bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controls on the Activation and Strength of a High-Latitude Convective Cloud Feedback
Authors: Abbot Dorian S. , Tziperman Eli 
Published: August 2008

Abstract
Previous work has shown that a convective cloud feedback can greatly increase high-latitude surface temperature upon the removal of sea ice and can keep sea ice from forming throughout polar night. This feedback activates at increased greenhouse gas concentrations. It may help to explain the warm “equable climates” of the late Cretaceous and early Paleogene eras (∼100 to ∼35 million years ago) and may be relevant for future climate under global warming. Here, the factors that determine the critical threshold CO2 concentration at which this feedback is active and the magnitude of the warming caused by the feedback are analyzed using both a highly idealized model and NCAR’s single-column atmospheric model (SCAM) run under Arctic-like conditions. The critical CO2 is particularly important because it helps to establish the relevance of the feedback for past and future climates.
Both models agree that increased heat flux into the high latitudes at low altitudes generally decreases the critical CO2. Increases in oceanic heat transport and in solar radiation absorbed during the summer should cause a sharp decrease in the critical CO2, but the effect of increases in atmospheric heat transport depends on its vertical distribution. It is furthermore found (i) that if the onset of convection produces more clouds and moisture, the critical CO2 should decrease, and the maximum temperature increase caused by the convective cloud feedback should increase and (ii) that reducing the depth of convection reduces the critical CO2 but has little effect on the maximum temperature increase caused by the convective cloud feedback. These results should help with interpretation of the strength and onset of the convective cloud feedback as found, for example, in Intergovernmental Panel on Climate Change (IPCC) coupled ocean–atmosphere models with different cloud and convection schemes.
Polarimetric Spectral Filter for Adaptive Clutter and Noise Suppression
Authors: Moisseev Dmitri N. , Chandrasekar V. 
Published: August 2008

Abstract
In this paper, spectral decompositions of differential reflectivity, differential phase, and copolar correlation coefficient are used to discriminate between weather and nonweather signals in the spectral domain. This approach gives a greater flexibility for discrimination between different types of scattering sources present in a radar observation volume. A spectral filter, which removes nonweather signals, is defined based on this method. The performance of this filter is demonstrated on the Colorado State University–University of Chicago–Illinois State Water Survey (CSU–CHILL) observations. It is shown that the resulting filter parameters are adaptively defined for each range sample and do not require an assumption on spectral properties of ground clutter.
Angiogenesis alteration by defibrotide: implications for its mechanism of action in severe hepatic veno-occlusive disease
Authors: Benimetskaya Luba , Wu Sijian , Voskresenskiy Anatoliy M. , Echart Cinara , Zhou Jin-Feng , Shin Joongho , Iacobelli Massimo , Richardson Paul , Ayyanar Kanyalakshmi , Stein C. A. 
Published: August 2008

AbstractDefibrotide (DF) is a mixture of porcine-derived single-stranded phosphodiester oligonucleotides (9-80-mer; average, 50-mer) that has been successfully used to treat severe hepatic veno-occlusive disease (sVOD) with multiorgan failure (MOF) in patients who have received cytotoxic chemotherapy in preparation for bone marrow transplantation. However, its mechanism of action is unknown. Herein, we show that DF and phosphodiester oligonucleotides can bind to heparin-binding proteins (eg, basic fibroblast growth factor [bFGF] but not vascular endothelial growth factor [VEGF] 165) with low nanomolar affinity. This binding occurred in a length- and concentration-dependent manner. DF can mobilize proangiogenic factors such as bFGF from their depot or storage sites on bovine corneal endothelial matrix. However, these molecules do not interfere with high-affinity binding of bFGF to FGFR1 IIIc but can replace heparin as a required cofactor for binding and hence cellular mitogenesis. DF also protects bFGF against digestion by trypsin and chymotrypsin and from air oxidation. In addition, DF binds to collagen I with low nanomolar affinity and can promote human microvascular endothelial cell-1 (HMEC-1) cell mitogenesis and tubular morphogenesis in three-dimensional collagen I gels. Thus, our data suggest that DF may provide a stimulus to the sinusoidal endothelium of a liver that has suffered a severe angiotoxic event, thus helping to ameliorate the clinical sVOD/MOF syndrome.
Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays
Authors: Graf Alexandra , Gasser Brigitte , Dragosits Martin , Sauer Michael , Leparc Germán G , Tüchler Thomas , Kreil David P , Mattanovich Diethard 
Published: August 2008

