bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intraocular lymphoma diagnosed by fine‐needle aspiration biopsy
Authors: Sarafzadeh Shaden , Corrêa Zélia M. , Dhamija Ashima , Augsburger James J. , Trichopoulos Nikolaos 
Published: July 2009

Acta Ophthalmol. 2010: 88: 705–710Abstract.Purpose:  To describe clinical experience in the diagnosis of intraocular lymphoma by fine‐needle aspiration biopsy (FNAB) in patients with one or more discrete intraocular infiltrative lesions and limited or absent intravitreal tumour cells.Methods:  Retrospective descriptive analysis of patients who underwent intraocular FNAB of a solid retinal, subretinal pigment epithelial or uveal tumour that proved to be a malignant lymphoma.Results:  After exclusions, our study group consisted of seven patients, each of whom had one or more discrete intraocular infiltrative lesions and limited or absent intravitreal tumour cells and underwent a diagnostic intraocular FNAB that confirmed malignant intraocular lymphoma cytopathologically. These included three patients with one or more geographic yellow subretinal pigment epithelial infiltrates and one patient each with a prominent nodular white subretinal pigment epithelial tumour, a rapidly developing solid placoid choroidal mass, a haemorrhagic retinal infiltrative lesion and an infiltrative iris tumour, respectively. A prominent feature of virtually all aspirates was a large proportion of degenerated lymphoid cells in the background. Cytologically intact tumour cells ranged from relatively homogeneous small round cells with large nucleus to cytoplasm ratio to pleomorphic large cells with irregular knob‐like nuclear protrusions. Immunocytochemical stains for lymphoid markers were helpful in confirming the pathological diagnosis of lymphoma in the five patients in whom this testing was performed.Conclusion:  FNAB was a useful diagnostic tool in the described subgroup of patients with suspected intraocular lymphoma. FNAB should be considered as a diagnostic option in selected patients with suspected intraocular lymphoma, especially if there are few or no vitreous cells.
Constructing a Philosophy of Science of Cognitive Science
Authors: Bechtel William 
Published: July 2009

AbstractPhilosophy of science is positioned to make distinctive contributions to cognitive science by providing perspective on its conceptual foundations and by advancing normative recommendations. The philosophy of science I embrace is naturalistic in that it is grounded in the study of actual science. Focusing on explanation, I describe the recent development of a mechanistic philosophy of science from which I draw three normative consequences for cognitive science. First, insofar as cognitive mechanisms are information‐processing mechanisms, cognitive science needs an account of how the representations invoked in cognitive mechanisms carry information about contents, and I suggest that control theory offers the needed perspective on the relation of representations to contents. Second, I argue that cognitive science requires, but is still in search of, a catalog of cognitive operations that researchers can draw upon in explaining cognitive mechanisms. Last, I provide a new perspective on the relation of cognitive science to brain sciences, one which embraces both reductive research on neural components that figure in cognitive mechanisms and a concern with recomposing higher‐level mechanisms from their components and situating them in their environments.
Morphology and biomass production of prairie cordgrass on marginal lands
Authors: BOE A. , OWENS V. , GONZALEZ‐HERNANDEZ J. , STEIN J. , LEE D. K. , KOO B. C. 
Published: July 2009

AbstractPrairie cordgrass (Spartina pectinataLink.) is indigenous throughout most of the continental United States and Canada to 60°N latitude and is well suited to marginal land too wet for maize (Zea maysL.) and switchgrass (Panicum virgatumL.). Evaluations of prairie cordgrass in Europe and North America indicated it has high potential for biomass production, relative to switchgrass, in short‐season areas. Our objective was to describe morphology and biomass production and partitioning in mature stands of ‘Red River’ prairie cordgrass and determine biomass production of natural populations on marginal land. This study was conducted from 2000 to 2008 in eastern South Dakota. Mean biomass production of mature stands of Red River was 12.7 Mg ha−1. Leaves composed >88% of the biomass, and 60% of the tillers had no internodes. Belowground biomass to a depth of approximately 25 cm, not including roots, was 21 Mg ha−1. Tiller density ranged from 683 tillers m−2for a 10‐year‐old stand to 1140 tillers m−2for a 4‐year‐old stand. The proaxis was composed of about eight phytomers, with rhizomes originating at proximal nodes and erect tillers at distal nodes. Vegetative propagation was achieved by both phalanx and guerilla growth. Differences among natural populations for biomass were expressed on gravelly marginal land. However, production, averaged across populations, was low (1.37 Mg ha−1) and comparable to ‘Cave‐In‐Rock’ switchgrass (1.67 Mg ha−1) over a 4‐year period. The large carbon storage capacity of prairie cordgrass in proaxes and rhizomes makes it useful for carbon sequestration purposes. Prairie cordgrass should be compared with switchgrass and other C4perennial grasses along environmental gradients to determine optimum landscape positions for each and to maximize bioenergy production and minimize inputs.
Value of the extracellular water ratio for assessment of cirrhotic patients with and without ascites
Authors: Hara Nagisa , Iwasa Motoh , Iwata Kazuko , Miyachi Hirohide , Tanaka Hideaki , Takeo Masaki , Fujita Naoki , Kobayashi Yoshinao , Takei Yoshiyuki 
Published: July 2009

