bluuebunny/crossref_metadata_2025 huggingface dataset:
Gauge invariant atomic orbital‐density functional theory prediction of accurate gas phase 1H and 13C NMR chemical shifts
Authors: Ebrahimi Hossein Pasha , Shaghaghi Hoora , Tafazzoli Mohsen
Published: November 2011

Hartree‐Fock and density functional theory methods at gauge invariant atomic orbital approach with different simplest basis sets were employed for the computation of chemical shifts. The wave functions for calculating gas‐phase 1H and 13C chemical shifts have been optimally selected using empirical models. The effects of electron correlation treatment, triple‐ξ valance shell, diffuse function, and polarization function on calculated chemical shifts have been discussed. Through empirical scaling of shielding, accurate predictions of 1H chemical shifts are achieved for the molecules studied, when considering small Pople basis sets. Gas phase experimental 1H chemical shifts in alcohols, amines and hydrocarbons were used to examine the theoretical optimal levels for obtaining the 1H chemical shift. In addition, this model has been used for 13C chemical shifts of gaseous hydrocarbons in relation to two different references. Furthermore, to assess the reliability of applied model for selection the most efficient wave function and calculation method two 24 factorial designs were considered and the results were discussed in this procedure. © 2011 Wiley Periodicals, Inc. Concepts Magn Reson Part A 38: 269–279, 2011
Transient expression of Ngn3 in Xenopus endoderm promotes early and ectopic development of pancreatic beta and delta cells
Authors: Oropez Daniel , Horb Marko
Published: November 2011

Promoting ectopic development of pancreatic beta cells from other cell types is one of the strategies being pursued for the treatment of diabetes. To achieve this, a detailed outline of the molecular lineage that operates in pancreatic progenitor cells to generate beta cells over other endocrine cell types is necessary. Here, we demonstrate that early transient expression of the endocrine progenitor bHLH protein Neurogenin 3 (Ngn3) favors the promotion of pancreatic beta and delta cell fates over an alpha cell fate, while later transient expression promotes ectopic development of all three endocrine cell fates. We found that short‐term activation of Ngn3 in Xenopus laevis endoderm just after gastrulation was sufficient to promote both early and ectopic development of beta and delta cells. By examining gene expression changes 4 h after Ngn3 activation we identified several new downstream targets of Ngn3. We show that several of these are required for the promotion of ectopic beta cells by Ngn3 as well as for normal beta cell development. These results provide new detail regarding the Ngn3 transcriptional network operating in endocrine progenitor cells to specify a beta cell phenotype and should help define new approaches to promote ectopic development of beta cells for diabetes therapy. genesis 50:271–285, 2012.© 2012 Wiley Periodicals, Inc.
Adapting the buccal micronucleus cytome assay for use in wild birds: Age and sex affect background frequency in pigeons
Authors: Shepherd G.L. , Somers C.M.
Published: November 2011

Micronucleus (MN) formation has been used extensively as a biomarker of damage from genotoxic exposures. The Buccal MN Cytome (BMCyt) assay provides a noninvasive means of quantifying MN frequency in humans, but it has not been developed for use in wildlife. We adapted the BMCyt assay for use in wild birds, with a focus on feral pigeons (Columba livia) as a potential indicator species. Five of six urban bird species sampled using oral cavity swabs produced sufficient buccal cells for the BMCyt assay. The body size of species sampled ranged almost 100‐fold (∼60 to 5,000 g), but was a not major factor influencing the number of buccal cells collected. Pigeon cells were stained and scored following published BMCyt assay protocols for humans, but with a modified fixation approach using heat and methanol. Pigeons had the same common nuclear abnormalities reported in human studies, and a similar background MN formation frequency of 0.88 MN/1,000 cells. Adult pigeons had on average a threefold higher rate of MN formation than juveniles, and males had a 1.4‐ to 2.2‐fold higher frequency than females. Domestic and feral pigeons did not differ in overall MN frequency. Our results indicate that the BMCyt assay can be used on wild birds, and could provide a means of assessing environmental genotoxicity in pigeons, a useful indicator species. However, bird age and sex are important factors affecting background MN frequency, and thereby the design of environmental studies. Environ. Mol. Mutagen., 2012. © 2011 Wiley Periodicals, Inc.
Modelling the bulk flow of a bedrock‐constrained, multi‐channel reach of the Mekong River, Siphandone, southern Laos
Authors: Van Tri P. D. , Carling Paul A. , Atkinson Peter M.
Published: November 2011

The general nature of bulk flow within bedrock single‐channel reaches has been considered by several studies recently. However, the flow structure of a bedrock‐constrained, large river with a multiple channel network has not been investigated previously. The multiple channel network of the Siphandone wetlands in Laos, a section of the Mekong River, was modelled using a steady one‐dimensional hydraulic model. The river network is characterized by a spatially‐varying channel‐form leading to significant changes in the bulk flow properties between and along the channels. The challenge to model the bulk flow in such a remote region was the lack of ideal boundary conditions. The flow models considered both low flow, high inbank and overbank flows and were calibrated using SPOT satellite sensor imagery and limited field data concerning water levels.

