dragica , Raskovic Sanvila , Tomic‐Spiric Vesna , Bulajic Milica , Bogic Mirjana , Bursuc Bogdana , Peric‐Popadic Aleksandra
Published: November 2013

Background

The increasing prevalence of allergic rhinitis (AR) is reported worldwide. Illness perception (IP) assessment is warranted in current routine clinical practice to assist communication between patients and medical staff, and improve adherence to treatment and disease outcome.

Objective

To investigate a group of patients with AR in terms of their IP by the Brief Illness Perception Questionnaire (BIPQ) and to correlate the findings with demographic and clinical features.

Methods

In this observational questionnaire‐based study, a successive series of patients treated for AR at the Allergology and Immunology Teaching Hospital, Clinical Centre of Serbia in Belgrade, were enrolled from September 2010 to January 2011, and 93 valid questionnaires were analyzed. Each item of the BIPQ assessed one dimension of IP like the consequences, timeline, personal control, treatment control, identity, coherence, emotional representation and concern.

Results

The patients' average age: 35.25 ± 12.42; male/female ratio: 0.79; the overall BIPQ score = 34.69 ± 11.89. The highest item‐related scores were found for treatment control (8.17 ± 2.28), illness understanding (7.34 ± 2.96) and emotional representation (6.30 ± 3.45), and the lowest for identity (4.8 ± 2.78) and affection (4.83 ± 2.65). Women compared with men perceive AR as a significantly more threatening disease (P = 0.04). No significant correlation between the BIPQ total or item‐related scores was found for any other demographic or clinical feature.

Conclusion

The BIPQ, which allows rapid assessment of IP and reveals gender differences in AR, is a convenient tool for use in routine clinical practice. Further investigation is needed to demonstrate how IP may influence patients' behavior in AR, treatment adherence and disease outcome.
Parietal blood oxygenation level‐dependent response evoked by covert visual search reflects set‐size effect in monkeys
Authors: Atabaki A. , Marciniak K. , Dicke P. W. , Karnath H.‐O. , Thier P.
Published: November 2013

Distinguishing a target from distractors during visual search is crucial for goal‐directed behaviour. The more distractors that are presented with the target, the larger is the subject's error rate. This observation defines the set‐size effect in visual search. Neurons in areas related to attention and eye movements, like the lateral intraparietal area (LIP) and frontal eye field (FEF), diminish their firing rates when the number of distractors increases, in line with the behavioural set‐size effect. Furthermore, human imaging studies that have tried to delineate cortical areas modulating their blood oxygenation level‐dependent (BOLD) response with set size have yielded contradictory results. In order to test whether BOLD imaging of the rhesus monkey cortex yields results consistent with the electrophysiological findings and, moreover, to clarify if additional other cortical regions beyond the two hitherto implicated are involved in this process, we studied monkeys while performing a covert visual search task. When varying the number of distractors in the search task, we observed a monotonic increase in error rates when search time was kept constant as was expected if monkeys resorted to a serial search strategy. Visual search consistently evoked robust BOLD activity in the monkey FEF and a region in the intraparietal sulcus in its lateral and middle part, probably involving area LIP. Whereas the BOLD response in the FEF did not depend on set size, the LIP signal increased in parallel with set size. These results demonstrate the virtue of BOLD imaging in monkeys when trying to delineate cortical areas underlying a cognitive process like visual search. However, they also demonstrate the caution needed when inferring neural activity from BOLD activity.