bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polymorphism of microcrystalline urate oxidase fromAspergillus flavus
Authors: Collings Ines , Watier Yves , Giffard Marion , Dagogo Sotonye , Kahn Richard , Bonneté Francoise , Wright Jonathan P. , Fitch Andrew N. , Margiolaki Irene 
Published: April 2010

Different polymorphs of rasburicase, a recombinant urate oxidase enzyme (Uox) fromAspergillus flavus, were obtained as a series of polycrystalline precipitates. Different crystallization protocols were followed in which the salt type, pH and polyethylene glycol 8000 (PEG 8000) concentration were varied. The related crystalline phases were characterized by means of high-resolution synchrotron X-ray powder diffraction. In all cases, Uox complexed with the inhibitor 8-azaxanthine (AZA) was not altered from its robust orthorhombicI222 phase by variation of any of the factors listed above. However, in the absence of AZA during crystallization ligand-free Uox was significantly affected by the type of salt, resulting in different crystal forms for the four salts tested: sodium chloride, potassium chloride, ammonium chloride and ammonium sulfate. Remarkable alterations of some of these phases were observed upon gradual increase of the exposure time of the sample to the synchrotron beam in addition to variation of the PEG 8000 concentration. When Uox was crystallized in Tris buffer or pure water in the absence of salt, a distinct polymorph of orthorhombic symmetry (P21212) was obtained that was associated with significantly altered lattice dimensions in comparison to a previously reported isosymmetrical structure. The latter form of Uox exhibits enhanced stability to variation of pH and PEG 8000 concentration accompanied by minor modifications of the unit-cell dimensions in the ranges under study. Accurate lattice parameters were extracted for all crystalline phases. This study reveals the rich phase diagram of Uox, a protein of high pharmaceutical importance, which is associated with an enhanced degree of polymorphism. The outcome of our analysis verifies previously reported results as well as demonstrating polymorphs that have altered unit-cell dimensions with respect to known structural models.
Analysis of multiple crystal forms ofBacillus subtilisBacB suggests a role for a metal ion as a nucleant for crystallization
Authors: Rajavel M. , Gopal B. 
Published: April 2010

Bacillus subtilisBacB is an oxidase that is involved in the production of the antibiotic bacilysin. This protein contains two double-stranded β-helix (cupin) domains fused in a compact arrangement. BacB crystallizes in three crystal forms under similar crystallization conditions. An interesting observation was that a slight perturbation of the crystallization droplet resulted in the nucleation of a different crystal form. An X-ray absorption scan of BacB suggested the presence of cobalt and iron in the crystal. Here, a comparative analysis of the different crystal forms of BacB is presented in an effort to identify the basis for the different lattices. It is noted that metal ions mediating interactions across the asymmetric unit dominate the different packing arrangements. Furthermore, a normalizedB-factor analysis of all the crystal structures suggests that the solvent-exposed metal ions decrease the flexibility of a loop segment, perhaps influencing the choice of crystal form. The residues coordinating the surface metal ion are similar in the triclinic and monoclinic crystal forms. The coordinating ligands for the corresponding metal ion in the tetragonal crystal form are different, leading to a tighter packing arrangement. Although BacB is a monomer in solution, a dimer of BacB serves as a template on which higher order symmetrical arrangements are formed. The different crystal forms of BacB thus provide experimental evidence for metal-ion-mediated lattice formation and crystal packing.
Structure of a monoclinic polymorph of human carbonic anhydrase II with a doubledaaxis
Authors: Robbins Arthur H. , Domsic John F. , Agbandje-McKenna Mavis , McKenna Robert 
Published: April 2010

The crystal structure of human carbonic anhydrase II with a doubledaaxis from that of the usually observed monoclinic unit cell has been determined and refined to 1.4 Å resolution. The diffraction data withh= 2n+ 1 were systematically weaker than those withh= 2n. Consequently, the scaling of the data, structure solution and refinement were challenging. The two molecules comprising the asymmetric unit are related by a noncrystallographic translation of ½ alonga, but one of the molecules has two alternate positions related by a rotation of approximately 2°. This rotation axis is located near the edge of the central β-sheet, causing a maximum distance disparity of 1.7 Å between equivalent atoms on the diametrically opposite side of the molecule. The crystal-packing contacts are similar to two sequential combined unit cells alongaof the previously determined monoclinic unit cell. Abnormally high finalRcrystandRfreevalues (20.2% and 23.7%, respectively) are not unusual for structures containing pseudo-translational symmetry and probably result from poor signal to noise in the weakh-odd data.
The human coronary collateral circulation
Authors: Seiler Christian 
Published: April 2010