The application of the model highlighted flow characteristics of a large multi‐channel network and also further indicated the field data that would be required to properly characterize the flow field empirically. Important results included the observation that adjacent channels within the network had different water surface slopes for the same moments in time; thus calibration data for modelling similar systems needs to account for these significant local differences. Further, the in‐channel hydraulic roughness coefficient strongly varied from one cross‐section to the next (Manning's ‘n’ range: 0·01 to 0·10). These differences were amplified during low flow but persisted in muted form during high discharges. Copyright © 2012 John Wiley & Sons, Ltd.
Predicting gully initiation: comparing data mining techniques, analytical hierarchy processes and the topographic threshold
Authors: Svoray Tal , Michailov Evgenia , Cohen Avraham , Rokah Lior , Sturm Arnon
Published: November 2011

Predicting gully initiation at catchment scale was done previously by integrating a geographical information system (GIS) with physically based models, statistical procedures or with knowledge‐based expert systems. However, the reliability and validity of applying these procedures are still questionable. In this work, a data mining (DM) procedure based on decision trees was applied to identify areas of gully initiation risk. Performance was compared with the analytic hierarchy process (AHP) expert system and with the commonly used topographic threshold (TT) technique. A spatial database was used to test the models, composed of a target variable (presence or absence of initial points) and ten independent environmental, climatic and human‐induced variables. The following findings emerged: using the same input layers, DM provided better predictive ability of gully initiation points than the application of both AHP and TT. The main difference between DM and TT was the very high overestimation inherent in TT. In addition, the minimum slope observed for soil detachment was 2°, whereas in other studies it is 3°. This could be explained by soil resistance, which is substantially lower in agricultural fields, while most studies test unploughed soil. Finally, rainfall intensity events >62.2 mm h‐1(for a period of 30 min) were found to have a significant effect on gully initiation. Copyright © 2012 John Wiley & Sons, Ltd.
Hypoxia and Hypoxia Inducible Factors: Diverse Roles in Liver Diseases
Authors: Nath Bharath , Szabo Gyongyi
Published: November 2011

Hypoxia has been shown to have a role in the pathogenesis of several forms of liver disease. The hypoxia inducible factors (HIFs) are a family of evolutionarily conserved transcriptional regulators that affect a homeostatic response to low oxygen tension and have been identified as key mediators of angiogenesis, inflammation, and metabolism. In this review we summarize the evidence for a role of HIFs across a range of hepatic pathophysiology. We describe regulation of the HIFs and review investigations that demonstrate a role for HIFs in the development of liver fibrosis, activation of innate immune pathways, hepatocellular carcinoma, as well as other liver diseases in both human disease as well as murine models. (Hepatology 2012;)
Hepatitis C and Non-Hodgkin Lymphoma: The Clinical Perspective
Authors: Hartridge-Lambert Sidonie K. , Stein Eytan M. , Markowitz Arnold J. , Portlock Carol S.
Published: November 2011

Hepatitis C virus (HCV) is a commonly transmitted infection that has both hepatic and extrahepatic repercussions. These range from the inflammatory to the oncologic with an undisputed link to hepatitis, liver cirrhosis, and hepatocellular carcinoma. Its role in the development of B cell non-Hodgkin lymphoma (B-NHL) is becoming better understood, leading to opportunities for research, therapy, and even prevention. Research in the field has progressed significantly over the last decade, with the number of patients diagnosed with HCV and B-NHL rising incrementally. It is therefore becoming crucial to fully understand the pathobiologic link of HCV in B cell lymphomagenesis and its optimal management in the oncologic setting. (Hepatology 2012)
Toll-like receptor 4–dependent Kupffer cell activation and liver injury in a novel mouse model of parenteral nutrition and intestinal injury
Authors: El Kasmi Karim C. , Anderson Aimee L. , Devereaux Michael W. , Fillon Sophie A. , Harris Kirk J. , Lovell Mark A. , Finegold Milton J. , Sokol Ronald J.
Published: November 2011

Infants with intestinal failure who are parenteral nutrition (PN)-dependent may develop cholestatic liver injury and cirrhosis (PN-associated liver injury: PNALI). The pathogenesis of PNALI remains incompletely understood. We hypothesized that intestinal injury with increased intestinal permeability combined with administration of PN promotes lipopolysaccharide (LPS)–Toll-like receptor 4 (TLR4) signaling dependent Kupffer cell (KC) activation as an early event in the pathogenesis of PNALI. We developed a mouse model in which intestinal injury and increased permeability were induced by oral treatment for 4 days with dextran sulphate sodium (DSS) followed by continuous infusion of soy lipid-based PN solution through a central venous catheter for 7 (PN7d/DSS) and 28 (PN28d/DSS) days. Purified KCs were probed for transcription of proinflammatory cytokines. PN7d/DSS mice showed increased intestinal permeability and elevated portal vein LPS levels, evidence of hepatocyte injury and cholestasis (serum aspartate aminotransferase, alanine aminotransferase, bile acids, total bilirubin), and increased KC expression of interleukin-6 (

Il6

), tumor necrosis factor α (

Tnf

α), and transforming growth factor β (

Tgf

β). Markers of liver injury remained elevated in PN28d/DSS mice associated with lobular inflammation, hepatocyte apoptosis, peliosis, and KC hypertrophy and hyperplasia. PN infusion without DSS pretreatment or DSS pretreatment alone did not result in liver injury or KC activation, even though portal vein LPS levels were elevated. Suppression of the intestinal microbiota with broad spectrum antibiotics or ablation of TLR4 signaling in

Tlr4

mutant mice resulted in significantly reduced KC activation and markedly attenuated liver injury in PN7d/DSS mice.

