bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations
Authors: Kiryu Hisanori , Asai Kiyoshi 
Published: February 2012

Abstract
Motivation: Measuring the effects of base mutations is a powerful tool for functional and evolutionary analyses of RNA structures. To date, only a few methods have been developed for systematically computing the thermodynamic changes of RNA secondary structures in response to base mutations.
Results: We have developed algorithms for computing the changes of the ensemble free energy, mean energy and the thermodynamic entropy of RNA secondary structures for exhaustive patterns of single and double mutations. The computational complexities are O(NW 2) (where N is sequence length and W is maximal base pair span) for single mutations and O(N 2 W 2) for double mutations with large constant factors. We show that the changes are relatively insensitive to GC composition and the maximal span constraint. The mean free energy changes are bounded ~7−9 kcal/mol and depend only weakly on position if sequence lengths are sufficiently large. For tRNA sequences, the most stabilizing mutations come from the change of the 5′-most base of the anticodon loop. We also show that most of the base changes in the acceptor stem destabilize the structures, indicating that the nucleotide sequence in the acceptor stem is highly optimized for secondary structure stability. We investigate the 22 tRNA genes in the human mitochondrial genome and show that non-pathogenic polymorphisms tend to cause smaller changes in thermodynamic variables than generic mutations, suggesting that a mutation which largely increases thermodynamic variables has higher possibility to be a pathogenic or lethal mutation.
Availability and implementation: The C++ source code of the Rchange software is available at http://www.ncrna.org/software/rchange/
Contact: kiryu-h@k.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Water temperature and timing of capelin spawning determine seabird diets
Authors: Davoren Gail K. , Penton Paulette , Burke Chantelle , Montevecchi William A. 
Published: February 2012

Abstract
Davoren, G. K., Penton, P., Burke, C., and Montevecchi, W. A. 2012. Water temperature and timing of capelin spawning determine seabird diets. – ICES Journal of Marine Science, 69: . The capelin (Mallotus villosus) is the focal forage fish in many northern marine ecosystems. Its capacity to respond to changes in ocean climate is explored and the usefulness of seabird diets as indicators evaluated by integrating the timing of capelin spawning and temperature (0–150 m) during gonadal development (February–June) with colony-based measures of prey deliveries to chicks of common murres (Uria aalge) and northern gannets (Morus bassanus) on the east coast of Newfoundland during the years 1991–1993 and 2003–2010. Great variation was observed in the timing of spawning, with similar annual trends in different regions of coastal Newfoundland. Spawning was later in years of colder-than-average temperature, although the importance of other variables (e.g. fish size) could not be ruled out. The relationship between temperature during gonadal development and timing of spawning was weak at demersal spawning sites, suggesting that timing may be regulated by other factors (e.g. temperature at spawning sites). When spawning was early in warmer years relative to chick-rearing, common murres delivered a lower percentage of energy-rich gravid capelin to their chicks and northern gannets delivered a lower percentage of capelin. Integrating multiple data sources will be important to monitor marine ecosystem health as ocean climate changes.
Fishing intensity metrics for use in overfishing determination
Authors: Cordue P. L. 
Published: February 2012

Abstract
Cordue, P. L. 2012. Fishing intensity metrics for use in overfishing determination. – ICES Journal of Marine Science, 69: 615–623. The issue of constructing a technically correct fishing intensity metric from the output of a stock assessment model is considered. Four metrics of annual overall “fishing intensity” are defined. The metrics are applicable to age- or length-structured stock assessment models, which may, or may not, include complex spatial and temporal structure in the population and the fisheries. Two of the metrics are termed “direct” as they are calculated from the model output in the given year. Equivalent annual U is a number-based exploitation rate, and equivalent annual F is an average fishing mortality rate. The other two metrics, equilibrium stock depletion (ESD) and spawning potential ratio (SPR), measure fishing intensity in terms of the potential long-term effect on the stock (via 1–ESD and 1–SPR). The use of the metrics for overfishing determination is illustrated with a simple, spatial, two-fishery model. Summary statistics, which are sometimes used as a measure of fishing intensity, such as total catch over a reference biomass, or a number-weighted F are shown to be technically invalid for overfishing determination. The common approach, for virtual population analysis assessments, of using an average F over a specified age range is also discussed.
First Report of Stem Canker Disease of Pitaya (Hylocereus undatus and H. polyrhizus) Caused by Neoscytalidium dimidiatum in Taiwan
Authors: Chuang M. F. , Ni H. F. , Yang H. R. , Shu S. L. , Lai S. Y. , Jiang Y. L. 
Published: February 2012

