bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of invasive candidal infection in critically ill patients with severeacute pancreatitis
Authors: Hall Alison M , Poole Lee AL , Renton Bryan , Wozniak Alexa , Fisher Michael , Neal Timothy , Halloran Christopher M , Cox Trevor , Hampshire Peter A 
Published: March 2013

Abstract
Introduction
Patients with severe acute pancreatitis are at risk of candidal infectionscarrying the potential risk of an increase in mortality. Since early diagnosis isproblematic, several clinical risk scores have been developed to identify patientsat risk. Such patients may benefit from prophylactic antifungal therapy whilethose patients who have a low risk of infection may not benefit and may be harmed.The aim of this study was to assess the validity and discrimination of existingrisk scores for invasive candidal infections in patients with severe acutepancreatitis.

Methods
Patients admitted with severe acute pancreatitis to the intensive care unit wereanalysed. Outcomes and risk factors of admissions with and without candidalinfection were compared. Accuracy and discrimination of three existing risk scoresfor the development of invasive candidal infection (Candida score, CandidaColonisation Index Score and the Invasive Candidiasis Score) were assessed.

Results
A total of 101 patients were identified from 2003 to 2011 and 18 (17.8%) of thesedeveloped candidal infection. Thirty patients died, giving an overall hospitalmortality of 29.7%. Hospital mortality was significantly higher in patients withcandidal infection (55.6% compared to 24.1%, P = 0.02). Candida colonisation was associated with subsequent candidal infection onmultivariate analysis. The Candida Colonisation Index Score was the most accuratetest, with specificity of 0.79 (95% confidence interval [CI] 0.68 to 0.88),sensitivity of 0.67 (95% CI 0.41 to 0.87), negative predictive value of 0.91 (95%CI 0.82 to 0.97) and a positive likelihood ratio of 3.2 (95% CI 1.9 to 5.5). TheCandida Colonisation Index Score showed the best discrimination with area underthe receiver operating characteristic curve of 0.79 (95% CI 0.69 to 0.87).

Conclusions
In this study the Candida Colonisation Index Score was the most accurate anddiscriminative test at identifying which patients with severe acute pancreatitisare at risk of developing candidal infection. However its low sensitivity maylimit its clinical usefulness.
The influence of gender on the epidemiology of and outcome from severe sepsis
Authors: Sakr Yasser , Elia Cristina , Mascia Luciana , Barberis Bruno , Cardellino Silvano , Livigni Sergio , Fiore Gilberto , Filippini Claudia , Ranieri Vito Marco 
Published: March 2013

Abstract
Introduction
The impact of gender on outcome in critically ill patients is unclear. Weinvestigated the influence of gender on the epidemiology of severe sepsis andassociated morbidity and mortality in a large cohort of ICU patients in the regionof Piedmont in Italy.

Methods
This was a post-hoc analysis of data from a prospective, multicenter,observational study in which all patients admitted to one of 24 participatingmedical and/or surgical ICUs between 3 April 2006 and 29 September 2006 wereincluded.

Results
Of the 3,902 patients included in the study, 63.5% were male. Female patients weresignificantly older than male patients (66 ± 16 years vs. 63 ± 16 years,P < 0.001). Female patients were less likely to have severe sepsisand septic shock on admission to the ICU and to develop these syndromes during theICU stay. ICU mortality was similar in men and women in the whole cohort (20.1%vs. 19.8%, P = 0.834), but in patients with severe sepsis wassignificantly greater in women than in men (63.5% vs. 46.4%, P = 0.007).In multivariate logistic regression analysis with ICU outcome as the dependentvariable, female gender was independently associated with a higher risk of ICUdeath in patients with severe sepsis (odds ratio = 2.33, 95% confidence interval =1.23 to 4.39, P = 0.009) but not in the whole cohort (odds ratio = 1.07,95% confidence interval = 0.87 to 1.34).