Abstract

Background
DNA Microarrays are regarded as a valuable tool for basic and applied research in microbiology. However, for many industrially important microorganisms the lack of commercially available microarrays still hampers physiological research. Exemplarily, our understanding of protein folding and secretion in the yeast Pichia pastoris is presently widely dependent on conclusions drawn from analogies to Saccharomyces cerevisiae. To close this gap for a yeast species employed for its high capacity to produce heterologous proteins, we developed full genome DNA microarrays for P. pastoris and analyzed the unfolded protein response (UPR) in this yeast species, as compared to S. cerevisiae.

Results
By combining the partially annotated gene list of P. pastoris with de novo gene finding a list of putative open reading frames was generated for which an oligonucleotide probe set was designed using the probe design tool TherMODO (a thermodynamic model-based oligoset design optimizer). To evaluate the performance of the novel array design, microarrays carrying the oligo set were hybridized with samples from treatments with dithiothreitol (DTT) or a strain overexpressing the UPR transcription factor HAC1, both compared with a wild type strain in normal medium as untreated control. DTT treatment was compared with literature data for S. cerevisiae, and revealed similarities, but also important differences between the two yeast species. Overexpression of HAC1, the most direct control for UPR genes, resulted in significant new understanding of this important regulatory pathway in P. pastoris, and generally in yeasts.

Conclusion
The differences observed between P. pastoris and S. cerevisiae underline the importance of DNA microarrays for industrial production strains. P. pastoris reacts to DTT treatment mainly by the regulation of genes related to chemical stimulus, electron transport and respiration, while the overexpression of HAC1 induced many genes involved in translation, ribosome biogenesis, and organelle biosynthesis, indicating that the regulatory events triggered by DTT treatment only partially overlap with the reactions to overexpression of HAC1. The high reproducibility of the results achieved with two different oligo sets is a good indication for their robustness, and underlines the importance of less stringent selection of regulated features, in order to avoid a large number of false negative results.
Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms
Authors: Honsa Erin , Fricke Thomas , Stephens Alex J , Ko Danny , Kong Fanrong , Gilbert Gwendolyn L , Huygens Flavia , Giffard Philip M 
Published: August 2008

Abstract

Background

Streptococcus agalactiae (Group B Streptococcus (GBS)) is an important human pathogen, particularly of newborns. Emerging evidence for a relationship between genotype and virulence has accentuated the need for efficient and well-defined typing methods. The objective of this study was to develop a single nucleotide polymorphism (SNP) based method for assigning GBS isolates to multilocus sequence typing (MLST)-defined clonal complexes.

Results
It was found that a SNP set derived from the MLST database on the basis of maximisation of Simpsons Index of Diversity provided poor resolution and did not define groups concordant with the population structure as defined by eBURST analysis of the MLST database. This was interpreted as being a consequence of low diversity and high frequency horizontal gene transfer. Accordingly, a different approach to SNP identification was developed. This entailed use of the "Not-N" bioinformatic algorithm that identifies SNPs diagnostic for groups of known sequence variants, together with an empirical process of SNP testing. This yielded a four member SNP set that divides GBS into 10 groups that are concordant with the population structure. A fifth SNP was identified that increased the sensitivity for the clinically significant clonal complex 17 to 100%. Kinetic PCR methods for the interrogation of these SNPs were developed, and used to genotype 116 well characterized isolates.

