bluuebunny/crossref_metadata_2025 huggingface dataset:
Equilibrium speciation dynamics in a model adaptive radiation of island lizards
Authors: Rabosky Daniel L. , Glor Richard E.
Published: December 2010

The relative importance of equilibrium and nonequilibrium processes in shaping patterns of species richness is one of the most fundamental questions in biodiversity studies. If equilibrium processes predominate, then ecological interactions presumably limit species diversity, potentially through diversity dependence of immigration, speciation, and extinction rates. Alternatively, species richness may be limited by the rate at which diversity arises or by the amount of time available for diversification. These latter explanations constitute nonequilibrium processes and can apply only to biotas that are unsaturated or far from diversity equilibria. Recent studies have challenged whether equilibrium models apply to biotas assembled through in situ speciation, as this process may be too slow to achieve steady-state diversities. Here we demonstrate that speciation rates in replicate Caribbean lizard radiations have undergone parallel declines to equilibrium conditions on three of four major islands. Our results suggest that feedback between total island diversity and per-capita speciation rates scales inversely with island area, with proportionately greater declines occurring on smaller islands. These results are consistent with strong ecological controls on species richness and suggest that the iconic adaptive radiation of Caribbean anoles may have reached an endpoint.
Kinetics of chain motions within a protein-folding intermediate
Authors: Neuweiler Hannes , Banachewicz Wiktor , Fersht Alan R.
Published: December 2010

Small proteins can fold remarkably rapidly, even in
μ
s. What limits their rate of folding? The Engrailed homeodomain is a particularly well-characterized example, which folds ultrafast via an intermediate, I, of solved structure. It is a puzzle that the helix2-turn-helix3 motif of the 3-helix bundle forms in approximately 2 
μ
s, but the final docking of preformed helix1 in I requires approximately 20 
μ
s. Simulation and structural data suggest that nonnative interactions may slow down helix docking. Here we report the direct measurement of chain motions in I by using photoinduced electron transfer fluorescence-quenching correlation spectroscopy (PET-FCS). We use a mutant that traps I at physiological ionic strength but refolds at higher ionic strength. A single Trp in helix3 quenches the fluorescence of an extrinsic label on contact with it. We placed the label along the sequence to probe segmental chain motions. At high ionic strength, we found two relaxations for all probed positions on the 2- and 20-
μ
s time scale, corresponding to the known folding processes, and a 200-ns phase attributable to loop closure kinetics in the unfolded state. At low ionic strength, we found only the 2-
μ
s and 200-ns phase for labels in the helix2-turn-helix3 motif of I, because the native state is not significantly populated. But for labels in helix1 we observed an additional approximately 10-
μ
s phase showing that it was moving slowly, with a rate constant similar to that for overall folding under native conditions. Folding was rate-limited by chain motions on a rough energy surface where nonnative interactions constrain motion.
Inositol polyphosphate 4-phosphatase II regulates PI3K/Akt signaling and is lost in human basal-like breast cancers
Authors: Fedele Clare G. , Ooms Lisa M. , Ho Miriel , Vieusseux Jessica , O'Toole Sandra A. , Millar Ewan K. , Lopez-Knowles Elena , Sriratana Absorn , Gurung Rajendra , Baglietto Laura , Giles Graham G. , Bailey Charles G. , Rasko John E. J. , Shields Benjamin J. , Price John T. , Majerus Philip W. , Sutherland Robert L. , Tiganis Tony , McLean Catriona A. , Mitchell Christina A.
Published: December 2010

Inositol polyphosphate 4-phosphatase-II (INPP4B) is a regulator of the phosphoinositide 3-kinase (PI3K) signaling pathway and is implicated as a tumor suppressor in epithelial carcinomas.
INPP4B
loss of heterozygosity (LOH) is detected in some human breast cancers; however, the expression of INPP4B protein in breast cancer subtypes and the normal breast is unknown. We report here that INPP4B is expressed in nonproliferative estrogen receptor (ER)-positive cells in the normal breast, and in ER-positive, but not negative, breast cancer cell lines. INPP4B knockdown in ER-positive breast cancer cells increased Akt activation, cell proliferation, and xenograft tumor growth. Conversely, reconstitution of INPP4B expression in ER-negative, INPP4B-null human breast cancer cells reduced Akt activation and anchorage-independent growth. INPP4B protein expression was frequently lost in primary human breast carcinomas, associated with high clinical grade and tumor size and loss of hormone receptors and was lost most commonly in aggressive basal-like breast carcinomas. INPP4B protein loss was also frequently observed in phosphatase and tensin homolog (PTEN)-null tumors. These studies provide evidence that INPP4B functions as a tumor suppressor by negatively regulating normal and malignant mammary epithelial cell proliferation through regulation of the PI3K/Akt signaling pathway, and that loss of INPP4B protein is a marker of aggressive basal-like breast carcinomas.
Hepatocyte-specific deletion of DDB1 induces liver regeneration and tumorigenesis
Authors: Yamaji Sachie , Zhang Mingjun , Zhang Jing , Endo Yoko , Bibikova Elena , Goff Stephen P. , Cang Yong
Published: December 2010