Conclusion
In this large regional Italian cohort of ICU patients, there were more male thanfemale admissions. The prevalence of severe sepsis was lower in women than in men,but female gender was independently associated with a higher risk of death in theICU for patients with severe sepsis.
Macrophage phenotypes during tissue repair
Authors: Novak Margaret L , Koh Timothy J 
Published: March 2013

Abstract
Review on tissue repair and M1-like to M2a-like macrophages, exhibiting important differences from in vitro phenotypes.
Mp are crucial for tissue repair and regeneration but can also contribute to tissue damage and fibrosis. Mp can adopt a variety of functional phenotypes in response to different stimuli; two of the best-characterized in vitro phenotypes are a proinflammatory “M1” phenotype, produced by exposure to IFN-γ and TNF-α, and an anti-inflammatory “M2a” phenotype, produced by IL-4 or IL-13. M2a Mp are frequently termed “wound healing” Mp, as they express factors that are important for tissue repair. This review will summarize current knowledge of Mp phenotypes during tissue repair and will argue that these in vivo Mp populations are heterogeneous and temporally regulated and do not conform to existing, in vitro-defined M1 or M2 phenotypes. Mp during the early stages of tissue repair exhibit a more proinflammatory phenotype than their later counterparts, which in turn may exhibit some M2a-associated characteristics. However, phenotypic markers that appear to be coregulated in cultured Mp can be expressed independently of each other in vivo. Additionally, M1- and M2-associated markers may be expressed simultaneously by actual tissue-repair Mp. Improved understanding of Mp phenotypes and their regulation may assist in generation of novel therapies based on manipulating Mp function to improve healing.
Central and haematopoietic interleukin-1 both contribute to ischaemic brain injury in mice
Authors: Denes Adam , Wilkinson Fiona , Bigger Brian , Chu Michael , Rothwell Nancy J. , Allan Stuart. M. 
Published: March 2013

Summary
Interleukin-1 (IL-1) is a key regulator of inflammation and ischaemic brain injury, but the contribution of central and peripheral sources of IL-1 to brain injury is not well understood. Here we show that haematopoietic-derived IL-1 is a key driver of ischaemic brain injury. Wild type (WT) mice transplanted with IL-1αβ-deficient bone marrow displayed a significant (40%) reduction in brain injury induced by focal cerebral ischaemia compared to WT mice transplanted with WT bone marrow. This was paralleled by improved neurological outcome and the almost complete absence of splenic-derived, but not liver-derived, IL-1α after stroke in WT mice lacking haematopoietic-derived IL-1. IL-1αβ knockout (KO) mice transplanted with IL-1αβ-deficient bone marrow showed a 60% reduction in brain injury compared to WT mice receiving WT bone marrow. Transplantation of WT bone marrow in IL-1αβ KO mice resulted in a similar level of blood-brain-barrier injury to that observed in WT mice receiving IL-1αβ-deficient bone marrow. Cerebral oedema after brain injury was reduced in IL-1αβ KO recipients irrespective of donor-derived IL-1, but a lack of haematopoetic IL-1 has also been associated with smaller brain oedema independently of recipient status. Thus, both central and haematopoietic-derived IL-1 are important contributors to brain injury after cerebral ischaemia. Identification of the cellular sources of IL-1 in the periphery could allow targeted interventions at these sites.
Erythropoietin attenuates cardiac dysfunction in experimental sepsis in mice via activation of the β-common receptor
Authors: Khan Areeg I. , Coldewey Sina M. , Patel Nimesh S. A. , Rogazzo Mara , Collino Massimo , Yaqoob Muhammed M. , Radermacher Peter , Kapoor Amar , Thiemermann Christoph 
Published: March 2013

SummaryThere is limited evidence that the tissue-protective effects of erythropoietin are mediated by a heterocomplex of the erythropoietin receptor and the β-common receptor (‘tissue-protective receptor’), which is pharmacologically distinct from the ‘classical’ erythropoietin receptor homodimer that is responsible for erythropoiesis. However, the role of the β-common receptor and/or erythropoietin in sepsis-induced cardiac dysfunction (a well known, serious complication of sepsis) is unknown. Here we report for the first time that the β-common receptor is essential for the improvements in the impaired systolic contractility afforded by erythropoietin in experimental sepsis. Cardiac function was assessed in vivo (echocardiography) and ex vivo (Langendorff-perfused heart) in wild-type and β-common receptor knockout mice, that were subjected to lipopolysaccharide (9 mg/kg body weight; young mice) for 16-18 hours or cecal ligation and puncture (aged mice) for 24 hours. Mice received erythropoietin (1000 IU/kg body weight) 1 hour after lipopolysaccharide or cecal ligation and puncture. Erythropoietin reduced the impaired systolic contractility (in vivo and ex vivo) caused by endotoxemia or sepsis in young as well as old wild-type mice in a β-common-receptor-dependent fashion. Activation by erythropoietin of the β-common receptor also resulted in the activation of well-known survival pathways (Akt and endothelial nitric oxide synthase) and inhibition of pro-inflammatory pathways (glycogen synthase kinase-3β, nuclear factor-κB and interleukin-1β). All the above pleiotropic effects of erythropoietin were lost in β-common receptor knockout mice. Erythropoietin attenuates the impaired systolic contractility associated with sepsis by activation of the β-common receptor, which, in turn, results in activation of survival pathways and inhibition of inflammation.
Mixing Enhancement Effect of Low-molecular-weight Organogelators for Thixotropic Organogel Creation
Authors: Ohsedo Yutaka , Watanabe Hisayuki , Oono Masashi , Tanaka Akihiro 
Published: March 2013