Eur J Clin Invest 2010; 40 (5): 465–476AbstractBackground  Coronary collaterals are an alternative source of blood supply to myocardium jeopardized by ischaemia. Well‐developed coronary collateral arteries in patients with coronary artery disease (CAD) mitigate myocardial infarcts and improve survival.Methods and results  Collateral arteries preventing myocardial ischaemia during brief vascular occlusion are present in 1/3 of patients with CAD. Among individuals without relevant coronary stenoses, there are preformed collateral arteries preventing myocardial ischaemia in 20–25%. Collateral flow sufficient to prevent myocardial ischaemia during coronary occlusion amounts to ‡25% of the normal flow through the open vessel. Myocardial infarct size, the most important prognostic determinant after such an event, is the product of coronary artery occlusion time, area at risk for infarction and the inverse of collateral supply. Coronary collateral flow can be assessed only during vascular occlusion of the collateral‐receiving artery. The gold standard for coronary collateral assessment is the measurement of intracoronary occlusive pressure‐ or velocity‐derived collateral flow index expressing collateral as a fraction of flow during vessel patency. Approximately one of five patients with CAD cannot be revascularized by percutaneous coronary intervention or coronary artery bypass grafting. Therapeutic promotion of collateral growth is a valuable treatment strategy in those patients.Conclusions  Promotion of collateral growth should aim at inducing the development of large conductive collateral arteries (i.e. arteriogenesis) and not so much the sprouting of capillary like vessels (i.e. angiogenesis). Large conductive collateral arteries appear to be effectively promoted via the activation of monocytes/macrophages by means of granulocyte‐colony stimulating factor or of augmenting coronary flow velocity.
Effect of experimental hyperglycaemia on renal haemodynamics in prediabetic patients with and without AT1 receptor blockade
Authors: Frank Helga , Pscherer Stefan , Fliser Danilo , Heemann Uwe 
Published: April 2010

Eur J Clin Invest 2010; 40 (5): 414–421AbstractBackground and objectives  To prevent diabetic nephropathy, knowledge about early renal impairment caused by a disturbed glucose homoeostasis is essential. The purpose of our study was to investigate haemodynamic changes of the kidney in subjects with impaired glucose tolerance (prediabetics, IGT) during experimental hyperglycaemia and the effect of angiotensin receptor blockade.Design  In our prospective case control study, we measured renal haemodynamics in 13 non‐albuminuric males with normal kidney function and IGT (diagnosed by an oral glucose tolerance test, OGTT) and in 13 matched controls with a normoglycemic response in the OGTT. Glomerular filtration rate (GFR) was assessed by determination of sinistrin clearance; renal plasma flow (RPF) by para‐aminohippuric acid clearance. All measurements were performed at rest and during hyperglycaemic stress testing (clamp technique; target blood glucose ∼170 mg dL−1). We examined renal effects of valsartan (4 weeks 160 mg day−1) at rest and during experimental hyperglycaemia. Metabolic (glycosylated haemoglobin, adiponectin) and inflammatory (high sensitive C‐reactive protein) parameters were compared with and without valsartan in both groups.Results  During experimental hyperglycaemia, GFR and RPF decreased significantly more in prediabetics compared with controls. Under valsartan, the hyperglycaemia induced decrease of GFR and RPF was blunted in part by valsartan. Hs‐CRP and HbA1c were significantly higher in prediabetics when compared with controls and improved both under valsartan. Adiponectin was lower in prediabetics and increased significantly under valsartan.Conclusions  Hyperglycaemia induces impairments of renal haemodynamics as well as inflammatory and metabolic parameters in subjects with impaired glucose tolerance, which improve under valsartan.
Community‐level effects of co‐occurring native and exotic ecosystem engineers
Authors: WARD JESSICA M. , RICCIARDI ANTHONY 
Published: April 2010