Conclusion
A five SNP method for dividing GBS into biologically valid groups has been developed. These SNPs are ideal for high throughput surveillance activities, and combining with more rapidly evolving loci when additional resolution is required.
Effect of benthic boundary layer transport on the productivity of Mono Lake, California
Authors: Bruce Louise C , Jellison Robert , Imberger Jörg , Melack John M 
Published: August 2008

Abstract
The significance of the transport of nutrient-rich hypolimnetic water via the benthic boundary layer (BBL) to the productivity of Mono Lake was studied using a coupled hydrodynamic and ecological model validated against field data. The coupled model enabled us to differentiate between the role of biotic components and hydrodynamic forcing on the internal recycling of nutrients necessary to sustain primary productivity. A 4-year period (1991–1994) was simulated in which recycled nutrients from zooplankton excretion and bacterially-mediated mineralization exceeded sediment fluxes as the dominant source for primary productivity. Model outputs indicated that BBL transport was responsible for a 53% increase in the flux of hypolimnetic ammonium to the photic zone during stratification with an increase in primary production of 6% and secondary production of 5%. Although the estimated impact of BBL transport on the productivity of Mono Lake was not large, significant nutrient fluxes were simulated during periods when BBL transport was most active.
A novel survival model of cardioplegic arrest and cardiopulmonary bypass in rats: a methodology paper
Authors: de Lange Fellery , Yoshitani Kenji , Podgoreanu Mihai V , Grocott Hilary P , Mackensen G Burkhard 
Published: August 2008

Abstract

Background
Given the growing population of cardiac surgery patients with impaired preoperative cardiac function and rapidly expanding surgical techniques, continued efforts to improve myocardial protection strategies are warranted. Prior research is mostly limited to either large animal models or ex vivo preparations. We developed a new in vivo survival model that combines administration of antegrade cardioplegia with endoaortic crossclamping during cardiopulmonary bypass (CPB) in the rat.

Methods
Sprague-Dawley rats were cannulated for CPB (n = 10). With ultrasound guidance, a 3.5 mm balloon angioplasty catheter was positioned via the right common carotid artery with its tip proximal to the aortic valve. To initiate cardioplegic arrest, the balloon was inflated and cardioplegia solution injected. After 30 min of cardioplegic arrest, the balloon was deflated, ventilation resumed, and rats were weaned from CPB and recovered. To rule out any evidence of cerebral ischemia due to right carotid artery ligation, animals were neurologically tested on postoperative day 14, and their brains histologically assessed.

Results
Thirty minutes of cardioplegic arrest was successfully established in all animals. Functional assessment revealed no neurologic deficits, and histology demonstrated no gross neuronal damage.

Conclusion
This novel small animal CPB model with cardioplegic arrest allows for both the study of myocardial ischemia-reperfusion injury as well as new cardioprotective strategies. Major advantages of this model include its overall feasibility and cost effectiveness. In future experiments long-term echocardiographic outcomes as well as enzymatic, genetic, and histologic characterization of myocardial injury can be assessed. In the field of myocardial protection, rodent models will be an important avenue of research.
Trichinella spiralis: nurse cell formation with emphasis on analogy to muscle cell repair
Authors: Wu Zhiliang , Sofronic-Milosavljevic Lj , Nagano Isao , Takahashi Yuzo 
Published: August 2008

Abstract

Trichinella infection results in formation of a capsule in infected muscles. The capsule is a residence of the parasite which is composed of the nurse cell and fibrous wall. The process of nurse cell formation is complex and includes infected muscle cell response (de-differentiation, cell cycle re-entry and arrest) and satellite cell responses (activation, proliferation and differentiation). Some events that occur during the nurse cell formation are analogous to those occurring during muscle cell regeneration/repair. This article reviews capsule formation with emphasis on this analogy.
Lateral dislocation of the knee joint after total knee arthroplasty: a case report
Authors: Ugutmen Ender , Ozkan Korhan , Unay Koray , Mahirogullari Mahir , Eceviz Engin , Taser Omer 
Published: August 2008

Abstract

Background
Total knee arthroplasty (TKA) is a successful therapy for functional improvement and pain relief in advanced symptomatic degeneration of the knee joint. But it can be associated with many complications, one of which is instability.

Case presentation
A 70-year-old woman was referred to our hospital because of right knee dislocation after TKA was performed on her right knee due to severe varus deformity and flexion contracture. This instability was caused by persistent MCL tightness and iatrogenic lateral collateral, arcuate ligament, and popliteus tendon injury.
The torn lateral collateral ligament and arcuate ligament were sutured with no. 2 non-absorbable (Ethibond) sutures with plication of the posterolateral knee capsule. A deep-dish liner was inserted to optimize soft tissue tension.