Abstract
In this study, we found that organogels composed of mixed alkylhydrazide derivatives with different alkyl chains as low-molecular-weight organogelators showed thixotropic properties, whereas organogels composed of a single alkylhydrazide component did not show such properties. With a two- or three-component system of alkylhydrazides, the transparency and mechanical properties of the resulting organogels were enhanced. This mixing enhancement for organogelators might be due to an improved network of closer and finer fibers compared to that in a one-component system.
Helix-sense-selective Polymerization of Substituted Acetylenes by Using an Isolated Rh Chiral Initiator with an Amino Acid Ligand
Authors: Zang Yu , Ohishi Tomoyuki , Aoki Toshiki , Teraguchi Masahiro , Kaneko Takashi 
Published: March 2013

Abstract
Helix-sense-selective polymerization (HSSP) of substituted acetylenes by using an isolated chiral Rh initiator with an amino acid ligand has been achieved. The sense of the helix of the main chain of the resulting polymer was controlled by the sign of the chirality of the ligand. The isolated initiator needed less of the chiral ligand and gave polymers having a higher [θ] value than the two component chiral initiator systems we reported previously. The resulting polymers had a higher Mw.
Selective Crystallization of W by Hydrothermal Treatment of Wastewater Containing W and Mo
Authors: Sasai Ryo , Hirata Koichiro 
Published: March 2013

Abstract
Tungsten was selectively recovered from wastewater containing W and Mo, as crystalline tungsten trioxide, by hydrothermal treatment. The optimal hydrothermal conditions for selective recovery of W involved treatment at 503 K for more than 8 h after adjusting the initial pH of the wastewater to 4.
Water-sliding Property of Polyacrylates with Different Fluoro Side Chains
Authors: Hirai Tomoyasu , Haraguchi Masayuki , Sakai Atsushi , Penaloza, Jr. David P , Ozawa Masaaki , Miyaji Katsuaki , Tanaka Keiji 
Published: March 2013

Abstract
The incorporation of fluoro-containing moieties into polymers can significantly change their surface properties. In this study, we synthesized two polyacrylates with different fluoro-containing side chains to give a better understanding of how the water-sliding property of polymers can be controlled.
Facile Synthesis of Thermally Stable Benzimidazolate-type Ionic Liquids
Authors: Tsuji Yuki , Ohno Hiroyuki 
Published: March 2013

Abstract
Novel azolate-type ionic liquids (ILs), alkyltributylphosphonium benzimidazolates (alkyl chain: methyl, butyl, and octyl), were prepared by neutralization of the corresponding alkyltributylphosphonium hydroxides with benzimidazole. All the azolate-type ILs prepared here showed high ionic conductivities above 10−3 S cm−1 at 80 °C, and good thermal stability over 300 °C. They are expected to be useful platforms for functional ILs having good thermal stabilities.
Synthesis of Silicon Quantum Dots Functionalized Chemically with Monosaccharides and Their Use in Biological Fluorescence Imaging
Authors: Nakahara Yoshio , Machiya Kazuki , Sato Toshiyuki , Nwe Ni Tar , Furuike Tetsuya , Tamura Hiroshi , Kimura Keiichi 
Published: March 2013

Abstract
Novel water-dispersible, pH-stable, and biocompatible quantum dots were synthesized through the surface modification of silicon quantum dots (SiQDs) with monosaccharides. The presence of the monosaccharide on the surface of the SiQDs was recognized by fluorescence measurements using its complementary lectin (concanavalin A). The fluorescence cell imaging was carried out by using SiQDs functionalized chemically with d-glucosamine, and it was shown that the SiQDs developed in this study are applicable as blue chromophores for biological fluorescence imaging.
Unequal Recombination and Evolution of the Mating-Type (MAT) Loci in the Pathogenic FungusGrosmannia clavigeraand Relatives
Authors: Tsui Clement K-M , DiGuistini Scott , Wang Ye , Feau Nicolas , Dhillon Braham , Bohlmann Jörg , Hamelin Richard C 
Published: March 2013