Conclusion :

These data suggest that intestinal-derived LPS activates KC through TLR4 signaling in early stages of PNALI. (Hepatology 2012)
The global burden of hepatitis E virus genotypes 1 and 2 in 2005
Authors: Rein David B. , Stevens Gretchen A. , Theaker Jordan , Wittenborn John S. , Wiersma Steven T.
Published: November 2011

We estimated the global burden of hepatitis E virus (HEV) genotypes 1 and 2 in 2005. HEV is an emergent waterborne infection that causes source-originated epidemics of acute disease with a case fatality rate thought to vary by age and pregnancy status. To create our estimates, we modeled the annual disease burden of HEV genotypes 1 and 2 for 9 of 21 regions defined for the Global Burden of Diseases, Injuries, and Risk Factors Study (the GBD 2010 Study), which represent 71% of the world's population. We estimated the seroprevalence of anti-HEV antibody and annual incidence of infection for each region using data from 37 published national studies and the DISMOD 3, a generic disease model designed for the GBD Study. We converted incident infections into three mutually exclusive results of infection: (1) asymptomatic episodes, (2) symptomatic disease, and (3) death from HEV. We also estimated incremental cases of stillbirths among infected pregnant women. For 2005, we estimated 20.1 (95% credible interval [Cr.I.]: 2.8–37.0) million incident HEV infections across the nine GBD Regions, resulting in 3.4 (95% Cr.I.: 0.5–6.5) million symptomatic cases, 70,000 (95% Cr.I.: 12,400–132,732) deaths, and 3,000 (95% Cr.I.: 1,892–4,424) stillbirths. We estimated a probability of symptomatic illness given infection of 0.198 (95% Cr.I.: 0.167–0.229) and a probability of death given symptomatic illness of 0.019 (95% Cr.I.: 0.017–0.021) for nonpregnant cases and 0.198 (95% Cr.I.: 0.169–0.227) for pregnant cases. Conclusion: The model was most sensitive to estimates of age-specific incidence of HEV disease. (Hepatology 2012)
Durandal: Fast exact clustering of protein decoys
Authors: Berenger Francois , Shrestha Rojan , Zhou Yong , Simoncini David , Zhang Kam Y. J.
Published: November 2011

In protein folding, clustering is commonly used as one way to identify the best decoy produced. Initializing the pairwise distance matrix for a large decoy set is computationally expensive. We have proposed a fast method that works even on large decoy sets. This method is implemented in a software called Durandal. Durandal has been shown to be consistently faster than other software performing fast exact clustering. In some cases, Durandal can even outperform the speed of an approximate method. Durandal uses the triangular inequality to accelerate exact clustering, without compromising the distance function. Recently, we have further enhanced the performance of Durandal by incorporating a Quaternion‐based characteristic polynomial method that has increased the speed of Durandal between 13% and 27% compared with the previous version. Durandal source code is available under the GNU General Public License at http://www.riken.jp/zhangiru/software/durandal_released_qcp.tgz. Alternatively, a compiled version of Durandal is also distributed with the nightly builds of the Phenix (http://www.phenix‐online.org/) crystallographic software suite (Adams et al., Acta Crystallogr Sect D 2010, 66, 213). © 2011 Wiley Periodicals, Inc. J Comput Chem, 2012
Meta‐analysis of endoscopic versus sublabial pituitary surgery
Authors: DeKlotz Timothy R. , Chia Stanley H. , Lu Wenxin , Makambi Kepher H. , Aulisi Edward , Deeb Ziad
Published: November 2011

Objectives/Hypothesis:

To determine whether the endoscopic or sublabial transseptal transsphenoidal approach for pituitary surgery has superior outcomes or decreased complication rates.

Study Design:

Retrospective meta‐analysis of literature.

Methods:

A MEDLINE search was conducted identifying all relevant literature in the English language from 1998 through 2010. Studies explicitly identifying pure sublabial or completely endoscopic approaches were included. Meta‐analysis comparing the two techniques was performed for multiple outcome measures utilizing a random effects approach.

Results:

A total of 21 endoscopic studies (n = 2,335) and 17 sublabial studies (n = 2,565) met inclusion criteria. Analysis revealed significantly superior rates of gross tumor resection (79% vs. 65%, P < .0001), as well as lower rates of cerebral spinal fluid leak (5% vs. 7%, P < .01), septal perforation (0% vs. 5%), and postoperative epistaxis (1% vs. 4%, P < .0001) for the endoscopic approach compared to the sublabial approach. There was no difference between the two techniques in the incidence of meningitis, diabetes insipidus, or resolution of hormonal abnormality. Hospital stay (P = .01) was shorter for endoscopic surgery compared to sublabial surgery, and there was no significant difference in terms of length of operation.