Pitaya (Hylocereus undatus and H. polyrhizus Britt. & Rose), a perennial succulent plant grown in the tropics, is becoming an emerging and important fruit plant in Taiwan. In September of 2009 and 2010, a number of pitaya plants were found to have a distinctive canker on stems. The disease expanded quickly to most commercial planting areas in Taiwan (e.g., Pintung, Chiayi, and Chunghua). Symptoms on the stem were small, circular, sunken, orange spots that developed into cankers. Pycnidia were erumpent from the surface of the cankers and the stems subsequently rotted. After surface disinfestation with 0.1% sodium hypochloride, tissues adjacent to cankers were placed on acidified potato dextrose agar (PDA) and incubated at room temperature for 1 week, after which colonies with dark gray-to-black aerial mycelium grew. Hyphae were branched, septate, and brown and disarticulated into 0- to 1-septate arthrospores. Sporulation was induced by culturing on sterile horsetail tree (Casuarina equisetifolia) leaves. Conidia (12.79 ± 0.72 × 5.14 ± 0.30 μm) from pycnidia were one-celled, hyaline, and ovate. The internal transcribed spacer (ITS) region of ribosomal DNA was PCR amplified with primers ITS1 and ITS4 (2) and sequenced. The sequence (GenBank Accession No. HQ439174) showed 99% identity to Neoscytalidium dimidiatum (Penz.) Crous & Slippers (GenBank Accession No. GQ330903). On the basis of morphology and nucleotide-sequence identity, the isolates were identified as N. dimidiatum (1). Pathogenicity tests were conducted in two replicates by inoculating six surface-sterilized detached stems of pitaya with either mycelium or conidia. Mycelial plugs from 2-day-old cultures (incubated at 25°C under near UV) were inoculated to the detached stems after wounding with a sterile needle. Conidial suspensions (103 conidia/ml in 200 μl) were inoculated to nonwounded stems. Noninoculated controls were treated with sterile medium or water. Stems were then incubated in a plastic box at 100% relative humidity and darkness at 30°C for 2 days. The symptoms described above were observed on inoculated stems at 6 to 14 days postinoculation, whereas control stems did not develop any symptoms. N. dimidiatum was reisolated from symptomatic tissues. To our knowledge, this is the first report of N. dimidiatum causing stem canker of pitaya. References: (1) P. W. Crous et al. Stud. Mycol. 55:235, 2006. (2) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al., eds. Academic Press, New York, 1990.
The contractile system as a negative regulator of the connexin 43 hemichannel
Authors: Ponsaerts Raf , Wang Nan , Himpens Bernard , Leybaert Luc , Bultynck Geert 
Published: February 2012

AbstractThe molecular mechanisms underlying the regulation of gap junction (GJ) channels based on the 43‐kDa connexin isoform (Cx43) have been studied extensively. GJ channels are formed by the docking of opposed hemichannels in adjacent cells. Mounting data indicate that unopposed Cx43 hemichannels are also functional in the plasma membrane. However, our understanding of how Cx43‐hemichannel opening and closing is regulated at the molecular level is only poorly understood. Recent work elucidated that actomyosin contractility inhibits potently Cx43 hemichannels. It is known that intracellular Ca2+ exerts a bell‐shaped‐dependent effect on Cx43‐hemichannel opening. While low‐intracellular [Ca2+] (<500 nM) provokes opening of the channel, high‐intracellular [Ca2+] (> 500 nM) favours closing of the channel. The mechanism underlying this negative regulation of Cx43‐hemichannel activity by high‐intracellular [Ca2+] seems to be dependent on the activation of the actomyosin contractile system. The activity of Cx43 hemichannels is critically controlled by molecular interactions between the intracellular loop and the C‐terminal tail. These interactions are essential for Cx43‐hemichannel opening in response to triggers such as cytosolic [Ca2+] rise or external [Ca2+] lowering. In this review, we present the hypothesis that the actomyosin contractile system can function as an important brake mechanism on Cx43‐hemichannel opening. By controlling loop–tail interactions, the contractile system would prevent aberrant or excessive opening of Cx43 hemichannels.
Killer cell immunoglobulin‐like receptor gene polymorphisms predispose susceptibility to Epstein‐Barr virus associated hemophagocytic lymphohistiocytosis in Chinese children
Authors: Qiang Qin , Zhengde Xie , Chunyan Liu , Zhizhuo Huang , Junmei Xu , Junhong Ai , Zheng Chengyun , Henter Jan‐Inge , Kunling Shen 
Published: February 2012