Summary1. Non‐indigenous ecosystem engineers can substantially affect native biodiversity by transforming the physical structure of habitats. In the Great Lakes–St. Lawrence River system, introduced dreissenid mussels (Dreissena polymorpha and D. bugensis) and the native benthic macroalga Cladophora act as ecosystem engineers by increasing substratum complexity and providing interstitial habitat for benthic macroinvertebrates.2. We manipulated the topography and perimeter‐to‐area ratio of patches of dreissenid mussels in a series of colonisation experiments conducted at two sites in the St. Lawrence River. Experimental substrata were variably colonised by Cladophora, prompting us to examine (i) how the topography of Dreissena patches affects benthic macroinvertebrate diversity and (ii) the extent to which the effects of Dreissena are altered by the presence of another habitat‐modifying organism (Cladophora).3. The results of our first experiment suggested that a patchy distribution of dreissenid mussels is an important driver of benthic diversity at small spatial scales. The results of our second and third experiments suggested that a native habitat engineer, Cladophora, modifies the impact of Dreissena on benthic macroinvertebrate communities.4. While macroalgal blooms have been linked to the large‐scale impacts of Dreissena on light and nutrient availability, Dreissena shells inhibited Cladophora growth at our experimental scale. These findings demonstrate that the interactions between habitat‐modifying species can complicate efforts to predict the community‐level effects of an invasion.
Subtle top‐down control of a freshwater meiofaunal assemblage by juvenile fish
Authors: DINEEN GERARD , ROBERTSON ANNE L. 
Published: April 2010

Summary1. Top‐down control of prey assemblages by fish predators has been clearly demonstrated in lakes (for zooplankton prey) and rivers (for macroinvertebrate prey). Fish predation can have a significant impact on the body size of prey assemblages; often large‐bodied prey are reduced in abundance, and indirect facilitation of small‐bodied prey occurs potentially initiating a trophic cascade.2. Benthic communities in aquatic ecosystems also include a numerous and functionally important meiofaunal‐sized component, but in freshwaters the impact of fish predation on meiofaunal assemblages is unknown. We used a laboratory microcosm study to explore the impact of juvenile fish predation on the abundance and size structure of a riverine meiofaunal assemblage.3. The presence of fish in our microcosms had no significant effect on overall meiofaunal (temporary and permanent) abundance. However, for the Copepoda, we found the first evidence of top‐down control of freshwater meiofaunal assemblages; in microcosms with juvenile fish, the abundance of large‐bodied Copepoda was significantly reduced, whereas small‐bodied Copepoda were significantly more abundant suggesting indirect facilitation.4. We conclude that predation by juvenile fish can alter the structure of freshwater meiofaunal assemblages, although we do not yet know whether these relatively subtle changes are overwhelmed by large‐scale events such as flow disturbances.
Modelling the impacts of flow regulation on fish distributions in naturally intermittent lowland streams: an approach for predicting restoration responses
Authors: BOND NICK , McMASTER DAMIEN , REICH PAUL , THOMSON JAMES R. , LAKE P. S. 
Published: April 2010

Summary1. Understanding the relationships between flow regime and the distribution of biota is critical for managing flows in regulated rivers. In northern Victoria, Australia, efforts are presently underway to restore a natural, intermittent flow regime to several streams which, for over 100 years, have received perennial diversions as part of a stock, irrigation and domestic water supply.2. Bayesian, model‐averaged, binomial regression was used to predict probabilities of occurrence for 13 fish species, including five non‐native species, based on hydrologic variables characterising both the current and modelled future flow regimes at 10 sites representing a range of hydrologic regimes (categorised here as heavily regulated, moderately regulated and unregulated).3. Regression models accurately predicted present probabilities of occurrence for most species across all sites. The models predicted a reduced likelihood of large, native, flow‐dependent species occurring at regulated sites following flow restoration. Predictions regarding the future distribution of widespread species including two small‐bodied native and four exotic species were less certain as current distributions of these widespread species were unrelated to hydrologic variables we examined and thus unlikely to be significantly affected by flow restoration. The distributions of two small native species currently restricted to unregulated sites are predicted to increase throughout the system.4. This study illustrates the effects of artificially induced perennial flow on lowland fish distributions. Furthermore, the combination of pre‐restoration data together with predictive modelling provides valuable insights into the likely outcomes of flow regime shifts.5. This study clearly demonstrates the value of combining empirical research and modelling in guiding environmental flow and ecosystem restoration decisions. Knowledge from the study is now helping guide management decisions and the development of mitigation strategies to protect highly valued species in the system from potential future threats.
Biological invasions and the dynamics of endemic diseases in freshwater ecosystems
Authors: POULIN R. , PATERSON R. A. , TOWNSEND C. R. , TOMPKINS D. M. , KELLY D. W. 
Published: April 2010