Conclusions:

The sublabial transsphenoidal approach has been the gold standard for pituitary surgery for many years. However, meta‐analysis of the recent literature demonstrates superior outcomes and decreased postoperative complications with the endoscopic approach, potentially justifying a shift toward endoscopic pituitary surgery.
Systematic review and meta‐analysis of the risk factors for sudden sensorineural hearing loss in adults
Authors: Lin Rui Jun , Krall Randall , Westerberg Brian D. , Chadha Neil K. , Chau Justin K.
Published: November 2011

Objectives/Hypothesis:

To review the medical literature evidence of potential risk factors for sudden sensorineural hearing loss (SSNHL) in the adult general population.

Study Design:

Systematic review of prospective and retrospective studies; meta‐analysis of case‐controlled studies.

Methods:

Three researchers independently reviewed MEDLINE (January 1, 1950–November 30, 2010), Embase (January 1, 1980–November 30, 2010), and Evidence‐Based Medicine Reviews databases in addition to conducting a manual reference search. Randomized controlled trials, prospective cohort studies, consecutive/nonconsecutive case series, and retrospective reviews in which a clear definition of SSNHL was stated were included in the study. Researchers individually extracted data regarding patient information and the presumed risk factors. Discrepancies were resolved by mutual consensus.

Results:

Twenty‐two articles met the inclusion criteria. Cardiovascular risk factors (smoking, increased alcohol consumption) appeared to be associated with a higher risk of developing SSNHL. A low level of serum folate may also be implicated as a risk factor. Factor V Leiden and MTHFR gene polymorphisms were found to occur more frequently in patients with SSNHL in several studies, suggesting these inherited prothrombophilic mutations could be independent risk factors of SSNHL.

Conclusions:

Acquired and inherited cardiovascular risk factors appeared to be associated with an increased risk of developing SSNHL.
The critical state behaviour of barodesy compared with the Matsuoka–Nakai failure criterion
Authors: Fellin Wolfgang , Ostermann Alexander
Published: November 2011

Barodesy is a new approach to constitutive modelling of soil. It is based on Goldscheider's principles and maps stretching directions onto corresponding stress directions with the help of a simple exponential function. This mapping also determines a critical state surface in principal stress space. The article investigates this surface and relates it to the well‐known Matsuoka–Nakai failure criterion. It turns out that the difference between these two surfaces is negligible for practical applications. Copyright © 2011 John Wiley & Sons, Ltd.
3‐miktoarm star terpolymers using triple click reactions: Diels–Alder, copper‐catalyzed azide‐alkyne cycloaddition, and nitroxide radical coupling reactions
Authors: Gunay Ufuk Saim , Durmaz Hakan , Gungor Eda , Dag Aydan , Hizal Gurkan , Tunca Umit
Published: November 2011

Well‐defined linear furan‐protected maleimide‐terminated poly(ethylene glycol) (PEG‐MI), tetramethylpiperidine‐1‐oxyl‐terminated poly(ε‐caprolactone) (PCL‐TEMPO), and azide‐terminated polystyrene (PS‐N3) or ‐poly(N‐butyl oxanorbornene imide) (PONB‐N3) were ligated to an orthogonally functionalized core (1) in a two‐step reaction mode through triple click reactions. In a first step, Diels–Alder click reaction of PEG‐MI with 1 was performed in toluene at 110 °C for 24 h to afford α‐alkyne‐α‐bromide‐terminated PEG (PEG‐alkyne/Br). As a second step, this precursor was subsequently ligated with the PCL‐TEMPO and PS‐N3 or PONB‐N3 in N,N‐dimethylformamide at room temperature for 12 h catalyzed by Cu(0)/Cu(I) through copper‐catalyzed azide‐alkyne cycloaddition and nitroxide radical coupling click reactions, yield resulting ABC miktoarm star polymers in a one‐pot mode. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
MANAGING THE FLOOD PULSE FOR OPTIMAL FISHERIES PRODUCTION IN THE ATCHAFALAYA RIVER BASIN, LOUISIANA (USA)
Authors: Alford J. B. , Walker M. R.
Published: November 2011

The Atchafalaya River Basin in south‐central Louisiana (USA) comprises the largest contiguous river–floodplain swamp in North America and functions as a distributary for the Mississippi River to the Gulf of Mexico. We assessed the impact of the annual flood pulse on fisheries production at a basin‐wide scale. We modelled flood duration (days/year Butte LaRose gauge height >3.6 m) and magnitude (mean daily gauge height) against long term (1987–2009) fishery‐independent and fishery‐dependent data on largemouth bass (Micropterus salmoides), crappie (Pomoxis spp.), blue catfish (Ictalurus furcatus), buffalofish (Ictiobus spp.), gizzard shad (Dorosoma cepedianum) and crayfish (Procambarus spp.). When the Atchafalaya River at Butte LaRose is at flood stage (≥ 3.6 m gauge height) for approximately 121–157 days/year, then annual relative abundances of largemouth bass, crappie, blue catfish and buffalofish are optimized during the fall (October–December). In contrast to the tenets of the flood pulse concept, gizzard shad abundance was optimized during low flow years, when flood duration is ≤10 days/year. Annual proportion of age‐1 largemouth bass was associated positively with flow magnitude during the previous year, whereas proportions of age‐2 largemouth bass and crappie were associated positively with flood magnitude 2 years prior to the fish sample. Results for commercial production metrics were ambiguous. Crayfish catches were associated positively with flood magnitude and duration, whereas gizzard shad landings peaked at a relatively small flood magnitude level and were not related to flood duration. Blue catfish and buffalofish annual landings were not influenced by the annual flood pulse. The annual flood pulse can be managed to optimize the availability of recreational (largemouth bass and crappie) and some commercial fisheries resources (blue catfish and crayfish). We estimate that a minimum discharge of 8807 m3 s−1 is required at the river's source for approximately 4–5 months during the winter–spring months to optimize fisheries production. Copyright © 2011 John Wiley & Sons, Ltd.
Quantitative estimation of insect diversity inhabitingCalotropis procerain industrial and nonindustrial areas of West Bengal, India
Authors: Jana Gautam , Chaki K. K. , Misra K. K.
Published: November 2011