Etiologic risk factors for hepatocellular carcinoma can be involved in the transformation process by directly targeting intracellular signaling pathways or by indirectly stimulating chronic cycles of hepatocyte destruction and regeneration. However, the contribution of these two routes to hepatocarcinogenesis has not been determined, partly because of the difficulty in distinguishing damaged and regenerated hepatocytes. Here we report that induced deletion of the damaged DNA binding protein 1 (DDB1) abrogates the self-renewing capacity of hepatocytes, resulting in compensatory proliferation of DDB1-expressing hepatocytes. Constitutive stimulation of this regeneration process leads to development of hepatocellular carcinoma, which surprisingly contains no disruption of the
DDB1
gene, indicating a cell-nonautonomous role of DDB1 inactivation in tumor initiation. Our results suggest that viruses and hepatoxins may cause liver tumors by simply driving hepatocyte turnover without directly targeting cancer cells.
Effects of a growth hormone-releasing hormone antagonist on telomerase activity, oxidative stress, longevity, and aging in mice
Authors: Banks William A. , Morley John E. , Farr Susan A. , Price Tulin O. , Ercal Nuran , Vidaurre Irving , Schally Andrew V.
Published: December 2010

Both deficiency and excess of growth hormone (GH) are associated with increased mortality and morbidity. GH replacement in otherwise healthy subjects leads to complications, whereas individuals with isolated GH deficiency such as Laron dwarfs show increased life span. Here, we determined the effects of treatment with the GH-releasing hormone (GHRH) receptor antagonist MZ-5-156 on aging in SAMP8 mice, a strain that develops with aging cognitive deficits and has a shortened life expectancy. Starting at age 10 mo, mice received daily s.c. injections of 10 μg/mouse of MZ-5-156. Mice treated for 4 mo with MZ-5-156 showed increased telomerase activity, improvement in some measures of oxidative stress in brain, and improved pole balance, but no change in muscle strength. MZ-5-156 improved cognition after 2 mo and 4 mo, but not after 7 mo of treatment (ages 12, 14 mo, and 17 mo, respectively). Mean life expectancy increased by 8 wk with no increase in maximal life span, and tumor incidence decreased from 10 to 1.7%. These results show that treatment with a GHRH antagonist has positive effects on some aspects of aging, including an increase in telomerase activity.
Your mistake is my mistake … or is it? Behavioural adjustments following own and observed actions in cooperative and competitive contexts
Authors: De Bruijn Ellen R. A. , Mars Rogier B. , Bekkering Harold , Coles Michael G. H.
Published: December 2010

A social speeded choice-reaction-time task was used to study adaptive behaviours following own and observed actions (errors and correct responses) in cooperative and competitive contexts. After making an erroneous response, the appropriate remedial action to avoid future errors in speeded reaction tasks is to slow down. Consistent with previous results, people indeed slow down following their own errors. Importantly, people who slow down most following own errors also slow down following observed errors in a cooperative situation. In a competitive context, a different pattern was found. People accelerated after errors from their opponent. The current findings demonstrate that the social context determines the way people respond to the errors of others, indicating that the neural systems that control remedial actions are highly flexible. These systems may underlie social adaptive behaviour, enabling people to respond flexibly to other people's actions in a wide variety of social contexts.
Predicting in vitro drug sensitivity using Random Forests
Authors: Riddick Gregory , Song Hua , Ahn Susie , Walling Jennifer , Borges-Rivera Diego , Zhang Wei , Fine Howard A.
Published: December 2010

Motivation: Panels of cell lines such as the NCI-60 have long been used to test drug candidates for their ability to inhibit proliferation. Predictive models of in vitro drug sensitivity have previously been constructed using gene expression signatures generated from gene expression microarrays. These statistical models allow the prediction of drug response for cell lines not in the original NCI-60. We improve on existing techniques by developing a novel multistep algorithm that builds regression models of drug response using Random Forest, an ensemble approach based on classification and regression trees (CART).

Results: This method proved successful in predicting drug response for both a panel of 19 Breast Cancer and 7 Glioma cell lines, outperformed other methods based on differential gene expression, and has general utility for any application that seeks to relate gene expression data to a continuous output variable.

Implementation: Software was written in the R language and will be available together with associated gene expression and drug response data as the package ivDrug at http://r-forge.r-project.org.

Contact:  riddickgp@mail.nih.gov

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Toward the estimation of the absolute quality of individual protein structure models
Authors: Benkert Pascal , Biasini Marco , Schwede Torsten
Published: December 2010

Motivation: Quality assessment of protein structures is an important part of experimental structure validation and plays a crucial role in protein structure prediction, where the predicted models may contain substantial errors. Most current scoring functions are primarily designed to rank alternative models of the same sequence supporting model selection, whereas the prediction of the absolute quality of an individual protein model has received little attention in the field. However, reliable absolute quality estimates are crucial to assess the suitability of a model for specific biomedical applications.

Results: In this work, we present a new absolute measure for the quality of protein models, which provides an estimate of the ‘degree of nativeness’ of the structural features observed in a model and describes the likelihood that a given model is of comparable quality to experimental structures. Model quality estimates based on the QMEAN scoring function were normalized with respect to the number of interactions. The resulting scoring function is independent of the size of the protein and may therefore be used to assess both monomers and entire oligomeric assemblies. Model quality scores for individual models are then expressed as ‘Z-scores’ in comparison to scores obtained for high-resolution crystal structures. We demonstrate the ability of the newly introduced QMEAN Z-score to detect experimentally solved protein structures containing significant errors, as well as to evaluate theoretical protein models.