Summary1. Biological invasions, still occurring worldwide at an alarming rate, are widely acknowledged as threats to the integrity and functioning of ecosystems. In addition to introducing disease, biological invasions have also been linked to sudden increases in the incidence or severity of previously existing diseases. We review and illustrate the potential direct and indirect impacts of introduced species on the dynamics of endemic parasites in freshwater ecosystems.2. Introduced species may trigger and sustain disease emergence by acting as competent hosts for endemic parasites in which infection is amplified and then ‘spilled back’ to native hosts. In contrast, if introduced species are not suitable hosts for endemic parasites but become infected anyway, they may act as sinks for parasites and thus dilute disease risk for native hosts.3. Another mechanism by which introduced species can influence endemic parasitic diseases is by altering the relative abundance of one of the parasite’s hosts in ways that could either enhance or reduce disease transmission to other native hosts in the parasite’s life cycle.4. Introduced species may also alter disease incidence and severity in native hosts through trait‐mediated indirect effects. For example, the introduced species could change the exposure or susceptibility of native hosts to infection by causing alterations in their behaviour or immunocompetence. Also, by directly changing physicochemical conditions and modifying environmental stressors introduced species may indirectly affect native host exposure and/or resistance to disease.5. A survey of parasites infecting introduced freshwater fish in four distinct geographical areas revealed that use of non‐indigenous hosts by endemic parasites is widespread, mostly involving parasites transmitted via the food chain.6. We conclude by presenting a framework, based on risk assessment, for the prediction and possible mitigation of the impact of introduced species on endemic diseases and by calling for greater recognition of the potential role of invasive species as triggers of endemic disease emergence.
Mast cells and angiogenesis in gastric carcinoma
Authors: Ribatti Domenico , Guidolin Diego , Marzullo Andrea , Nico Beatrice , Annese Tiziana , Benagiano Vincenzo , Crivellato Enrico 
Published: April 2010

SummaryPrevious studies have shown that increased vascularity is associated with haematogenous metastasis and poor prognosis in gastric cancer. The role of mast cells in gastric cancer angiogenesis has not been clarified completely. In this study, we correlated microvascular density and tryptase‐ and chymase‐positive mast cells with histopathological type in gastric cancer. Specimens of primary gastric adenocarcinomas obtained from 30 patients who had undergone curative gastrectomy were investigated immunohistochemically by using anti‐CD31 antibody to stain endothelial cells and anti‐tryptase and anti‐chymase antibodies to stain mast cells. The results showed that stage IV gastric carcinoma has a higher degree of vascularization than other stages and that both tryptase‐ and chymase‐positive mast cells increase in parallel with malignancy grade even if the density of chymase‐positive mast cells was significantly lower than the density of tryptase‐positive mast cells and is highly correlated with the extent of angiogenesis. This study has demonstrated that mast cell density correlates with angiogenesis and progression of patients with gastric carcinoma. Understanding the mechanisms of gastric cancer angiogenesis provides a basis for a rational approach to the development of an antiangiogenic therapy in patients with this malignancy.
Palaeoecology of Southeast Asian megafauna‐bearing sites from the Pleistocene and a review of environmental changes in the region
Authors: Louys Julien , Meijaard Erik 
Published: April 2010

