bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying the Predictability of Winter River Flow in Iberia. Part I: Interannual Predictability
Authors: Gámiz-Fortis Sonia , Pozo-Vázquez David , Trigo Ricardo M. , Castro-Díez Yolanda 
Published: June 2008

Abstract
The interannual variability and predictability of the winter streamflow of the main Iberian Peninsula international rivers (Douro, Tejo, and Guadiana) are examined for the period 1923–2004. In the first part of this paper, a singular spectral analysis was carried out to isolate the main oscillatory components of the streamflow series. Results showed a similar model structure for the three rivers, including the following components: (i) a nonlinear trend that contains variability at periods of 20–30 yr, (ii) modulated amplitude oscillations with associated periods in the bands 2–3, 4–5, and 6–8 yr, and (iii) a red noise process. These models accounts for the bulk of winter river flow variance, ranging between 64% (Guadiana) and 96% (Douro). In general, the amount of variability associated with the low-frequency component is similar to that associated with the interannual variability. The analysis of the association between the North Atlantic Oscillation (NAO) and the streamflow variability proved this relationship to be complex and nonstationary. In particular, it is found that only when the NAO presents high amplitude oscillations is this mode capable of dominating the streamflow variability.
In Part II, autoregressive-moving-average (ARMA) models were fitted to the filtered streamflow series and an interannual forecasting experiment was conducted. Results were tested against the raw streamflow series. The percentage of variance explained by the models ranged from 25% to 62%. Additionally, the ARMA models presented useful one-year-ahead forecasting skills. Particularly during the validation period (1986–2004) the models performed between 51% and 53% better than climatology. The skill against persistence proved to be much greater, indicating that the climatology is a better benchmark than persistence for streamflow forecasting in Iberia. Finally, the developed models were, in most cases, able to accurately predict the phase of the streamflow, with a percentage of agreement that ranged from 54% to 90% throughout the validation period.
Tripleclouds: An Efficient Method for Representing Horizontal Cloud Inhomogeneity in 1D Radiation Schemes by Using Three Regions at Each Height
Authors: Shonk Jonathan K. P. , Hogan Robin J. 
Published: June 2008

Abstract
Radiation schemes in general circulation models currently make a number of simplifications when accounting for clouds, one of the most important being the removal of horizontal inhomogeneity. A new scheme is presented that attempts to account for the neglected inhomogeneity by using two regions of cloud in each vertical level of the model as opposed to one. One of these regions is used to represent the optically thinner cloud in the level, and the other represents the optically thicker cloud. So, along with the clear-sky region, the scheme has three regions in each model level and is referred to as “Tripleclouds.” In addition, the scheme has the capability to represent arbitrary vertical overlap between the three regions in pairs of adjacent levels. This scheme is implemented in the Edwards–Slingo radiation code and tested on 250 h of data from 12 different days. The data are derived from cloud retrievals using radar, lidar, and a microwave radiometer at Chilbolton, southern United Kingdom. When the data are grouped into periods equivalent in size to general circulation model grid boxes, the shortwave plane-parallel albedo bias is found to be 8%, while the corresponding bias is found to be less than 1% using Tripleclouds. Similar results are found for the longwave biases. Tripleclouds is then compared to a more conventional method of accounting for inhomogeneity that multiplies optical depths by a constant scaling factor, and Tripleclouds is seen to improve on this method both in terms of top-of-atmosphere radiative flux biases and internal heating rates.
Necessity of Routine Pelvic Radiograph in the Pediatric Blunt Trauma Patient
Authors: Ramirez Dana W. E. , Schuette Jennifer J. , Knight Vinita , Johnson Elizabeth , Denise Justin , Walker Allen R. 
Published: June 2008

Background Pelvic radiographs are obtained frequently in pediatric blunt trauma. The authors hypothesize that there are clinical indicators that can predict pelvic fracture on a pelvic radiograph in the pediatric blunt trauma patient with a Glasgow Coma Scale score of 14 or 15. Methods A retrospective case-control study of 33 patients with pelvic fractures and 63 patients without pelvic fractures was performed. Results 8 evaluated clinical indicators showed that pelvic contusions and abrasions ( P = .026), hip/pelvic pain ( P<.001), abdominal pain and distension ( P = .006), back pain ( P = .080), hip held in rotation at presentation ( P = .026), and femur deformity/pain ( P = .002) were independently predictive of pelvic fracture. In combination, absence of hip/pelvic pain, pelvic contusions and abrasions, abdominal pain/distension, and femur deformity/pain showed a negative predictive value of 87%. Conclusion Clinical indicators may be useful in determining the need for pelvic radiographs in awake and alert pediatric blunt trauma patients.
Stretching Positions for the Posterior Capsule of the Glenohumeral Joint
Authors: Izumi Tomoki , Aoki Mitsuhiro , Muraki Takayuki , Hidaka Egi , Miyamoto Shigenori 
Published: June 2008