In a comprehensive QMEAN Z-score analysis of all experimental structures in the PDB, membrane proteins accumulate on one side of the score spectrum and thermostable proteins on the other. Proteins from the thermophilic organism Thermatoga maritima received significantly higher QMEAN Z-scores in a pairwise comparison with their homologous mesophilic counterparts, underlining the significance of the QMEAN Z-score as an estimate of protein stability.

Availability: The Z-score calculation has been integrated in the QMEAN server available at: http://swissmodel.expasy.org/qmean.

Contact:  torsten.schwede@unibas.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cucumber mosaic virus 2b-Deficient Mutant Causes Limited, Asymptomatic Infection of Bell Pepper
Authors: Masiri Jongkit , Velasquez Nubia V. , Murphy John F.
Published: December 2010

Cucumber mosaic virus Fast New York strain (CMV-Fny) containing a mutated 2b protein (CMV-FnyΔ2b) was evaluated for the ability to infect ‘Calwonder’ bell pepper (Capsicum annuum) plants in comparative tests with the parent virus, CMV-Fny. Plants inoculated with CMV-FnyΔ2b did not develop local or systemic symptoms of infection, whereas CMV-Fny-infected plants developed systemic chlorosis by 7 days post inoculation (dpi), followed by mosaic and leaf deformation. Virus accumulation, determined by enzyme-linked immunosorbent assay (ELISA), revealed that CMV-FnyΔ2b accumulated in inoculated Calwonder leaves and inconsistently infected some noninoculated leaves at a low titer but was not detected in the youngest, noninoculated leaves. Immuno-tissue blot tests did not detect CMV-FnyΔ2b in the stems of infected plants, whereas CMV-Fny accumulated throughout the length of the stems of inoculated plants. In two experiments, protoplasts were isolated from Calwonder leaves, inoculated with viral RNAs of CMV-Fny or CMV-FnyΔ2b, and tested by ELISA for infection. In both experiments, less CMV-FnyΔ2b than CMV-Fny accumulated in protoplasts. These results suggest that the CMV 2b protein is needed for systemic infection of Calwonder pepper plants and for accumulation of the virus in inoculated protoplasts.
Clinical Significance of Soluble TNF Receptor in Japanese Patients with Non‐Alcoholic Steatohepatitis
Authors: Tokushige Katsutoshi , Hashimoto Etsuko , Tsuchiya Noriko , Kaneda Hiroyuki , Taniai Makiko , Shiratori Keiko
Published: December 2010

Abstract: Background: Soluble tumor necrosis factor receptor (sTNFR) is reported to be a good indicator of TNF production and severity in inflammatory diseases. To investigate the clinical significance of sTNFR in non‐alcoholic steatohepatitis (NASH), we measured the serum levels of soluble TNF receptor‐1 and ‐2.

Patients and Methods: We analyzed 82 NASH patients and 15 healthy subjects (control). The grades of fibrosis, inflammation and fatty deposit were evaluated on liver biopsy. The serum levels of sTNFR‐1 and ‐2 were measured by ELISA.

Results: There was significant correlation between platelet count and sTNFRs. The titers of sTNFR‐2 in NASH patients with diabetes mellitus (DM) were higher than in those without DM. The serum levels of sTNFRs in NASH patients with advanced fibrosis were increased compared with those of control and NASH patients with low‐grade fibrosis. Soluble TNFRs in patients with moderate inflammation were increased compared to those of control and patients with mild inflammation. There was no significant association between fatty deposit grade and sTNFRs.

Conclusion: Soluble TNFRs have a significant correlation with fibrosis in NASH.
Lymphocyte subset reconstitution after unrelated cord blood or bone marrow transplantation in children
Authors: Rénard Cécile , Barlogis Vincent , Mialou Valérie , Galambrun Claire , Bernoux Delphine , Goutagny Marie Pierre , Glasman Laurence , Loundou Anderson Dieudonné , Poitevin‐Later Françoise , Dignat‐George Françoise , Dubois Valérie , Picard Christophe , Chabannon Christian , Bertrand Yves , Michel Gérard
Published: December 2010

We report the post‐transplant lymphocyte subset recovery of 226 children treated with Unrelated Cord Blood transplant (UCBT) (n = 112) or Unrelated Bone Marrow Transplant (UBMT) (n = 114) for malignant or non‐malignant diseases. Absolute numbers of natural killer (NK), B and T cells were monitored by flow cytometry up to 5 years post‐transplant. Immunological endpoints were: time to achieve a CD3+ cell count >0·5 and 1·5 × 109/l, CD4+ > 0·2 and 0·5 × 109/l, CD8+ > 0·25 × 109/l, CD19+ > 0·2 × 109/l, NK > 0·1 × 109/l. These endpoints were analysed through the use of cumulative incidence curves in the context of competing risks. CD8+ T cell recovery was delayed after UCBT with a median time to reach CD8+ T cells > 0·25 × 109/l of 7·7 months whereas it was 2·8 months in UBMT (P < 0·001). B cell recovery was better in UCBT, with a median time to reach CD19+ cells > 0·2 × 109/l of 3·2 months in UCBT and 6·4 months in UBMT (P = 0·03). Median time for CD4+ T cell and NK cell recovery was similar in UCBT and UBMT. CD4+ T cells recovery was negatively correlated to age (better reconstitution in younger patients, P = 0·002). CD8+ T cells recovery was shorter in recipients with a positive cytomegalovirus serology (P = 0·001).
Extraction of microbial proteome from soil: potential and limitations assessed through a model study
Authors: Giagnoni L. , Magherini F. , Landi L. , Taghavi S. , Modesti A. , Bini L. , Nannipieri P. , Van der lelie D. , Renella G.
Published: December 2010