This paper compares the species richnesses, Bray–Curtis similarities, species diversities, evennesses, and the results of various analyses (multivariate, logarithmic series, and lognormal distribution analyses) of insects from four orders (viz., Hemiptera, Orthoptera, aculeate Hymenoptera, and Coleoptera) inhabiting a medicinal plant,Calotropis proceraamong eight sites within industrial and nonindustrial zones in the Purba Medinipur district (erstwhile Midnapore), West Bengal, India. Both cluster analysis and principal component analysis indicate an effect of industrialization on the diversity of the four insect orders. The species community at each site exhibits an almost pure lognormal distribution. Bootstrap estimation of species diversity also points to the effect of industrialization. A comparison of the values ofxandN/Sof the logarithmic series indicates a typical relationship between the species community and its diversity. The number of unique species among the eight study sites is 6 according to jackknife estimation. Beta‐diversity analysis of the samples shows the impact of industrialization on the abundances and species richness of the insects. Altogether, 16 types of analytical procedure are applied for this purpose, and their suitabilities for this kind of data set are assessed. Disturbance, probably due to industrial emissions, has changed the compositions and structures of the insect communities out to a distance of at least 6 km from the core industrial area.
Evaluation of Biodiesel Derived from Camelina sativa Oil
Authors: Soriano Nestor U. , Narani Akash
Published: November 2011

Biodiesel derived from camelina as well as other feedstocks including palm, mustard, coconut, sunflower, soybean and canola were prepared via the conventional base‐catalyzed transesterification with methanol. Fatty acid profiles and the fuel properties of biodiesel from different vegetable oils were analyzed and tested in accordance with ASTM D6751. Camelina biodiesel contains 10–12%, 37–40%, and 48–50% saturated, monounsaturated and polyunsaturated components, respectively. Some fuel properties of camelina biodiesel are comparable to that of sunflower biodiesel including kinematic viscosity (40 °C), flash point, cloud point, cold filter plugging point, and oil stability index. However, camelina biodiesel exhibited the poorest oxidative stability, highest distillation temperature and has the highest potential to form coke during combustion, all of which are attributed to the high amounts of n‐3‐fatty acids in camelina oil. While neat camelina biodiesel may exhibit undesirable fuel properties, it is very comparable with soybean biodiesel at the B20 level.
Using Sybil for interactive comparative genomics of microbes on the web
Authors: Riley David R. , Angiuoli Samuel V. , Crabtree Jonathan , Dunning Hotopp Julie C. , Tettelin Hervé
Published: November 2011

Motivation: Analysis of multiple genomes requires sophisticated tools that provide search, visualization, interactivity and data export. Comparative genomics datasets tend to be large and complex, making development of these tools difficult. In addition to scalability, comparative genomics tools must also provide user-friendly interfaces such that the research scientist can explore complex data with minimal technical expertise.

Results: We describe a new version of the Sybil software package and its application to the important human pathogen Streptococcus pneumoniae. This new software provides a feature-rich set of comparative genomics tools for inspection of multiple genome structures, mining of orthologous gene families and identification of potential vaccine candidates.

Availability: The S.pneumoniae resource is online at http://strepneumo-sybil.igs.umaryland.edu. The software, database and website are available for download as a portable virtual machine and from http://sourceforge.net/projects/sybil.

Contact:  driley@som.umaryland.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Serum levels of microRNAs in patients with heart failure
Authors: Goren Yaron , Kushnir Michal , Zafrir Barak , Tabak Sarit , Lewis Basil S. , Amir Offer
Published: November 2011

Aims

Diagnosis and risk stratification of patients with heart failure remain a challenge. The small non‐coding RNAs known as microRNAs regulate gene expression and seem to play an important role in the pathogenesis of heart failure. In the current study, we aim to characterize the levels of microRNAs in the sera of chronic systolic heart failure patients vs. controls and assess the possible correlation between elevation in the levels of specific microRNAs and clinical prognostic parameters in heart failure patients.