ABSTRACTEpstein‐Barr virus associated hemophagocytic lymphohistiocytosis (EBV‐HLH) has a high mortality rate among children. The pathogenesis of, and underlying predisposing factors for, EBV‐HLH are as yet unclear; however, natural killer cells may play a key role in progression of the disease. This study attempted to determine whether killer cell immunoglobulin‐like receptor (KIR) gene polymorphisms are responsible for susceptibility to EBV‐HLH. Of the 125 children with EBV infection studied, 59 had EBV‐HLH and 66 patients had EBV associated infectious mononucleosis (IM) without HLH. The control group was 146 normal children without immune deficiency. KIR polymorphisms were determined by polymerase chain reaction with sequence‐specific primers. KIR polymorphism data were analyzed using the X2 test or Fisher's exact test. The overall observed carrier frequency (OF) of KIR2DS5 was significantly higher in EBV‐HLH patients than in IM patients and normal controls (49.2% versus 31.8%, P = 0.048; 49.2% versus 31.5%, P = 0.018, respectively), and the odds ratios (95% confidence interval) were 2.071 (1.001–4.286) and 2.101(1.132–3.900) respectively. The OF of KIR3DS1 was significantly higher in the EBV‐HLH patients than in the IM patients (47.4% versus 24.6%, P  =  0.012), but not different from normal controls. In summary, KIR polymorphisms may be involved in the development of EBV‐HLH, with KIR2DS5 promoting susceptibility to this disease. The obtained KIR data will enrich the understanding of genetic relationships among diseases associated with EBV infection in children.
Production and properties of lipase of Aeromonas sobria
Authors: Takahashi Eizo , Ito Hidenobu , Kobayashi Hidetomo , Yamanaka Hiroyasu , Takeda Yoshifumi , Balakrish Nair Gopinath , Arimoto Sakae , Negishi Tomoe , Okamoto Keinosuke 
Published: February 2012

ABSTRACT Aeromonas have been isolated from a wide variety of aquatic environments. However the number of Aeromonas in sea water is extremely small compared to that in fresh water. In in vitro culture, Aeromonas can grow in mediums containing NaCl at a concentration of 3.0%, this concentration corresponding to that of sea water. It is unclear why the number of Aeromonas is low in sea water. Exoproteins of bacteria are thought to be important for bacterial growth and survival in the environment. Previously, the present authors have shown that mediums containing 3.0% NaCl suppress production of two proteases, serine protease and metalloprotease. In this experiment, other exoproteins whose production is influenced by the amount of NaCl in the medium were analyzed. A protein whose production is repressed in medium containing 3.0% NaCl was found and purified. Biological assay of the purified protein showed that it degrades tributyrin and hydrolyzes para‐nitrophenyl‐fatty acylesters. These results show that the protein is a lipase. Subsequently, the nucleotide sequence of the gene encoding the lipase was determined and the amount of mRNA of the lipase gene in the cells measured. It was found that transcription of the gene is not inhibited by NaCl in the medium. This result indicates that the lipase might be synthesized, but the folding process to become an active structure does not progress smoothly in a medium containing 3.0% NaCl.
Inhibition of p53 transcriptional activity by human cytomegalovirus UL44
Authors: Kwon Yejin , Kim Mi‐Na , Young Choi Eun , Heon Kim Jung , Hwang Eung‐Soo , Cha Chang‐Yong 
Published: February 2012