Conclusion
This is a very severe complication, and surgeons must be cautious about ligament balancing and soft tissue resection during TKA for severe varus and valgus deformities.
Ball and socket ankle joint in connection with bilateral tarsal synostosis in a boy with congenital absence of the portal vain: a novel malformation complex
Authors: Zandieh Shahin , Vakil-Adli Anosheh , Hochreiter Josef , Grill Franz , Klaushofer Klaus , Al Kaissi Ali 
Published: August 2008

Abstract

Background
Contracted valgus flat foot in the adolescent is frequently caused by tarsal synostosis or synchondrosis. These synostoses are prevalently symptomatic during adolescence, when by ossifying they block the subtalar joint in valgus. Careful and detailed examinations might reveal additional abnormalities.

Case presentation
A 16-year-old boy of Austrian origin presented with contracted valgus foot associated with tarsal hypomobility and pain. Talonavicular synostosis with ball and socket ankle joint was detected via lateral radiographs and 3 DCT scan. Preoperative laboratory investigations revealed leucocytopenia, and thrombopenia. Computerised abdominal tomography showed portal vein atresia and portopulmonary hypertension.

Conclusion
Clinical research is the corner stone to elucidate the aetiological understandings in patients with malformation complex. The latter is a critical task for the development of scientific bases for preventive strategies. Careful examination for these abnormalities should lead the clinician to earlier referral of patients for additional examination by a specialised medical team. This often enables more focused care for the individual and better characterisation/documentation of the malformation complex. The association of tarsal synostosis and the previously unreported associated occurrences of congenital absence of the portal vein, portopulmonary hypertension, cardiomegaly and splenomegaly have been encountered. We stress that our present patient illustrates and supports the pathophysiological hypotheses that have previously proposed for the concurrent existence of absent portal vein, hepatic nodular hyperplasia and portopulmonary hypertension. Nevertheless, no previous single report signifies the existence of tarsal synostosis in connection with the above-mentioned abnormalities.
TH-17 cells in rheumatoid arthritis
Authors: Shahrara Shiva , Huang QiQuan , Mandelin Arthur M , Pope Richard M 
Published: August 2008

Abstract
Introduction
The aim of this study was to quantify the number of T-helper (TH)-17 cells present in rheumatoid arthritis (RA) synovial fluid (SF) and to determine the level of interleukin (IL)-17 cytokine in RA, osteoarthritis (OA) and normal synovial tissue, as well as to examine SF macrophages for the presence of IL-23, IL-27 and interferon (IFN)-γ.

Methods
Peripheral blood (PB) mononuclear cells from normal and RA donors and mononuclear cells from RA SF were examined either without stimulation or after pretreatment with IL-23 followed by stimulation with phorbol myristate acetate (PMA) plus ionomycin (P/I). The abundance of TH-17 cells in RA SF was determined by flow cytometry. IL-17 levels were quantified in synovial tissue from RA, OA and normal individuals by ELISA and IL-23 was identified in SFs by ELISA. RA SF and control in vitro differentiated macrophages were either untreated or treated with the toll-like receptor (TLR) 2 ligand peptidoglycan, and then IL-23, IL-27 and IFN-γ mRNA levels were quantified by real-time polymerase chain reaction (RT-PCR).

Results
Treatment with P/I alone or combined with IL-23 significantly increased the number of TH-17 cells in normal, RA PB and RA SF. With or without P/I plus IL-23, the percentage of TH-17 cells was higher in RA SF compared with normal and RA PB. IL-17 levels were comparable in OA and normal synovial tissues, and these values were significantly increased in RA synovial tissue. Although IL-17 was readily detected in RA SFs, IL-23 was rarely identified in RA SF. However, IL-23 mRNA was significantly increased in RA SF macrophages compared with control macrophages, with or without TLR2 ligation. IL-27 mRNA was also significantly higher in RA SF compared with control macrophages, but there was no difference in IL-27 levels between RA and control macrophages after TLR2 ligation. IFN-γ mRNA was also detectable in RA SF macrophages but not control macrophages and the increase of IFN-γ mRNA following TLR2 ligation was greater in RA SF macrophages compared with control macrophages.