Proteomics is the study of functions and regulation of biological systems based on the analysis of the protein expression profile, and there is a general agreement that soil proteomics may be a tool for better soil management. Because of the ability of soils to stabilize extracellular proteins by various mechanisms, development of soil proteomics needs an assessment of the efficiency of protein extraction from various soil types. We evaluated the possibility of extraction of soil microbial proteome by inoculating Cupriavidus metallidurans CH34, which has a known proteome, into sterile sand, kaolinite, montmorillonite and a mixture of sand, kaolinite, montmorillonite, goethite and humic acids. One hour after inoculation, the viability of C. metallidurans was determined by the colony‐forming units method (CFU), the amount of extracted proteins was determined by the Bradford method and the bacterial proteome was analysed by the two‐dimensional gel electrophoresis technique (2D‐GE). The bacterial number was 2.5 × 106 CFU g−1 of soil in all microcosms, whereas the total extracted protein content varied from 98.1 to 1268 µg g−1 in the various microcosms, but was undetectable in the inoculated montmorillonite. The number of protein spots from the bacterial culture and the inoculated microcosms varied between 317 and 591, with 54 variable spots among the pure culture and the microcosms. No protein spots were detected in the 2D‐GE from the montmorillonite microcosm. The 2D‐GE of artificial soil microcosms showed a protein pattern that was different from those of pure culture and sand and kaolinite microcosms. The results confirm the importance of clay‐specific surface area and CEC in protein adsorption as montmorillonite alone had the largest sorptive capacity, and show that the artificial soil used also had a large sorptive capacity for microbial proteins. Globally, the results indicate that the extraction of proteins from soils is strongly influenced by the clay type and organic matter content, and that poor protein extraction efficiency may reduce the potential of soil proteomics.
Hepatitis A outbreaks: the effect of a mass vaccination programme
Authors: Torner N. , Broner S. , Martinez A. , Godoy P. , Batalla J. , Dominguez A. ,   the Hepatitis A Surveillance Group of Catalonia
Published: December 2010

Summary.  A Hepatitis A vaccination programme of people belonging to risk groups begun in Catalonia in 1995 and a universal vaccination programme of pre‐adolescents 12 years of age with the hepatitis A + B vaccine was added in 1998. The aim of the study was to investigate the characteristics of hepatitis A outbreaks occurring in Catalonia between 1991 and 2007 to determine the associated risk factors and optimize the use of vaccination. Incidence rates of outbreaks, cases and hospitalizations associated with outbreaks and the rate ratios (RR) of person‐to‐person transmission outbreaks between the periods before and after mass vaccination and their 95% confidence intervals (CI) were calculated. A rate of 2.45 outbreaks per million persons per year was found. The rate of cases affected in these outbreaks was 1.28 per 105 persons per year and the rate of hospitalizations was 0.45 per million persons per year. In person‐to‐person outbreaks, the highest incidence rate (5.26 and 6.33 per million persons per year) of outbreaks according to the age of the index case was in the 5 to 14 year age group in both periods (RR:0.83; 95% CI:0.48–1.43). A significant increase was observed in the 25 to 44 year age group (RR: 0.35; 95% CI 0.14–0.77). Hepatitis A vaccination has made an important impact on burden and characteristics of outbreaks and could provide greater benefits to the community if the vaccine was administrated to children during their first years of life.
Effect of maintenance therapy with low‐dose peginterferon for recurrent hepatitis C after living donor liver transplantation
Authors: Ueda Y. , Marusawa H. , Kaido T. , Ogura Y. , Oike F. , Mori A. , Ogawa K. , Yoshizawa A. , Hatano E. , Miyagawa‐Hayashino A. , Haga H. , Egawa H. , Takada Y. , Uemoto S. , Chiba T.
Published: December 2010