ABSTRACTHuman cytomegalovirus (HCMV) stimulates cellular synthesis of DNA and proteins and induces transition of the cell cycle from G1 to S and G2/M phase, in spite of increased amounts of p53 in the infected cells. The immediate early protein IE2–86 kDa (IE86) tethers a transcriptional repression domain to p53; however, its repression of p53 function is not enough to abrogate the G1 checkpoint function of p53. Other HCMV proteins that suppress the activity of p53 were investigated in this study. Of the HCMV proteins that bind to p53 when assessed by immunoprecipitation and immunoblot analysis, HCMV UL44 was chosen as a candidate protein. It was found that reporter gene containing p53 consensus sequence was activated by transfection with wild type p53, but when plasmids of p53 with IE86 or UL44 were co‐transfected, p53 transcriptional activity was decreased to 3–7% of the p53 control in a dose‐dependent manner. When the deletion mutant of UL44 was co‐transected with p53, the carboxyl one‐third portion of UL44 had little effect on inhibition of p53 transcriptional activity. The amount of mRNA p21 was measured in H1299 by real time PCR after transfection of the combination of p53 and UL44 vectors and it was found that p21 transcription by p53 was inhibited dose‐dependently by UL44. Increased G0/G1 and decreased S phases in p53 wild type‐transfected H1299 cells were recovered to the level of p53 mutant type‐transfected ones by the additional transfection of UL44 in a dose‐dependent manner. In conclusion, the transcriptional activity of p53 is suppressed by UL44 as well as by IE86.
Iron deficiency affects plant defence responses and confers resistance to Dickeya dadantii and Botrytis cinerea
Authors: KIEU NAM PHUONG , AZNAR AUDE , SEGOND DIEGO , RIGAULT MARTINE , SIMOND‐CÔTE ELIZABETH , KUNZ CAROLINE , SOULIE MARIE‐CHRISTINE , EXPERT DOMINIQUE , DELLAGI ALIA 
Published: February 2012

SUMMARYIron is an essential element for most living organisms, and pathogens are likely to compete with their hosts for the acquisition of this element. The bacterial plant pathogen Dickeya dadantii has been shown to require its siderophore‐mediated iron uptake system for systemic disease progression on several host plants, including Arabidopsis thaliana. In this study, we investigated the effect of the iron status of Arabidopsis on the severity of disease caused by D. dadantii. We showed that symptom severity, bacterial fitness and the expression of bacterial pectate lyase‐encoding genes were reduced in iron‐deficient plants. Reduced symptoms correlated with enhanced expression of the salicylic acid defence plant marker gene PR1. However, levels of the ferritin coding transcript AtFER1, callose deposition and production of reactive oxygen species were reduced in iron‐deficient infected plants, ruling out the involvement of these defences in the limitation of disease caused by D. dadantii. Disease reduction in iron‐starved plants was also observed with the necrotrophic fungus Botrytis cinerea. Our data demonstrate that the plant nutritional iron status can control the outcome of an infection by acting on both the pathogen's virulence and the host's defence. In addition, iron nutrition strongly affects the disease caused by two soft rot‐causing plant pathogens with a large host range. Thus, it may be of interest to take into account the plant iron status when there is a need to control disease without compromising crop quality and yield in economically important plant species.
Fourth‐line rescue therapy with rifabutin in patients with three Helicobacter pylori eradication failures
Authors: Gisbert J. P. , Castro‐Fernandez M. , Perez‐Aisa A. , Cosme A. , Molina‐Infante J. , Rodrigo L. , Modolell I. , Cabriada J. L. , Gisbert J. L. , Lamas E. , Marcos E. , Calvet X. 
Published: February 2012

SummaryBackgroundIn some cases, Helicobacter pylori infection persists even after three eradication treatments.AimTo evaluate the efficacy of an empirical fourth‐line rescue regimen with rifabutin in patients with three eradication failures.MethodsDesign: Multicentre, prospective study. Patients: In whom the following three treatments had consecutively failed: first (PPI + clarithromycin + amoxicillin); second (PPI + bismuth + tetracycline + metronidazole); third (PPI + amoxicillin + levofloxacin). Intervention: A fourth regimen with rifabutin (150 mg b.d.), amoxicillin (1 g b.d.) and a PPI (standard dose b.d.) was prescribed for 10 days. Outcome: Eradication was confirmed by 13C‐urea breath test 4–8 weeks after therapy. Compliance and tolerance: Compliance was determined through questioning and recovery of empty medication envelopes. Adverse effects were evaluated using a questionnaire.ResultsOne‐hundred patients (mean age 50 years, 39% men, 31% peptic ulcer/69% functional dyspepsia) were included. Eight patients did not take the medication correctly (in six cases due to adverse effects). Per‐protocol and intention‐to‐treat eradication rates were 52% (95% CI = 41–63%) and 50% (40–60%). Adverse effects were reported in 30 (30%) patients: nausea/vomiting (13 patients), asthenia/anorexia (8), abdominal pain (7), diarrhoea (5), fever (4), metallic taste (4), myalgia (4), hypertransaminasemia (2), leucopenia (<1,500 neutrophils) (2), thrombopenia (<150 000 platelets) (2), headache (1) and aphthous stomatitis (1). Myelotoxicity resolved spontaneously in all cases.ConclusionsEven after three previous H. pylori eradication failures, an empirical fourth‐line rescue treatment with rifabutin may be effective in approximately 50% of the cases. Therefore, rifabutin‐based rescue therapy constitutes a valid strategy after multiple previous eradication failures with key antibiotics, such as clarithromycin, metronidazole, tetracycline and levofloxacin.
The effect of short time periods of pre‐operative warming in the prevention of peri‐operative hypothermia
Authors: Horn E.‐P. , Bein B. , Böhm R. , Steinfath M. , Sahili N. , Höcker J. 
Published: February 2012

