bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revisiting amino acid substitution matrices for identifying distantly related proteins
Authors: Yamada Kazunori , Tomii Kentaro 
Published: November 2013

Abstract
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

ABSTRACTFoxtail 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.
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.
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

AbstractSecreted 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

AbstractPost‐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

AbstractThe 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

SummaryAlthough 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

AbstractBackground and aimsMinimum 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.MethodsQualitative 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.ResultsAlcohol 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.ConclusionsIf 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

AbstractAimsTo 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).DesignCross‐sectional.SettingSydney, Australia.Participants and measurementsA total of 300 IDU were administered a structured interview examining the prevalence and severity of CPA and drug use histories.FindingsOf 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).ConclusionsSevere 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

SummaryBackgroundThere 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.AimTo provide information on alternative treatments for the management of these patients.MethodsA 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.ResultsSeveral 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.ConclusionThere 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

ObjectivesThe 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.MethodsA 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.ResultsThe 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.ConclusionsResults 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.
Zebrafish: A model vertebrate suitable for the analysis of human genetic disorders
Authors: Ota Satoshi , Kawahara Atsuo 
Published: November 2013

AbstractZebrafish 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

AbstractIntroductionThe 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.ObjectivesThe 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.MethodsFor 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.ResultsCompared 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.ConclusionsThe 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.