Summary.  Approximately 30% of patients who have recurrent hepatitis C after liver transplantation achieve sustained virological response (SVR) by taking a combination therapy of pegylated interferon and ribavirin. For the remaining non‐SVR patients, an effective management treatment has not yet been established. In this study, efficacy of long‐term peginterferon maintenance therapy for non‐SVR patients was evaluated. Forty patients who had previously received the combination therapy for hepatitis C after living donor liver transplantation were classified into one of the following three groups: the SVR group (n = 11); the non‐SVR‐IFN group (n = 17), which received low‐dose peginterferon maintenance therapy for non‐SVR patients; and the non‐SVR‐Withdrawal group (n = 12), which discontinued the interferon treatment. We then compared histological changes among these three groups after 2 or more years follow‐up. Activity grade of liver histology improved or remained stable in patients in the SVR and non‐SVR‐IFN groups, but deteriorated in half of the patients in the non‐SVR‐Withdrawal group. Fibrosis improved or remained stable in 10 of 11 SVR patients and in 13 of 17 non‐SVR‐IFN patients, but deteriorated in all non‐SVR‐Withdrawal patients. Mean changes in fibrosis stage between pretreatment and final liver biopsy were −0.18, +0.06 and +2.2 in the SVR, non‐SVR‐IFN and non‐SVR‐Withdrawal groups, respectively. Fibrosis stage deteriorated to F3 or F4 significantly more rapidly in the non‐SVR‐Withdrawal group than in the other two groups. In conclusion, continuing long‐term maintenance therapy with peginterferon prevented histological progression of hepatitis C in patients who had undergone living donor liver transplantation.
Overcoming methodical limits of standard RHD genotyping by next‐generation sequencing
Authors: Stabentheiner S. , Danzer M. , Niklas N. , Atzmüller S. , Pröll J. , Hackl C. , Polin H. , Hofer K. , Gabriel C.
Published: December 2010

Background and objectives  Molecular variations of the RHD gene may result in the reduced expression of the D antigen and altered Rh phenotypes. In many occasions, they cannot be typed reliably by standard serological methods. Sequence‐based typing is the gold standard to determine rare and unknown RHD genotypes. For this pilot study, sequence‐based typing by standard Sanger sequencing was compared to a newly established next‐generation sequencing approach based on pyrosequencing.

Materials and methods  Twenty‐six DNA samples were selected after primary serological testing exhibiting a weak reaction in Rh phenotype. Parallel sequence analysis of the complete coding sequence including adjacent intronic sequences allowed a comparison of the methodical potency in mutation detection of Sanger with next‐generation sequencing.

Results  Sanger sequencing revealed 39 RHD polymorphisms in 21 of 26 samples in the RHD coding region, while pyrosequencing detected all but two alterations resulting in a concordance rate of 94·9% and clearly revealed a heterozygous compound mutation in one sample with RHDψ and Weak D type 4 alleles. The resolution of cis/trans linkage of polymorphisms and exact characterization of a 37 bp duplication was achieved by next‐generation sequencing.

Conclusion  Our data suggest that next‐generation sequencing offers a new development for high‐throughput and clonal sequencing for molecular RHD genotyping. However, further attempts in the methodical set‐up have to be undertaken prior to validation and introduction as a routine service.
Flowering phenological pattern in crowns of four temperate deciduous tree species and its reproductive implications
Authors: Tal O.
Published: December 2010

Temperate deciduous forest trees flower in spring, a period that starts when the trees lack leaves and when weather is unpredictable, including frost events, and ends when the forest becomes green and vertical microclimatic gradients are established. This paper asks whether there are spatio‐temporal patterns in the development of flowering in trees, and how they relate to reproductive processes. Using a crane, flowering phenology was studied in the crowns of ca. 200 trees of four species, from early spring (ash) through the period of leaf‐unfolding (maples) to early summer (lime). Flowering levels in different crown regions were documented quantitatively and repeatedly during the flowering season and compared among individuals and among species. Early‐flowering trees displayed a clear and consistent acropetalous and centrifugal flowering pattern, while this pattern disappeared in species that flowered after leaves unfolded. This pattern was superposed on the basic flowering rhythm of each species, and was influenced by effects of direct sunlight, acting at a small scale in early spring and at a large scale in early summer. As this acropetalous centrifugal pattern contrasts the microclimatic gradients that develop only after leaves unfold, it might indicate physiological processes in the ‘awakening’ of trees, as well as evolutionary processes that took place in temperate trees during adaptation to a temperate climate.
A new species ofMelampsorarust onSalix elbursensisfrom Iran
Authors: Damadi S. M. , Pei M. H. , Smith J. A. , Abbasi M.
Published: December 2010

A rust fungus was found causing stem cankers on 1‐ to 5‐year‐old stems ofSalix elbursensisin the north west of Iran. The rust also forms uredinia on leaves and flowers of the host willow. Light and scanning electron microscopy revealed that the new rust is morphologically distinct from severalMelampsoraspecies occurring on the willows taxonomically close toS. elbursensis, but indistinguishable fromMelampsora larici‐epitea. Examination of the internal transcribed spacer (ITS) region of the ribosomal DNA suggested that the rust fungus is phylogenetically close toMelampsora allii‐populinaandMelampsora pruinosaeonPopulusspp. Based on both the morphological characteristics and the ITS sequence data, the rust is described as a new species –Melampsora iranicasp. nov.
SCHOLARLY PAPER: The nursing care traditional Chinese node
Authors: Mu Pei‐Fan
Published: December 2010

Mu P‐F. International Journal of Nursing Practice 2010; 16: 645–646 The nursing care traditional Chinese node
SCHOLARLY PAPER: Cochrane nursing care field nursing care clinical trial database node
Authors: Hopp Lisa
Published: December 2010

Hopp L. International Journal of Nursing Practice 2010; 16: 647–648 Cochrane nursing care field nursing care clinical trial database node
Benefits of first‐half intensive haemodiafiltration for the removal of uraemic solutes
Authors: NAGAOKA YUME , MATSUMOTO HIROSHI , OKADA TOMONARI , IWASAWA HIDEAKI , TOMARU RYO , WADA TOSHIKAZU , GONDO ASAKO , NAKAO TOSHIYUKI
Published: December 2010

Aim:  Haemodiafiltration (HDF) is the most efficient blood purification method and can remove a wide spectrum of solutes of different molecular weights (MW). The purpose of this study was to investigate whether the removed amounts of solutes, especially the larger molecules, could be increased by changing the HDF filtration procedure.