AbstractSexual reproduction in fungi is regulated by the mating-type (MAT) locus where recombination is suppressed. We investigated the evolution of MAT loci in eight fungal species belonging to Grosmannia and Ophiostoma (Sordariomycetes, Ascomycota) that include conifer pathogens and beetle symbionts. The MAT1-2 idiomorph/allele was identified from the assembled and annotated Grosmannia clavigera genome, and the MAT locus is flanked by genes coding for cytoskeleton protein (SLA) and DNA lyase. The synteny of these genes is conserved and consistent with other members in Ascomycota. Using sequences from SLA and flanking regions, we characterized the MAT1-1 idiomorph from other isolates of G. clavigera and performed dotplot analysis between the two idiomorphs. Unexpectedly, the MAT1-2 idiomorph contains a truncated MAT1-1-1 gene upstream of the MAT1-2-1 gene that bears the high-mobility-group domain. The nucleotide and amino acid sequence of the truncated MAT1-1-1 gene is similar to its homologous copy in the MAT1-1 idiomorph in the opposite mating-type isolate, except that positive selection is acting on the truncated gene and the alpha(α)-box that encodes the transcription factor has been deleted. The MAT idiomorphs sharing identical gene organization were present in seven additional species in the Ophiostomatales, suggesting that the presence of truncated MAT1-1-1 gene is a general pattern in this order. We propose that an ancient unequal recombination event resulted in the ancestral MAT1-1-1 gene integrated into the MAT1-2 idiomorph and surviving as the truncated MAT1-1-1 genes. The α-box domain of MAT1-1-1 gene, located at the same MAT locus adjacent to the MAT1-2-1 gene, could have been removed by deletion after recombination due to mating signal interference. Our data confirmed a 1:1 MAT/sex ratio in two pathogen populations, and showed that all members of the Ophiostomatales studied here including those that were previously deemed asexual have the potential to reproduce sexually. This ability can potentially increase genetic variability and can enhance fitness in new, ecological niches.
Strain Specific Genotype−Environment Interactions and Evolutionary Potential for Body Mass in Brook Charr (Salvelinus fontinalis)
Authors: Crespel Amélie , Bernatchez Louis , Audet Céline , Garant Dany 
Published: March 2013

AbstractDiscriminating between genetic and environmental causes of phenotypic variation is an essential requirement for understanding the evolutionary potential of populations. However, the extent to which genetic variation differs among conspecific groups and environments during ontogeny has rarely been investigated. In this study, the genetic basis of body mass was measured in three divergent strains of brook charr (Salvelinus fontinalis) in different rearing environments and at different time periods. The results indicate that body mass was a heritable trait in all strains but that the level of heritability greatly differed among strains. Moreover, heritability estimates of each strain varied differently according to environmental rearing conditions, and cross-environments correlations were all significantly lower than unity, indicating strain-specific patterns of genotype–environment interactions. Heritability estimates also varied throughout ontogeny and decreased by 50% from 9 to 21 months of age. This study highlights the divergence in genetic architecture and evolutionary potential among these strains and emphasizes the importance of considering the strain-specific potential of the response to selection according to environmental variation.
Distinct 3-O-Sulfated Heparan Sulfate Modification Patterns Are Required forkal-1−Dependent Neurite Branching in a Context-Dependent Manner inCaenorhabditis elegans
Authors: Tecle Eillen , Diaz-Balzac Carlos A , Bülow Hannes E 
Published: March 2013

AbstractHeparan sulfate (HS) is an unbranched glycosaminoglycan exhibiting substantial molecular diversity due to multiple, nonuniformly introduced modifications, including sulfations, epimerization, and acetylation. HS modifications serve specific and instructive roles in neuronal development, leading to the hypothesis of a HS code that regulates nervous system patterning. Although the in vivo roles of many of the HS modifications have been investigated, very little is known about the function of HS 3-O-sulfation in vivo. By examining patterning of the Caenorhabditis elegans nervous system in loss of function mutants of the two 3-O-sulfotransferases, hst-3.1 and hst-3.2, we found HS 3-O-sulfation to be largely dispensable for overall neural development. However, generation of stereotypical neurite branches in hermaphroditic-specific neurons required hst-3.1, hst-3.2, as well as an extracellular cell adhesion molecule encoded by kal-1, the homolog of Kallmann Syndrome associated gene 1/anosmin-1. In contrast, kal-1−dependent neurite branching in AIY neurons required catalytic activity of hst-3.2 but not hst-3.1. The context-dependent requirement for hst-3.2 and hst-3.1 indicates that both enzymes generate distinct types of HS modification patterns in different cell types, which regulate kal-1 to promote neurite branching. We conclude that HS 3-O-sulfation does not play a general role in establishing the HS code in C. elegans but rather plays a specialized role in a context-dependent manner to establish defined aspects of neuronal circuits.
A Genomic Survey of Reb Homologs Suggests Widespread Occurrence of R-Bodies in Proteobacteria
Authors: Raymann Kasie , Bobay Louis-Marie , Doak Thomas G , Lynch Michael , Gribaldo Simonetta 
Published: March 2013