Methods and results

The levels of 186 microRNAs were measured in the sera of 30 stable chronic systolic heart failure patients and 30 controls using quantitative reverse transcription–polymerase chain reaction (qRT–PCR). The differences in microRNA levels between the two groups were characterized, and a score, based on the levels of four specific microRNAs with the most significant increase in the heart failure group (miR‐423‐5p, miR‐320a, miR‐22, and miR‐92b), was defined. The score was used to discriminate heart failure patients from controls with a sensitivity and specificity of 90%. Moreover, in the heart failure group, there was a significant association between the score and important clinical prognostic parameters such as elevated serum natriuretic peptide levels, a wide QRS, and dilatation of the left ventricle and left atrium (r = 0.63, P = 3e‐4; P = 0.009; P = 0.03; and P = 0.01, respectively).

Conclusions

Elevated serum levels of specific microRNAs: miR‐423‐5p, miR‐320a, miR‐22, and miR‐92b, identify systolic heart failure patients and correlate with important clinical prognostic parameters.
Conexibacter

arvalis sp. nov., isolated from a cultivated field soil sample
Authors: Seki Tamae , Matsumoto Atsuko , Shimada Risa , Inahashi Yuki , Ōmura Satoshi , Takahashi Yōko
Published: November 2011

Two bacterial strains, designated KV-962T and KV-963, were isolated from soil collected from a field in Japan. Cells of both strains were Gram-staining-positive, non-spore-forming, short rod-shaped and motile. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains were related to

Conexibacter woesei

DSM 14684T, with a similarity value of 98.6 %. These strains possessed MK-7 (H4) as the sole menaquinone and contained C18 : 1ω9c, C17 : 1ω6c and iso-C16 : 0 as the major fatty acids. On the basis of genotypic and phenotypic characteristics, strain KV-962T and KV-963 were indicated as a novel species of the genus

Conexibacter

, for which the name
Conexibacter

arvalis sp. nov. is proposed. The type strain is KV-962T ( = DSM 23288T  = NBRC 106558T)
Georgenia satyanarayanai sp. nov., an alkaliphilic and thermotolerant amylase-producing actinobacterium isolated from a soda lake
Authors: Srinivas A. , Rahul K. , Sasikala Ch. , Subhash Y. , Ramaprasad E. V. V. , Ramana Ch. V.
Published: November 2011

A Gram-stain-positive, oxidase-negative, starch-hydrolysing, actinobacterium (strain JC82T) was isolated from a soda lake in Lonar, India. Based on 16S rRNA gene sequence similarity studies, strain JC82Tbelonged to the genusGeorgeniaand was most closely related toGeorgenia muralis1A-CT(96.8 %) and other members of the genusGeorgenia(<96.5 %). The DNA G+C content of strain JC82Twas 73.4 mol%. The cell-wall amino acids were alanine, glutamic acid and lysine with peptidoglycan type A4α. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, an unidentified lipid (L1) and an unidentified glycolipid (GL3). The predominant isoprenoid quinone was menaquinone MK-8(H4). Anteiso-C15 : 0was the predominant fatty acid and significant proportions of iso-C14 : 0, C14 : 0, C16 : 0, iso-C15 : 0and iso-C16 : 0were also detected. Strain JC82Tproduced thermostable alkaline amylase. The results of physiological and biochemical tests allowed a clear phenotypic differentiation of strain JC82Tfrom all other members of the genusGeorgenia. Based on these data, strain JC82Trepresents a novel species of the genusGeorgenia, for which the nameGeorgenia satyanarayanaisp. nov. is proposed. The type strain is JC82T( = KCTC 19802T = NBRC 107612T).
Plantactinospora endophytica sp. nov., an actinomycete isolated from Camptotheca acuminata Decne., reclassification of

Actinaurispora siamensis

as Plantactinospora siamensis comb. nov. and emended descriptions of the genus

Plantactinospora

and

Plantactinospora mayteni
Authors: Zhu Wen-Yong , Zhao Li-Xing , Zhao Guo-Zhen , Duan Xue-Wei , Qin Sheng , Li Jie , Xu Li-Hua , Li Wen-Jun
Published: November 2011

A novel endophytic actinomycete, designated strain YIM 68255T, was isolated from healthy leaves of Camptotheca acuminata Decne. collected in Yunnan province, south-west China and characterized by using a polyphasic approach. The strain formed well-developed substrate mycelium, but no aerial mycelium. It grew at 10–45 °C, at pH 5–10 (optimum pH 7) and in the presence of 0–3 % (w/v) NaCl. The DNA G+C content was 73.0 mol%. Phylogenetic analyses showed that strain YIM 68255T belonged to the genus

Plantactinospora

. However, it exhibited some differences from

Plantactinospora mayteni

YIM 61359T and the level of DNA–DNA relatedness was 42.7±1.3 %. Based on comparative analysis of physiological and chemotaxonomic data, it is proposed that strain YIM 68255T represents a novel species of the genus

Plantactinospora

, Plantactinospora endophytica sp. nov., with strain YIM 68255T ( = DSM 45387T = CCTCC AA 209047T) as the type strain. In addition, it is also proposed that

Actinaurispora siamensis

Thawai et al. 2010 be transferred to the genus

Plantactinospora

as Plantactinospora siamensis comb. nov. [type strain CM2-8T ( = JCM 15677T = BCC 34762T)] based on chemotaxonomic characteristics and phylogenetic analysis. Emended descriptions of the genus