Methods:  A new first‐half intensive HDF treatment (F‐HDF) was designed, whereby convective clearance is intensively forced during the first half of a HDF session. We compared the removed amounts of solutes in the same group of nine patients treated by F‐HDF, constant rate‐replacing HDF (C‐HDF) and a high‐flux haemodialysis (HD).

Results:  F‐HDF can remove significantly larger amounts of α1‐microglobulin (MG), molecular weight (MW) 33 000, compared with HD and C‐HDF (30.1 ± 15.1 vs 12.4 ± 0.3, 15.0 ± 3.1 mg, P < 0.01). Regarding the removal amounts and clear space of β2MG, MW 11 800, there were no significant differences between the three treatment modalities. Regarding amounts of creatinine, urea nitrogen and phosphorus, there were no significant differences between the three treatment modalities.

Conclusion:  In post‐replacement HDF with a high‐flux membrane dialyzer, the method used in the present study in which replacement is completed during the first half of the process, is associated with a greater rate of larger molecule removal than the conventional uniform replacement method.
Novel groups of Gammaproteobacteria catalyse sulfur oxidation and carbon fixation in a coastal, intertidal sediment
Authors: Lenk Sabine , Arnds Julia , Zerjatke Katrice , Musat Niculina , Amann Rudolf , Mußmann Marc
Published: December 2010

The oxidation of hydrogen sulfide is essential to sulfur cycling in marine habitats. However, the role of microbial sulfur oxidation in marine sediments and the microorganisms involved are largely unknown, except for the filamentous, mat‐forming bacteria. In this study we explored the diversity, abundance and activity of sulfur‐oxidizing prokaryotes (SOP) in sulfidic intertidal sediments using 16S rRNA and functional gene sequence analyses, fluorescence in situ hybridization (FISH) and microautoradiography. The 16S rRNA gene analysis revealed that distinct clades of uncultured Gammaproteobacteria are important SOP in the tidal sediments. This was supported by the dominance of gammaproteobacterial sequences in clone libraries of genes encoding the reverse dissimilatory sulfite reductase (rDSR) and the adenosine phosphosulfate reductase (APR). Numerous sequences of all three genes grouped with uncultured autotrophic SOP. Accordingly, Gammaproteobacteria accounted for 40–70% of all 14CO2‐incorporating cells in surface sediments as shown by microautoradiography. Furthermore, phylogenetic analysis of all three genes consistently suggested a discrete population of SOP that was most closely related to the sulfur‐oxidizing endosymbionts of the tubeworm Oligobrachia spp. FISH showed that members of this population (WS‐Gam209 group) were abundant, reaching up to 1.3 × 108 cells ml−1 (4.6% of all cells). Approximately 25% of this population incorporated CO2, consistent with a chemolithoautotrophic metabolism most likely based on sulfur oxidation. Thus, we hypothesize that novel, gammaproteobacterial SOP attached to sediment particles may play a more important role for sulfide removal and primary production in marine sediments than previously assumed.
Developing and Utilizing Network Resources: Roles of Political Skill
Authors: Wei Li‐Qun , Chiang Flora F. T. , Wu Long‐Zeng
Published: December 2010

abstract

This study examines the role of political skill in thedevelopmentandutilizationof network resources at the individual level. Drawing on the behavioural and network perspectives as well as political skill literature, we propose that political skill increases one's network resources (developing network), which will benefit his/her performance and career success. Moreover, political skill is hypothesized to strengthen the relationships between network resources and performance and career outcomes (utilizing network). A two‐wave study on a sample of 281 supervisor–subordinate dyads from six electronic firms in China confirms our hypotheses. Our examination of the dual role of political skill facilitates a better understanding of the networking process from the perspective of individual skill/behaviour, thus enriching the behavioural theory and network literature. Implications are discussed and directions for future research are suggested.
The Poverty Reduction Strategy Approach Six Years On: An Examination of Principles and Practice in Uganda
Authors: Canagarajah Sudharshan , Diesen Arthur van
Published: December 2010

It is over six years since the World Bank and the IMF started promoting a PRS approach to development management in low‐income countries. The 2005 review endorsed the approach, but highlighted the need for a renewed focus on the principles underpinning it: country ownership; results orientation; comprehensiveness; partnership focus; and long‐term outlook. Uganda is often hailed as one of the best PRS performers. This article finds that Uganda's Poverty Eradicaton Action Plan (PEAP) has brought significant gains to development management, but that its performance against several of the PRS principles is disappointing. A return to these principles could improve the practice of the government and development partners around the PEAP – a finding likely to be applicable to many countries implementing a PRS.
THE ETHICS OF IMPOSSIBLE AND POSSIBLE CHANGES TO HUMAN NATURE
Authors: MURPHY TIMOTHY F.
Published: December 2010