Background Various stretches have been introduced for the posterior shoulder; however, little quantitative analysis to measure stretching of the posterior capsule has been performed. Hypothesis The current shoulder stretching program is not sufficient to stretch the entire posterior capsule. Study Design Controlled laboratory study. Methods Using 8 fresh-frozen cadaver shoulders (average age, 82.4 years), 8 stretching positions for the posterior capsule were simulated by passive internal rotation. Stretching positions of 0°, 30°, 60°, and 90° of elevation in the scapular plane; 60° of flexion; 60° of abduction; 30° of extension; and 60° of flexion and horizontal adduction were adopted. Strain was measured in the upper, middle, and lower parts of the capsule. The measurement of strain was instituted from reference length. Results With internal rotation, mean strain on the upper capsule was 3.02% at 0° of elevation and 3.35% at 30° of extension. Strain on the middle capsule at 0° and 30° elevation was 0.78% and 4.77%, respectively; on the lower capsule, it was 5.65% and 2.24% at 30° and 60° of elevation, respectively, and 2.88% at 30° of extension. Increase in strains of the upper, middle, and lower capsule with internal rotation at 0°, 30°, and 60° of elevation were statistically significant, respectively ( P < .01). Other shoulder positions demonstrated no positive strain values. Conclusions Based on the results of this cadaver study, large strains on the posterior capsule of the shoulder were obtained at a stretching position of 30° of elevation in the scapular plane with internal rotation for the middle and lower capsule, while a stretching position of 30° of extension with internal rotation was effective for the upper and lower capsule. Clinical Relevance The current posterior capsule stretching program of the shoulder was not sufficient to stretch the entire posterior capsule.
Original Research: Local TAT-p27Kip1 Fusion protein inhibits cell proliferation in rat Carotid arteries
Authors: Neukamm Birgit , Miyakawa Ayumi A. , Fukada Sandra Y. , de Andrade Claudia R. , Pacheco Fernando P. , da Silva Thaís G. , Ramalho Leandra N. Z. , de Oliveira Ana Maria , Krieger Jose E. 
Published: June 2008

Introduction: p27Kip1 is a cyclin kinase inhibitor that induces cell cycle arrest. In this study, the efficacy of fusion protein TAT- p27Kip1 to inhibit cell proliferation in rat perivascular injured carotid arteries was tested. Methods: The cDNA of p27Kip1 and GFP (green fluorescein protein) fused to the TAT epitope, which allows cell penetration, yielded TAT-p27 Kip1 and TAT-GFP fusion proteins. In vitro biological activity on cell proliferation was evaluated by [3H] thymidine DNA incorporation in rabbit aortic endothelial cells (REC). An in vivo model used a silicone collar filled with saline positioned around the carotid vessel for 14 days to produce an increased adventitia cross-sectional area. Results: TAT-p27Kip1 inhibited REC proliferation in vitro using either 100, 200, and 500 nM compared to control (88.2 ± 4.4, 81.3 ± 7, 71.9 ± 4.2 vs. 100 ± 6.7%, N = 3, respectively, p < 0 .05). This response was stable for purified proteins stored at -20•C for at least 23 days. In vivo , TAT-p27Kip1 solution reduced adventitia cross-sectional area in a dose-dependent manner compared to TAT-GFP (area in mm2 — TAT-p27Kip1: 200 nM, 0.160 ± 0.018; 500 nM, 0.050 ± 0.005 vs. TAT-GFP: 500 nM, 0.595 ± 0.066 vs. the contralateral: 0.047 ± 0.005, N = 7, p < 0 .01). Conclusion: Taken together, these results provide evidence that TAT-p27Kip1 can inhibit vascular cells proliferation. It is the first successful demonstration that the cell permeable TAT-p27Kip1 has potential as a vascular anti-proliferative agent.
Id1 is a common downstream target of oncogenic tyrosine kinases in leukemic cells
Authors: Tam Winnie F. , Gu Ting-Lei , Chen Jing , Lee Benjamin H. , Bullinger Lars , Fröhling Stefan , Wang Andrew , Monti Stefano , Golub Todd R. , Gilliland D. Gary 
Published: June 2008