Abstract
Bacteria and eukaryotes are involved in many types of interaction in nature, with important ecological consequences. However, the diversity, occurrence, and mechanisms of these interactions often are not fully known. The obligate bacterial endosymbionts of Paramecium provide their hosts with the ability to kill sensitive Paramecium strains through the production of R-bodies, highly insoluble coiled protein ribbons. R-bodies have been observed in a number of free-living bacteria, where their function is unknown. We have performed an exhaustive survey of genes coding for homologs of Reb proteins (R-body components) in complete bacterial genomes. We found that reb genes are much more widespread than previously thought, being present in representatives of major Proteobacterial subdivisions, including many free-living taxa, as well as taxa known to be involved in various kinds of interactions with eukaryotes, from mutualistic associations to pathogenicity. Reb proteins display very good conservation at the sequence level, suggesting that they may produce functional R-bodies. Phylogenomic analysis indicates that reb genes underwent a complex evolutionary history and allowed the identification of candidates potentially involved in R-body assembly, functioning, regulation, or toxicity. Our results strongly suggest that the ability to produce R-bodies is likely widespread in Proteobacteria. The potential involvement of R-bodies in as yet unexplored interactions with eukaryotes and the consequent ecological implications are discussed.
On the Mutational Topology of the Bacterial Genome
Authors: Foster Patricia L , Hanson Andrew J , Lee Heewook , Popodi Ellen M , Tang Haixu 
Published: March 2013

AbstractBy sequencing the genomes of 34 mutation accumulation lines of a mismatch-repair defective strain of Escherichia coli that had undergone a total of 12,750 generations, we identified 1625 spontaneous base-pair substitutions spread across the E. coli genome. These mutations are not distributed at random but, instead, fall into a wave-like spatial pattern that is repeated almost exactly in mirror image in the two separately replicated halves of the bacterial chromosome. The pattern is correlated to genomic features, with mutation densities greatest in regions predicted to have high superhelicity. Superimposed upon this pattern are regional hotspots, some of which are located where replication forks may collide or be blocked. These results suggest that, as they traverse the chromosome, the two replication forks encounter parallel structural features that change the fidelity of DNA replication.
Novel Proteins Required for Meiotic Silencing by Unpaired DNA and siRNA Generation inNeurospora crassa
Authors: Hammond Thomas M , Xiao Hua , Boone Erin C , Decker Logan M , Lee Seung A , Perdue Tony D , Pukkila Patricia J , Shiu Patrick K T 
Published: March 2013

AbstractDuring meiosis in the filamentous fungus Neurospora crassa, unpaired genes are identified and silenced by a process known as meiotic silencing by unpaired DNA (MSUD). Previous work has uncovered six proteins required for MSUD, all of which are also essential for meiotic progression. Additionally, they all localize in the perinuclear region, suggesting that it is a center of MSUD activity. Nevertheless, at least a subset of MSUD proteins must be present inside the nucleus, as unpaired DNA recognition undoubtedly takes place there. In this study, we identified and characterized two new proteins required for MSUD, namely SAD-4 and SAD-5. Both are previously uncharacterized proteins specific to Ascomycetes, with SAD-4 having a range that spans several fungal classes and SAD-5 seemingly restricted to a single order. Both genes appear to be predominantly expressed in the sexual phase, as molecular study combined with analysis of publicly available mRNA-seq datasets failed to detect significant expression of them in the vegetative tissue. SAD-4, like all known MSUD proteins, localizes in the perinuclear region of the meiotic cell. SAD-5, on the other hand, is found in the nucleus (as the first of its kind). Both proteins are unique compared to previously identified MSUD proteins in that neither is required for sexual sporulation. This homozygous-fertile phenotype uncouples MSUD from sexual development and allows us to demonstrate that both SAD-4 and SAD-5 are important for the production of masiRNAs, which are the small RNA molecules associated with meiotic silencing.