Some commentators speak freely about genetics being poised to change human nature. Contrary to such rhetoric, Norman Daniels believes no such thing is plausible since ‘nature’ describes characteristic traits of human beings as a whole. Genetic interventions that do their work one individual at a time are unlikely to change the traits of human beings as a class. Even so, one can speculate about ways in which human beings as a whole could be genetically altered, and there is nothing about that venture that could not be deliberated in the way other high‐impact questions can be evaluated. There might well come a time when it would be defensible to use genetics to change human beings as a class, in order to protect people in the face of changed environmental circumstances or to enhance existing capacities. Moreover, if one understands human nature not in an empirically descriptive way but in a metaphysical way having implications about human behavior, it can make sense to talk about de‐naturing individuals through genetic changes. Even under a metaphysical conception of human nature, however, one can still imagine that people in the future might want to alter their traits in pursuit of another normative idea of a good and valuable life, and genetic modifications might function as a pathway to that change.
INTENSIVE CARE TRIAGE: PRIORITY SHOULD BE INDEPENDENT OF WHETHER PATIENTS ARE ALREADY RECEIVING INTENSIVE CARE
Authors: HOPE TONY , MCMILLAN JOHN , HILL ELAINE
Published: December 2010

Intensive care units (ICUs) are not always able to admit all patients who would benefit from intensive care. Pressure on ICU beds is likely to be particularly high during times of epidemics such as might arise in the case of swine influenza. In making choices as to which patients to admit, the key US guidelines state that significant priority should be given to the interests of patients who are already in the ICU over the interests of patients who would benefit from intensive care but who have not been admitted. We examine four reasons that in principle might justify such a prioritization rule and conclude that none is convincing. We argue that the current location of patients should not, in principle, affect their priority for intensive care. We show, however, that under some but not all circumstances, maximizing lives saved by intensive care might require continuing to treat in the ICU a patient already admitted rather than transferring that patient out of the unit in order to admit a sicker patient who would also benefit more from intensive care. We conclude that further modelling is required in order to clarify what practical policies would maximize lives saved by intensive care.
Models of power and the deletion of participation in a classroom literacy event
Authors: Jacobs Gloria E.
Published: December 2010

This article uses the analytic lens of power relations and models of power to examine how the participation of two students in an urban US eighth‐grade English language arts class was symbolically and literally deleted. The researcher asks why do some students fail despite being placed in a technologically rich educational environment that ostensibly draws on best practices? Drawing on data collected during an academic year, the author uses a telling case of a dyad engaged in on‐line research and the creation of a PowerPoint presentation to illustrate how the students try to participate and complete the assignment but experience failure. The author raises questions about the context of the students' lives as well as the nature of the classroom instruction and assessment structure. It is argued that further research into the nature of participation is needed to address the lack of student success in urban schools.
METHODOLOGICAL CHOICES IN KELSEY'S ECCENTRIC EXISTENCE
Authors: THIEL JOHN E.
Published: December 2010

This article explores the methodological choices that shape David Kelsey's magnum opus Eccentric Existence: A Theological Anthropology (2009). These choices are explicit, and elucidated by Kelsey primarily in the introductory sections of this work. Considered in turn are Kelsey's rejection of a modern, apologetical approach to the theological task, his recovery of a premodern commitment to explaining the logic of beliefs rather than the logic of coming to belief, his explication of theological anthropology through a God‐centered, Trinitarian, understanding of the biblical plot, and his decision to elucidate the human person theologically through an appreciation of the canonical Wisdom literature, which valorizes humanity's created goodness. It concludes by assessing Kelsey's project as an unsystematic systematic theology, a notion he develops as well in his earlier Imagining Redemption (2005).
Staff beliefs about why people with learning disabilities self‐harm: a Q‐methodology study
Authors: Dick Katie , Gleeson Kate , Johnstone Lucy , Weston Clive
Published: December 2010

Accessible summary

 Staff beliefs about why people with learning disabilities self‐harm are important because they can affect the way that staff respond to the behaviour.

 Staff who work with people with learning disabilities said why they think people with learning disabilities self‐harm.

 Staff had many different views on why people with learning disabilities self‐harm. Staff thought that people with learning disabilities self‐harm because they are distressed. Some staff said it is difficult to understand why people with learning disabilities self‐harm. Some staff said people self‐harm because of their learning disabilities.

 It would be useful for staff to receive more training about self‐harm. This could improve care for people with learning disabilities who self‐harm.

Staff beliefs about self‐harm can influence staff responses to the behaviour. Existing research into staff beliefs about self‐harm by people with learning disabilities is limited, with qualitative research restricted to forensic services. The aim of this study was to use Q‐methodology to explore staff beliefs about why people with learning disabilities self‐harm. Five distinct viewpoints were identified: self‐harm is individual, complex and emotionally meaningful; self‐harm is a means to communicate distress, whether or not you have learning disabilities; self‐harm is difficult to understand but seems to be a way to modify emotional states; self‐harm is a result of having learning disabilities and being different; and self‐harm is meaningful within relationships. These viewpoints represent the variety of theories and discussions in the literature. It is proposed that some of these viewpoints may result in more helpful responses to self‐harm than others. Therefore, further staff training that promotes skills in developing a comprehensive and individual understanding of self‐harm is recommended.
The combination of primary sclerosing cholangitis and CCR5‐Δ32 in recipients is strongly associated with the development of nonanastomotic biliary strictures after liver transplantation
Authors: op den Dries Sanna , Buis Carlijn I. , Adelmeijer Jelle , Van der Jagt Eric J. , Haagsma Elizabeth B. , Lisman Ton , Porte Robert J.
Published: December 2010

Background: The role of the immune system in the pathogenesis of nonanastomotic biliary strictures (NAS) after orthotopic liver transplantation (OLT) is unclear. A loss‐of‐function mutation in the CC chemokine receptor 5 (CCR5‐Δ32) leads to changes in the immune system, including impaired chemotaxis of regulatory T cells.