SummaryThe aim of our study was to evaluate the performance of different durations of active pre‐operative skin‐surface warming (pre‐warming) to prevent peri‐operative hypothermia and postoperative shivering. We randomly assigned 200 patients, scheduled for surgery of 30–90 min under general anaesthesia, to receive passive insulation or forced‐air skin surface warming for 10, 20 or 30 min. Body temperature was measured at the tympanic membrane. Shivering was graded by visual inspection. There were significant differences in changes of core temperature between the non‐pre‐warmed group and all the pre‐warmed groups (p < 0.00001), but none between the three pre‐warmed groups (p = 0.54). Without pre‐warming, 38/55 (69%) patients became hypothermic (< 36 °C) at the end of anaesthesia, whereas only 7/52 (13%), 3/43 (7%) and 3/50 (6%) patients following 10, 20 or 30 min pre‐warming, respectively, became hypothermic (p < 0.001 vs no pre‐warming). Shivering was observed in 10 patients without, and in three, three and one patients with pre‐warming in the respective groups (p = 0.02). Pre‐warming of patients for only 10 or 20 min before general anaesthesia mostly prevents hypothermia and reduces shivering.
The role of statin therapy in the prevention of atrial fibrillation: a meta‐analysis of randomized controlled trials
Authors: Fang Wen‐tong , Li Hong‐jian , Zhang Haibo , Jiang Su 
Published: February 2012

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT• Atrial fibrillation (AF) is the most common clinically significant cardiac arrhythmia, and AF is associated with relatively higher all‐cause mortality in both men and women.• However, there are limited treatment options for AF.• Statins are hypothesized to have a benefit against arrhythmias in addition to well‐established secondary prevention benefit for atherosclerotic coronary artery disease, yet the data are inconsistentWHAT THIS STUDY ADDS• Statin therapy was significantly associated with a decreased risk of incidence or recurrence of AF.• The benefit of statin therapy seemed more markedly in secondary prevention than primary prevention.• These results provided some evidence for the benefit of statins beyond their lipid‐lowering activityAIMS The use of statins has been suggested to protect against atrial fibrillation (AF) in some clinical observational and experimental studies but has remained inadequately explored. This study was designed to examine whether statins can reduce the risk of AF.METHODS Meta‐analysis of randomized, controlled trials with use of statins on incidence or recurrence of AF was performed.RESULTS Twenty studies with 23 577 patients were included in the analysis. Seven studies investigated the use of statins in patients with AF, 11 studies investigated the primary prevention of statins in patients without AF, and two studies investigated mixed populations of patients. The incidence or recurrence of AF occurred in 1543 patients. Overall, statin therapy was significantly associated with a decreased risk of AF compared with control (odds ratio 0.49, 95% confidence interval 0.37–0.65; P < 0.00001). A beneficial effect was found in the atorvastatin subgroup and the simvastatin subgroup, but not in the pravastatin subgroup or the rosuvastatin subgroup. The benefit of statin therapy appeared to be more pronounced in secondary prevention (odds ratio 0.34, 95% confidence interval 0.18–0.64; P < 0.0008) than in primary prevention (odds ratio 0.54, 95% confidence interval 0.40–0.74; P < 0.0001).CONCLUSIONS Statin therapy was significantly associated with a decreased risk of incidence or recurrence of AF. Heterogeneity was explained by differences in statin types, patient populations and surgery types. The benefit of statin therapy seemed more pronounced in secondary than in primary prevention.