Conclusion
These observations support a role for TH-17 cells in RA. Our observations do not strongly support a role for IL-23 in the generation of TH-17 cells in the RA joint, however, they suggest strategies that enhance IL-27 or IFN-γ might modulate the presence of TH-17 cells in RA.
Circulating immune complexes contain citrullinated fibrinogen in rheumatoid arthritis
Authors: Zhao Xiaoyan , Okeke Nwora Lance , Sharpe Orr , Batliwalla Franak M , Lee Annette T , Ho Peggy P , Tomooka Beren H , Gregersen Peter K , Robinson William H 
Published: August 2008

Abstract
Introduction
There is increasing evidence that autoantibodies and immune complexes (ICs) contribute to synovitis in rheumatoid arthritis (RA), yet the autoantigens incorporated in ICs in RA remain incompletely characterised.

Methods
We used the C1q protein to capture ICs from plasma derived from human RA and control patients. Antibodies specific for immunoglobulin were used to detect ICs, and fibrinogen antibodies were used to detect fibrinogen-containing ICs. RA and control plasma were separated by liquid chromatography, and fractions then characterised by ELISA, immunoblotting and mass spectrometry. Immunohistochemical staining was performed on rheumatoid synovial tissue.

Results
C1q-immunoassays demonstrated increased levels of IgG (p = 0.01) and IgM (p = 0.0002) ICs in plasma derived from RA patients possessing anti-cyclic citrullinated peptide (CCP+) autoantibodies as compared with healthy controls. About one-half of the anti-CCP+ RA possessed circulating ICs containing fibrinogen (p = 0.0004). Fractionation of whole RA plasma revealed citrullinated fibrinogen in the high molecular weight fractions that contained ICs. Positive correlations were observed between fibrinogen-containing ICs and anti-citrullinated fibrinogen autoantibodies, anti-CCP antibody, rheumatoid factor and certain clinical characteristics. Immunohistochemical staining demonstrated co-localisation of fibrinogen, immunoglobulin and complement component C3 in RA pannus tissue. Mass spectrometry analysis of immune complexes immunoprecipitated from RA pannus tissue lysates demonstrated the presence of citrullinated fibrinogen.

Conclusion
Circulating ICs containing citrullinated fibrinogen are present in one-half of anti-CCP+ RA patients, and these ICs co-localise with C3 in the rheumatoid synovium suggesting that they contribute to synovitis in a subset of RA patients.
Hyperosmotic stress enhances cytokine production and decreases phagocytosis in vitro
Authors: Otto Natalie M , Schindler Ralf , Lun Andreas , Boenisch Olaf , Frei Ulrich , Oppert Michael 
Published: August 2008

Abstract
Introduction
Hyperglycemia is associated with negative outcomes in various settings of critical illness; infectious complications, especially, seem to be increased. On the other hand, intensive insulin therapy (IIT) has been shown to improve outcome in clinical trials. Whether normoglycemia itself or the application of insulin is responsible for the observed findings is unknown. We therefore tested the effect of glucose and insulin on various immune functions in vitro.

Methods
Human peripheral blood mononuclear cells (PBMCs) were incubated ex vivo with low doses of lipopolysaccharide (LPS). PBMCs were incubated with various osmotic agents, insulin, or a combination of both. Interleukin (IL)-6 and IL-1 cytokine response was measured by enzyme-linked immunosorbent assay. In addition, we investigated the effects of glucose on phagocytosis and oxidative burst in human granulocytes.

Results
Increasing concentrations of both glucose and mannitol significantly enhanced LPS-induced cytokine production. Insulin alone did not alter cytokine production and had only a minor influence in combination with glucose. Phagocytosis and oxidative burst were significantly reduced with increasing concentrations of glucose and mannitol.

Conclusion
Hyperglycemia may lead to inflammation by enhancing cytokine production via the direct effects of hyperosmotic stress. Impaired phagocytosis and oxidative burst under hyperglycemia may weaken defense mechanisms of the host. Our in vitro findings may help to explain the beneficial effects of IIT not only in diabetic but also in critically ill patients.