Abstract
Oncogenic tyrosine kinases, such as BCR-ABL, TEL-ABL, TEL-PDGFβR, and FLT3-ITD, play a major role in the development of hematopoietic malignancy. They activate many of the same signal transduction pathways. To identify the critical target genes required for transformation in hematopoietic cells, we used a comparative gene expression strategy in which selective small molecules were applied to 32Dcl3 cells that had been transformed to factor-independent growth by these respective oncogenic alleles. We identified inhibitor of DNA binding 1 (Id1), a gene involved in development, cell cycle, and tumorigenesis, as a common target of these oncogenic kinases. These findings were prospectively confirmed in cell lines and primary bone marrow cells engineered to express the respective tyrosine kinase alleles and were also confirmed in vivo in murine models of disease. Moreover, human AML cell lines Molm-14 and K562, which express the FLT3-ITD and BCR-ABL tyrosine kinases, respectively, showed high levels of Id1 expression. Antisense and siRNA based knockdown of Id1-inhibited growth of these cells associated with increased p27Kip1 expression and increased sensitivity to Trail-induced apoptosis. These findings indicate that Id1 is an important target of constitutively activated tyrosine kinases and may be a therapeutic target for leukemias associated with oncogenic tyrosine kinases.
Adenosine receptors in regulation of dendritic cell differentiation and function
Authors: Novitskiy Sergey V. , Ryzhov Sergey , Zaynagetdinov Rinat , Goldstein Anna E. , Huang Yuhui , Tikhomirov Oleg Y. , Blackburn Michael R. , Biaggioni Italo , Carbone David P. , Feoktistov Igor , Dikov Mikhail M. 
Published: June 2008

AbstractDifferentiation of functional dendritic cells (DCs) critically depends on the microenvironment. DCs differentiate in hypoxic tumor sites and inflamed or damaged tissue. Because local concentrations of adenosine reach high physiologically relevant levels in these conditions, we assessed the expression of adenosine receptors and the effect of their activation on differentiation of human monocytes and mouse peritoneal macrophages and hematopoietic progenitor cells (HPCs) into myeloid DCs. Stimulation of adenosine receptors skews DC differentiation toward a distinct cell population characterized by expression of both DC and monocyte/macrophage cell surface markers. Pharmacologic analysis and experiments with cells from A2B adenosine receptor knockout mice identified A2B receptor as the mediator of adenosine effects on DCs. Unlike normal myeloid DCs, adenosine-differentiated DCs have impaired allostimulatory activity and express high levels of angiogenic, pro-inflammatory, immune suppressor, and tolerogenic factors, including VEGF, IL-8, IL-6, IL-10, COX-2, TGF-β, and IDO. They promoted tumor growth if injected into tumors implanted in mice. Using adenosine desaminase knockout animals, we showed that DCs with proangiogenic phenotype are highly abundant under conditions associated with elevated levels of extracellular adenosine in vivo. Adenosine signaling through A2B receptor is an important factor of aberrant DC differentiation and generation of tolerogenic, angiogenic, and proinflammatory cells.
Biologic and genetic characterization of the novel amyloidogenic lambda light chain–secreting human cell lines, ALMC-1 and ALMC-2
Authors: Arendt Bonnie K. , Ramirez-Alvarado Marina , Sikkink Laura A. , Keats Jonathan J. , Ahmann Gregory J. , Dispenzieri Angela , Fonseca Rafael , Ketterling Rhett P. , Knudson Ryan A. , Mulvihill Erin M. , Tschumper Renee C. , Wu Xiaosheng , Zeldenrust Steven R. , Jelinek Diane F. 
Published: June 2008