AbstractAim To reconstruct the palaeoenvironments of megafauna‐bearing sites from Pleistocene Southeast Asia, and to describe general environmental changes in the region.Location Indochina and Sundaland, including Myanmar, Laos, Vietnam, Cambodia, Thailand, the Malay Peninsula, Borneo, Sumatra and Java.Methods This study reconstructs the habitat types of 25 Pleistocene sites in Southeast Asia through a synecological (community‐based) method. This method specifically targets medium‐ and large‐bodied mammals, and ecovariables that could be directly assessed from species lists were chosen. The methods allow the reconstruction of fossil sites as closed (continuous tree cover), mixed (heterogeneous tree cover) and open (very limited to no tree cover) through discriminant functions analysis of community guild structure.Results Four Pleistocene sites can confidently be assigned to one of the three habitat types. Tam Hang (south), a Middle Pleistocene site from Laos, is classified as mixed. Ban Fa Suai, a Middle Pleistocene site from Thailand, is also classified as mixed. Trinil, a Middle Pleistocene site from Java, is classified as open. Lastly, Hang Hum II, a Late Pleistocene site from Vietnam, is classified as open. Insufficient species are present in the fossil faunas of remaining sites to allow statistically confident habitat assignment. Nevertheless, conditional habitat assignments can be achieved, and these are largely congruent with other palaeoenvironmental evidence.Main conclusions Medium‐ and large‐bodied mammals are the most frequently recovered mammals from Pleistocene sites in Southeast Asia. Previous palaeoenvironmental reconstructions of these sites have been hampered by this body size bias, as well as by limited site and faunal descriptions. However, our analysis demonstrates that reconstructions can still be achieved for megafauna‐bearing sites in the region. The reconstructions suggest that through much of the Pleistocene, Southeast Asia had significant areas of mixed habitats, and that the widespread distribution of rain forests, such as found today, was a relatively rare phenomenon.
The role of IL‐1β in reduced IL‐7 production by stromal and epithelial cells: a model for impaired T‐cell numbers in the gut during HIV‐1 infection
Authors: Thang P. H. , Ruffin N. , Brodin D. , Rethi B. , Cam P. D. , Hien N. T. , Lopalco L. , Vivar N. , Chiodi F. 
Published: April 2010

Abstract.  Thang PH, Ruffin N, Brodin D, Rethi B, Cam PD, Hien NT, Lopalco L, Vivar N, Chiodi F (Karolinska Institutet, Stockholm, Sweden; National Institute of Hygiene and Epidemiology, Hanoi, Vietnam; San Raffaele Scientific Institute, Milan, Italy). The role of IL‐1β in reduced IL‐7 production by stromal and epithelial cells: a model for impaired T‐cell numbers in the gut during HIV‐1 infection. J Intern Med 2010; 268: 181–193.Objectives.  Interleukin (IL)‐7 is a key cytokine in T‐cell homeostasis. Stromal cells, intestinal epithelial cells and keratinocytes are known to produce this cytokine. The mechanisms and cellular factors regulating IL‐7 production are still unclear. We assessed whether IL‐1β and interferon (IFN)‐γ, cytokines produced during inflammatory conditions, may impact on IL‐7 production.Design.  We used human intestinal epithelial cells (DLD‐1 cell line) and bone marrow stromal cells (HS27 cell line), known to produce IL‐7; IL‐7 production was evaluated at the mRNA and protein levels. To assess whether treatment of HS27 cells with IL‐1β and/or IFN‐γ leads to changes in the gene expression of cytokines, Toll‐like receptors (TLRs) and chemokines, we analysed gene expression profiles using the whole‐genome microarray Human Gene 1.0 ST.Results.  We found that IFN‐γ enhanced the expression of IL‐7 mRNA (P < 0.001) in both cell lines. IL‐1β treatment led to a significant down‐regulation (P < 0.001) of IL‐7 mRNA expression in both cell lines. The IL‐7 concentration in supernatants collected from treated DLD‐1 and HS27 cell cultures reflected the trend of IL‐7 mRNA levels. The gene profiles revealed dramatic changes in expression of cytokines and their receptors (IL‐7/IL‐7Rα; IL‐1α,IL‐1β/IL‐1R1; IFN‐γ/IFN‐γR1), of IFN regulatory factors (IRF‐1 and 2), of TLRs and of important chemo‐attractants for T cells. The microarray results were verified by additional methods.Conclusions.  Our results are discussed in the setting of inflammation and T‐cell survival in the gut compartment during HIV‐1 infection where stromal and epithelial cells may produce factors that contribute to impaired IL‐7 homeostasis and homing of T cells.