Aim: To investigate the impact of the CCR5‐Δ32 mutation on the development of NAS.

Methods: In 384 OLTs, we assessed the CCR5 genotype in donors and recipients and correlated this with the occurrence of NAS.

Results: The CCR5‐Δ32 allele was found in 65 (16.9%) recipients. The cumulative incidence of NAS at 5 years was 6.5% in wild‐type (Wt) recipients vs 17.2% for carriers of the CCR5‐Δ32 allele (P<0.01). In recipients with CCR5‐Δ32, 50% of all NAS occurred >2 years after OLT, compared with 10% in the Wt group. In multivariate regression analysis, the adjusted risk of developing NAS was four‐fold higher in recipients with CCR5‐Δ32 (P<0.01). The highest risk of NAS was seen in patients transplanted for primary sclerosing cholangitis (PSC), who also carried CCR5‐Δ32 (relative risk 5.4, 95% confidence interval 2.2–12.9; P<0.01). Donor CCR5 genotype had no impact on the occurrence of NAS.

Conclusions: Patients with the CCR5‐Δ32 mutation have a four‐fold higher risk of developing NAS, compared with Wt recipients. This risk is even higher in patients with CCR5‐Δ32 transplanted for PSC. Late development of NAS is significantly more present in patients with CCR5‐Δ32. These data suggest that the immune system plays a critical role in the development of NAS after OLT.
Limitations in predicting dyebath exhaustion using optical spectroscopy
Authors: Günay Melih , Jasper Warren J
Published: December 2010

There are practical limitations in predicting dyebath concentrations and dyebath exhaustion using absorbance measurements from optical spectroscopy. The purpose of this paper is to examine the common assumptions of prediction models that cause prediction errors, and especially when multiple dye combinations are used. If a linear model is used to map absorbance to concentration, then five assumptions must hold: measurement repeatability, linear scaling, spectral additivity, linear independence of the constituent spectra and the absence of spectral morphing. Violation of one or more of these assumptions will lead to errors in predicting the concentrations of dyes in a dyebath and subsequent exhaustion calculations.
Model for blood collections management
Authors: Lowalekar Harshal , Ravichandran N.
Published: December 2010

BACKGROUND: A typical blood bank gets its major supply of blood from organizing blood donation camps. The quantity of blood collected in the blood donation drives is random and it might be sensible to cut off the supply at some level to reduce the wastages by overcollection.

STUDY DESIGN AND METHODS: In this paper we introduce two new cutoff level policies and compare their performance with the policy of collecting all the available supply at blood collection drives, which is quite prevalent among the blood banks. We develop a simulation model for collection that enables such comparison on the basis of shortages, wastages, and total costs.

RESULTS AND CONCLUSION: The results obtained from the simulation model for a real‐life situation show that the cutoff level policies are better than the unrestricted collection policy in controlling total costs. They also result in less wastage in the system for a given level of shortages.
Governing on the Edges: Globalization of Production and the Challenge to Public Administration in the Twenty‐First Century
Authors: Abonyi George , Van Slyke David M.
Published: December 2010

Globalization means many things for governments around the world in terms of governance. Questions that are left unexplored in the public administration literature are what changes in the globalization of production mean for governments and their relationships with business and civil society, and what the implications are for public administration. The authors develop a conceptual framework that governments can use to shape their interactions with business in more strategically and mutually beneficial ways. The data are derived from extensive fieldwork in the emerging economies of Southeast Asia. Key challenges to government include the importance of understanding global value chains, value chain‐related trade facilitation, investment in logistics, the strengthening of enterprise clusters, effective education, skill development and training, and the governance risks inherent in value chains and networks. The essay concludes with a discussion of five key considerations for public administration in thinking, planning, and acting strategically in relationships with the private sector regarding the globalization of production. These considerations are crucial for creating business environments that strengthen economic development and manage societal concerns in ways that are aligned with public values.
At Your Service? Volunteering and National Service in 2020
Authors: Nesbit Rebecca , Brudney Jeffrey L.
Published: December 2010

This article evaluates the potential of the Edward M. Kennedy Serve America Act of 2009 to raise the level of volunteering and national service in the United States, particularly among young people, and its implications for public administration in 2020. The act would increase service‐learning opportunities and national service placements substantially. Research suggests that participation in these activities is associated with increased volunteering, civic and political engagement, and interest in a career in government or nonprofit service, especially among African Americans and Hispanics. These results hold considerable promise for the practice of public administration in 2020. The authors find that their effectuation depends not only on increasing federal service programs significantly and continuing growth in funding, but also on addressing important challenges, such as the ability of public policy to increase volunteering, volunteer management capacity to support these efforts, the role of volunteering in addressing pressing social issues, and reaching disadvantaged populations.