Plantactinospora

and

Plantactinospora mayteni

are also provided.
Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species
Authors: Kim Ok-Sun , Cho Yong-Joon , Lee Kihyun , Yoon Seok-Hwan , Kim Mincheol , Na Hyunsoo , Park Sang-Cheol , Jeon Yoon Seong , Lee Jae-Hak , Yi Hana , Won Sungho , Chun Jongsik
Published: November 2011

Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have not been considered. Here, the next generation database, named EzTaxon-e, is formally introduced. This new database covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature. In addition to an identification function based on Basic Local Alignment Search Tool (blast) searches and pairwise global sequence alignments, a new objective method of assessing the degree of completeness in sequencing is proposed. All sequences that are held in the EzTaxon-e database have been subjected to phylogenetic analysis and this has resulted in a complete hierarchical classification system. It is concluded that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes and offers a valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates. The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/.
A multi‐layer contextual model for recommender systems in digital libraries
Authors: Dehghani Zohreh , Afshar Ebrahim , Jamali Hamid R. , Nematbakhsh Mohammad Ali
Published: November 2011

Purpose

The aim of this paper is to investigate contextual information that has an impact on the process of selection and decision making in recommender systems (RSs) in digital libraries.

Design/methodology/approach

Using a grounded theory method of qualitative research, semi‐structured interviews were carried out with 22 information specialists, and IT and computer engineering students and professors. Data resulting from interviews were analysed in two stages using open coding, followed by axial and selective coding.

Findings

The central idea (concept) developed in this study, named scientific research ground (SRG), is an information ground users step into with scholarly purposes. Within SRG they start interacting with information systems. SRG has contexts which situate users in a range of situations while interacting with information systems. Users' characteristics such as purpose, activity, literacy, mental state, expectations, and assumptions, occupational and social status are some contexts that should be taken into account for making a recommendation.

Research limitations/implications

This study sought to explore contextual information in the academic community and the academic contextual information cannot be generalized to RSs in other environments such as e‐commerce.

Practical implications

Identifying and implementing contextual information in information systems can help make better recommendations as well as improve interaction between users and information systems.

Originality/value

Based on the SRG idea and its contexts, a multi‐layer contextual model for a recommender system is proposed.
Medical image resources used by health care professionals
Authors: Sedghi Shahram , Sanderson Mark , Clough Paul
Published: November 2011

Purpose

Medicine is heavily dependent on images and health care professionals use medical images for clinical, educational and research purposes. This paper aims to investigate the resources used by health care professionals while searching for medical images.

Design/methodology/approach

The research is based on a qualitative study that uses the Straussian version of grounded theory and involved 29 health care professionals from various health and biomedical departments working within Sheffield Teaching Hospitals NHS (National Health Service) Foundation Trust. Data collection was carried out using semi‐structured interviews and think‐aloud protocols.

Findings

The findings show that health care professionals seek medical images in a variety of visual information sources, including those found online and from published medical literature. The research also identified a number of difficulties that health care professionals face when searching for medical images in various image resources.

Originality/value

There have been few studies that investigated the image resources used by health care professionals. Thus, this study contributes to the understanding of medical image resources and information needs of health care professionals. A clear understanding of the medical image information needs of health care professionals is also vital to the design process and development of medical image retrieval systems.
How are XML‐based Marc 21 and Dublin Core records indexed and ranked by general search engines in dynamic online environments?
Authors: Hossein Farajpahlou A. , Tabatabai Faeze
Published: November 2011

Purpose

The aim of this paper is to examine the indexing quality and ranking of XML content objects containing Dublin Core and MARC 21 metadata elements in dynamic online information environments by general search engines such as Google and Yahoo!

Design/methodology/approach

In total, 100 XML content objects were divided into two groups: those with DCXML elements and those with MARCXML elements. Both groups were published on the web site www.marcdcmi.ir in late July 2009 and were online until June 2010. The web site was introduced to Google and Yahoo! search engines. The indexing quality of metadata elements embedded in the content objects in a dynamic online information environment and their indexing and ranking capabilities were compared and examined.

Findings

Google search engine was able to retrieve fully all the content objects through their Dublin Core and MARC 21 metadata elements; Yahoo! search engine, however, did not respond at all. Results of the study showed that all Dublin Core and MARC 21 metadata elements were indexed by Google search engine. No difference was observed between indexing quality and ranking of DCXML metadata elements with that of MARCXML. The results of the study revealed that neither the XML‐based Dublin Core Metadata Initiative nor MARC 21 demonstrate any preference regarding access in dynamic online information environments through Google search engine.

Practical implications

The findings can provide useful information for search engine designers.

Originality/value

The present study was conducted for the first time in dynamic environments using XML‐based metadata elements. It can provide grounds for further studies of this kind.
The effect of funding on academic research impact: a case study of Iranian publications
Authors: Jowkar Abdolrasoul , Didegah Fereshteh , Gazni Ali
Published: November 2011

Purpose

This paper's aim is to examine the citation impact of Iranian funded research publications and compare it with research which received no funding.