AbstractPrimary systemic amyloidosis (AL) is a rare monoclonal plasma cell (PC) disorder characterized by the deposition of misfolded immunoglobulin (Ig) light chains (LC) in vital organs throughout the body. To our knowledge, no cell lines have ever been established from AL patients. Here we describe the establishment of the ALMC-1 and ALMC-2 cell lines from an AL patient. Both cell lines exhibit a PC phenotype and display cytokine-dependent growth. Using a comprehensive genetic approach, we established the genetic relationship between the cell lines and the primary patient cells, and we were also able to identify new genetic changes accompanying tumor progression that may explain the natural history of this patient's disease. Importantly, we demonstrate that free lambda LC secreted by both cell lines contained a beta structure and formed amyloid fibrils. Despite absolute Ig LC variable gene sequence identity, the proteins show differences in amyloid formation kinetics that are abolished by the presence of Na2SO4. The formation of amyloid fibrils from these naturally secreting human LC cell lines is unprecedented. Moreover, these cell lines will provide an invaluable tool to better understand AL, from the combined perspectives of amyloidogenic protein structure and amyloid formation, genetics, and cell biology.
European Organization for Research and Treatment of Cancer and International Society for Cutaneous Lymphoma consensus recommendations for the management of cutaneous B-cell lymphomas
Authors: Senff Nancy J. , Noordijk Evert M. , Kim Youn H. , Bagot Martine , Berti Emilio , Cerroni Lorenzo , Dummer Reinhard , Duvic Madeleine , Hoppe Richard T. , Pimpinelli Nicola , Rosen Steven T. , Vermeer Maarten H. , Whittaker Sean , Willemze Rein 
Published: June 2008

AbstractPrimary cutaneous B-cell lymphomas (CBCL) represent approximately 20% to 25% of all primary cutaneous lymphomas. With the advent of the World Health Organization-European Organization for Research and Treatment of Cancer (EORTC) Consensus Classification for Cutaneous Lymphomas in 2005, uniform terminology and classification for this rare group of neoplasms were introduced. However, staging procedures and treatment strategies still vary between different cutaneous lymphoma centers, which may be because consensus recommendations for the management of CBCL have never been published. Based on an extensive literature search and discussions within the EORTC Cutaneous Lymphoma Group and the International Society for Cutaneous Lymphomas, the present report aims to provide uniform recommendations for the management of the 3 main groups of CBCL. Because no systematic reviews or (randomized) controlled trials were available, these recommendations are mainly based on retrospective studies and small cohort studies. Despite these limitations, there was consensus among the members of the multidisciplinary expert panel that these recommendations reflect the state-of-the-art management as currently practiced in major cutaneous lymphoma centers. They may therefore contribute to uniform staging and treatment and form the basis for future clinical trials in patients with a CBCL.
Prediction of enzyme function by combining sequence similarity and protein interactions
Authors: Espadaler Jordi , Eswar Narayanan , Querol Enrique , Avilés Francesc X , Sali Andrej , Marti-Renom Marc A , Oliva Baldomero 
Published: June 2008

Abstract

Background
A number of studies have used protein interaction data alone for protein function prediction. Here, we introduce a computational approach for annotation of enzymes, based on the observation that similar protein sequences are more likely to perform the same function if they share similar interacting partners.

Results
The method has been tested against the PSI-BLAST program using a set of 3,890 protein sequences from which interaction data was available. For protein sequences that align with at least 40% sequence identity to a known enzyme, the specificity of our method in predicting the first three EC digits increased from 80% to 90% at 80% coverage when compared to PSI-BLAST.

Conclusion
Our method can also be used in proteins for which homologous sequences with known interacting partners can be detected. Thus, our method could increase 10% the specificity of genome-wide enzyme predictions based on sequence matching by PSI-BLAST alone.
Phagocytosis of Aspergillus fumigatus conidia by primary nasal epithelial cells in vitro
Authors: Botterel Françoise , Gross Karine , Ibrahim-Granet Oumaïma , Khoufache Khaled , Escabasse Virginie , Coste André , Cordonnier Catherine , Escudier Estelle , Bretagne Stéphane 
Published: June 2008

Abstract

Background
Invasive aspergillosis, which is mainly caused by the fungus Aspergillus fumigatus, is an increasing problem in immunocompromised patients. Infection occurs by inhalation of airborne conidia, which are first encountered by airway epithelial cells. Internalization of these conidia into the epithelial cells could serve as a portal of entry for this pathogenic fungus.