Aims:  Ascites, which often complicates liver cirrhosis, is reported to be a factor that worsens the outcome. The aims of this study were to quantify body water compartment changes in cirrhotic patients, with and without ascites, and to elucidate the value of body water analysis for predicting the development of ascites.Methods:  A total of 109 cirrhotic patients, with and without ascites, and 65 controls were studied. Intra‐ and extracellular water (ECW) in the whole body and in the arm, leg and trunk were measured using the recently developed 8‐electrodes multiple‐frequency bioelectrical impedance analyzer. Furthermore, patients without ascites were followed to an episode of ascites or death.Results:  Patients with liver cirrhosis had significantly higher ECW ratios than controls. ECW ratios were increased in cirrhotic patients with moderate and severe disease. The ECW ratio of the trunk showed highly significant changes in cirrhotic patients with ascites. The ECW ratio correlated with age, serum albumin, and prothrombin time. A relative expansion of ECW and low albumin were predictive of further episodes of ascites (log‐rank 6.94, P < 0.01). In multivariate analysis, the ECW ratio was independently associated with the development of ascites.Conclusion:  Liver cirrhosis was characterized by a redistribution of body water. The ECW ratio is a reliable tool for quantification of redistribution of body water and can predict the development of ascites.
New scoring system for predicting relapse after lamivudine‐induced hepatitis B e‐antigen loss in chronic hepatitis B patients
Authors: Song Byung‐Cheol , Cui Xiu Ji , Cho Yoo‐Kyung , Choi Eun Kwang , Hyun Soyoung , Song Hyun Joo , Kim Heung Up 
Published: July 2009

Aim:  In endemic areas of hepatitis B virus (HBV) infection, lamivudine‐induced hepatitis B e‐antigen (HBeAg) loss is not durable. We developed a scoring system to predict the relapse after lamivudine‐induced HBeAg loss.Methods:  Of 93 HBeAg‐positive chronic hepatitis B patients receiving lamivudine therapy, we studied the 30 patients who achieved HBeAg loss. Qualitative polymerase chain reaction assays for HBV DNA were performed after HBeAg loss; if results were negative on two consecutive occasions, lamivudine treatment was stopped. Serum HBV DNA levels at the time of HBeAg loss were determined using stored serum by the Cobas Amplicor HBV Monitor Kit.Results:  Cumulative relapse rates were 44%, 55.8% and 59.8%, after 1, 2 and 5 years, respectively. Univariate analysis showed that the risk factors for relapse were age (≥ 30 years), HBV DNA level (≥ 60 IU/mL) at the time of HBeAg loss and liver cirrhosis. Independent risk factors for relapse were age (odds ratio [OR], 4.3; 95% confidence interval [CI], 1.2–17.6) and serum HBV DNA level at the time of HBeAg loss (OR, 5.1; 95% CI, 1.3–21.6). We developed a scoring system based on these independent risk factors. No relapse was observed for patients with a risk score of 0. For patients with a risk score of 1, the relapse rates were 41%, 49% and 56% at 1, 2 and 5 years, respectively. All patients with a risk score of 2 relapsed (P = 0.01).Conclusion:  Our new scoring system may be useful for predicting relapses in patients with lamivudine‐induced HBeAg loss. Treatment strategies should be individualized according to risk score.
Sediment-hosted gas hydrates: new insights on natural and synthetic systems
Authors: Long D. , Lovell M. A. , Rees J. G. , Rochelle C. A. 
Published: July 2009

Abstract
In the public's imagination, hydrates are seen as either a potential new source of energy to be exploited as the world uses up its reserves of oil and gas or as a major environmental hazard. Scientists, however, have expressed great uncertainty as to the global volume of hydrates and have reached little agreement on how they might be exploited. Both of these uncertainties can be reduced by a better understanding of how hydrates are held within sediments. There are conflicting ideas as to whether hydrates are disseminated within selected lithologies or trapped within fractures comparable to mineral lodes. To resolve this, hydrates have to be examined at all scales ranging from using seismics to microscopic studies. Their position within sediments also influences the stability of methane hydrate in responding to pressure and temperature and how the released gas might transfer to the ocean, atmosphere, or to a transport mechanism for recovery. These results also run parallel with the studies of carbon dioxide hydrate, which is being considered as a potential sequestion medium.
Gas hydrate crystallite size investigations with high-energy synchrotron radiation
Authors: Klapp S. A. , Klein H. , Kuhs W. F. 
Published: July 2009