Design/methodology/approach

Using a bibliometric method, the study investigated 80,300 Iranian publications published from 2000 to 2009 in SCI‐EXPANDED to discover the percentage of funded publications and to determine the citation impact of these publications in comparison with unfunded ones.

Findings

The results of the study showed that around 12.5 per cent of Iranian publications were funded and the number of funded publications has increased dramatically over the last four years. The citation impact of funded publications was higher in almost all of the subject fields. The highest number of funded publications belonged to the universities subordinate to The Ministry of Science, Research and Technology.

Originality/value

The impact and quality of research is influenced by different factors, for instance receiving funding and research facilities. As this issue has not been previously examined in Iran, the present study determines whether funding can influence the impact of Iranian research.
The impact of New Zealand's disclosure reform on differential managerial disclosure behaviour for good news versus bad news firms
Authors: Marsden Alastair , Poskitt Russell , Wang Yinjian
Published: November 2011

Purpose

The purpose of this paper is to investigate the impact of the introduction of New Zealand's statutory‐backed continuous disclosure regime enacted in December 2002 on the differential disclosure behaviour of New Zealand firms with good and bad earnings news.

Design/methodology/approach

This paper examines the level of information disclosure, analyst forecast error and forecast dispersion, abnormal returns and abnormal volumes for firms with good and bad news earnings announcements in a sample period surrounding reforms to New Zealand's continuous disclosure regime.

Findings

The authors find evidence that the pre‐announcement information flow was poorer prior to the reform for bad news firms compared to good news firms, in terms of greater analysts' forecast dispersion and a larger abnormal price reaction to the actual earnings announcement. Second, the reform reduced the asymmetry of information flow between good and bad news firms, with the differences in analysts' forecast dispersion and abnormal price reaction dissipating after the reform.

Research limitations/implications

The findings suggest that the reforms to New Zealand's continuous disclosure regime have reduced managers' propensity to withhold bad news and improved the quality of information provided to investors by firms with bad earnings news.

Originality/value

This study improves our understanding of the impact of disclosure reform on the behaviour of managers in a market with relatively low liquidity and less litigation risk in comparison to larger and more developed markets.
Does the change of accounting regulation on employee share options give rise to greater scope for earnings management?
Authors: Nee Ang Hong , Pinnuck Matthew
Published: November 2011

Purpose

The purpose of this paper is to address the concern about the impact of accounting regulatory change pertaining to employee share options (ESOs) on earnings management. Following Australia's adoption of International Financial Reporting Standards (IFRS) in 2005, companies are required to recognise the fair value of ESOs as expenses. Due to inherent imprecision in the estimate of ESO's fair value, the regulatory change from disclosure to recognition was widely claimed to potentially give rise to an alternative mechanism to manage earnings. This study provides empirical evidence on whether the regulatory change leads to earnings management problems.

Design/methodology/approach

This study uses the regulatory change in accounting for ESOs to provide a direct test of earnings management between disclosed versus recognised regimes for the same sample of firms. The sample consists of Australian firms from S&P/ASX300 for the period from 2003 to 2006.

Findings

The results show that, although the accounting regulatory change from disclosure to recognition may provide an alternative earnings management vehicle, there is no evidence of this occurring. There could be several reasons for this finding. First, the statistical tests lack power. Second, there are stricter audit tests on recognised amounts than on disclosed amounts. Third, given the concern of excessive pay and the close scrutiny of compensation, managers may have already understated ESO values in the disclosure regime. Finally, managers have limited time and resources and the effort involved in the adoption of IFRS in 2005 could have restricted the time available to manage earnings via the ESO reporting channel.

Originality/value

This study adds to the limited research on whether a change in accounting regulation for employee share options from disclosure to recognition gives rise to greater scope for earnings management. One reason for the lack of empirical evidence in the research is due to the problem of designing a test. Bernard and Schipper suggest that within‐firm studies have limitations for comparing the effects of recognition versus disclosure when the change is driven by an estimate becoming more reliable. A cross‐sectional study is also problematic due to self‐selection bias if firms can choose between disclosure versus recognition. This study circumvents potential design problems raised by Bernard and Schipper by setting a test using regulatory change which allows the test to be compared directly using the same company.
Australasian cash flow reporting regulation: value relevant?
Authors: Malone Christopher B. , Wongchoti Udomsak , Mitchell Alan J.
Published: November 2011

Purpose

This paper provides empirical support for the introduction of cash flow disclosure regulation issued by Australasian accounting bodies, AASB and NZICA (formerly NZSA), between 1987 and 1992.

Design/methodology/approach

The empirical analysis uses a long window event study format on a panel of 5,368 firm‐year observations between 1996 and 2005.

Findings

The cash flow disclosures required in the regulation are associated with significant abnormal return responses. These effects are robust to the inclusion of other factors linked to abnormal returns such as movements in profitability, size and leverage. We also find support for the proposition that the cash flow effects are conditioned on the quality of the firm, as proxied by q. The market is better and more easily informed with the information required under the revised reporting regime.

Research limitations/implications

The analysis would have been improved with better access to pre‐reform period data.

Originality/value

There is no other study on Australasian markets which looks at the value impacts of cash flow information in relation to this regulatory change. Such a study has also never been done on New Zealand companies.