Results
We used an in vitro model of primary cultures of human nasal epithelial cells (HNEC) at an air-liquid interface. A. fumigatus conidia were compared to Penicillium chrysogenum conidia, a mould that is rarely responsible for invasive disease. Confocal microscopy, transmission electron microscopy, and anti-LAMP1 antibody labeling studies showed that conidia of both species were phagocytosed and trafficked into a late endosomal-lysosomal compartment as early as 4 h post-infection. In double immunolabeling experiments, the mean percentage of A. fumigatus conidia undergoing phagocytosis 4 h post-infection was 21.8 ± 4.5%. Using combined staining with a fluorescence brightener and propidium iodide, the mean rate of phagocytosis was 18.7 ± 9.3% and the killing rate 16.7 ± 7.5% for A. fumigatus after 8 h. The phagocytosis rate did not differ between the two fungal species for a given primary culture. No germination of the conidia was observed until 20 h of observation.

Conclusion
HNEC can phagocytose fungal conidia but killing of phagocytosed conidia is low, although the spores do not germinate. This phagocytosis does not seem to be specific to A. fumigatus. Other immune cells or mechanisms are required to kill A. fumigatus conidia and to avoid further invasion.
LuxS-independent formation of AI-2 from ribulose-5-phosphate
Authors: Tavender Timothy J , Halliday Nigel M , Hardie Kim R , Winzer Klaus 
Published: June 2008

Abstract

Background
In many bacteria, the signal molecule AI-2 is generated from its precursor S-ribosyl-L-homocysteine in a reaction catalysed by the enzyme LuxS. However, generation of AI-2-like activity has also been reported for organisms lacking the luxS gene and the existence of alternative pathways for AI-2 formation in Escherichia coli has recently been predicted by stochastic modelling. Here, we investigate the possibility that spontaneous conversion of ribulose-5-phosphate could be responsible for AI-2 generation in the absence of luxS.

Results
Buffered solutions of ribulose-5-phosphate, but not ribose-5-phosphate, were found to contain high levels of AI-2 activity following incubation at concentrations similar to those reported in vivo. To test whether this process contributes to AI-2 formation by bacterial cells in vivo, an improved Vibrio harveyi bioassay was used. In agreement with previous studies, culture supernatants of E. coli and Staphylococcus aureus luxS mutants were found not to contain detectable levels of AI-2 activity. However, low activities were detected in an E. coli pgi-eda-edd-luxS mutant, a strain which degrades glucose entirely via the oxidative pentose phosphate pathway, with ribulose-5-phosphate as an obligatory intermediate.

Conclusion
Our results suggest that LuxS-independent formation of AI-2, via spontaneous conversion of ribulose-5-phosphate, may indeed occur in vivo. It does not contribute to AI-2 formation in wildtype E. coli and S. aureus under the conditions tested, but may be responsible for the AI-2-like activities reported for other organisms lacking the luxS gene.
Expression of Brugmansia candida Hyoscyamine 6beta-Hydroxylase gene in Saccharomyces cerevisiae and its potential use as biocatalyst
Authors: Cardillo Alejandra B , Talou Julián Rodríguez , Giulietti Ana M 
Published: June 2008

Abstract

Background
Tropane alkaloids, mainly hyoscyamine and scopolamine, are widely used in medicine due to their anticholinergic activity. Scopolamine has a higher demand being the more valuable alkaloid due to its fewer side effects and higher physiological activity. Anisodamine (6β-hydroxyhyoscyamine) is the intermediate in the conversion of hyoscyamine into scopolamine. Current studies report that this alkaloid is potentially applicable in medicine. The gene that codifies for Hyoscyamine 6-β hydroxylase, the enzyme responsible for hyoscyamine hydroxylation and epoxidation, leading to scopolamine was isolated from Brugmansia candida.

Results
The h6h cDNA was cloned into pYES2.1 and pYES2.1/V5-His-TOPO vectors to produce an untagged and a tagged protein, respectively. The H6H enzyme was produced in Saccharomyces cerevisiae in order to obtain a biological catalyst for potential industrial applications. Protein extracts of the induced yeast were analyzed by Western blot. The expression was detected 4 h after induction and no degradation was observed during the period assayed. The tagged and the untagged proteins were able to transform hyoscyamine, showing a functional expression of the h6h cDNA.

Conclusion
The strains obtained in this work are promising and potentially applicable in biocatalytic processes.