Abstract

The grain sizes of gas hydrate crystallites are largely unknown in natural samples. Single grains are hardly detectable with electron or optical microscopy. For the first time, we have used high-energy synchrotron diffraction to determine grain sizes of six natural gas hydrates retrieved from the Bush Hill region in the Gulf of Mexico and from ODP Leg 204 at the Hydrate Ridge offshore Oregon from varying depth between 1 and 101 metres below seafloor. High-energy synchrotron radiation provides high photon fluxes as well as high penetration depth and thus allows for investigation of bulk sediment samples. Gas hydrate grain sizes were measured at the Beam Line BW 5 at the HASYLAB/Hamburg. A ‘moving area detector method’, originally developed for material science applications, was used to obtain both spatial and orientation information about gas hydrate grains within the sample. The gas hydrate crystal sizes appeared to be (log-)normally distributed in the natural samples. All mean grain sizes lay in the range from 300 to 600 µm with a tendency for bigger grains to occur in greater depth. Laboratory-produced methane hydrate, aged for 3 weeks, showed half a log-normal curve with a mean grain size value of
c
. 40 µm. The grains appeared to be globular shaped.
Exploration strategy for economically significant accumulations of marine gas hydrate
Authors: Kleinberg R. L. 
Published: July 2009

Abstract
There are at present no validated methods for reliably finding economically significant accumulations of natural gas hydrate in marine environments. The seismic bottom simulating reflector (BSR) has been regarded as a primary indicator of hydrate presence in marine environments, but the presence of a BSR conveys no information about the abundance of hydrate in the sediments above it. Seafloor features such as gas seeps, pockmarks or hydrate outcrops may be qualitative markers of deeper hydrate presence, but cannot be interpreted quantitatively. Another approach to exploration geophysics is required to find exploitable gas hydrate reservoirs with high reliability. It is known that in many cases gas is supplied to the gas hydrate stability zone primarily through faults or fractures. In a certain range of gas flux, these fissures should become mineralized with gas hydrate and form vertical or subvertical dykes. The dip and strike of these dykes are controlled by the principal stress directions, which can be predetermined. Thus multiple hydrate dykes are expected to be parallel. Even if the greatest volume of gas hydrate is to be found in sub-horizontal permeable beds, the steeply dipping mineralized conduits that fed gas to them may be the most reliable marker of substantial subsurface hydrate presence. Geological and geophysical survey methods sensitive to parallel arrays of vertical and subvertical hydrate dykes are presented.
Gas hydrate forming fluids on the NE Sakhalin slope, Sea of Okhotsk
Authors: Mazurenko L. L. , Matveeva T. V. , Prasolov E. M. , Shoji H. , Obzhirov A. I. , Jin Y. K. , Poort J. , Logvina E. A. , Minami H. , Sakagami H. , Hachikubo A. , Salomatin A. S. , Salyuk A. N. , Prilepskiy E. B. ,   CHAOS 2003 Scientific Team
Published: July 2009

Abstract

An area of focused fluid venting off NE Sakhalin, Sea of Okhotsk, was investigated in 2003 during the 31st and 32nd international expeditions of R/V
Akademik M. A. Lavrentyev
within the framework of the CHAOS Project. More than 40 structures related to seafloor gas venting were discovered and gas hydrates were sampled from three of these: CHAOS, Hieroglyph and Kitami. Geochemical analyses were used to define the mechanisms of gas hydrate accumulation and the sources of fluids involved. Chemical and isotopic analyses of the interstitial and hydrate waters suggest that hydrates were formed from seawater (or
in-situ
pore water) and an ascending fluid enriched in salts. Hydrate formation occurs at locations of the most intensive saline water upflow, and this is probably a function of the gas solubility in water in equilibrium with hydrate. The water involved in gas hydrate formation consists of about 70% pore water derived from the host sediment and 30% from the ascending fluid. The overall isotopic composition of the ‘fluid’ taking part in hydrate formation was calculated as
δ
2
H≈−11‰ and δ
18
O≈−1.5‰.
Mapping hydrate stability zones offshore Scotland
Authors: Camps A. P. , Long D. , Rochelle C. A. , Lovell M. A. 
Published: July 2009

Abstract
One practical method to reduce environmentally damaging greenhouse gas emissions is through the geological storage of carbon dioxide. Deep, warm storage of carbon dioxide is currently taking place at Sleipner, North Sea and Weyburn, Canada. It is, however, also possible to store carbon dioxide as a liquid and hydrate in cool, sub-seabed sediments. Offshore north and west of Scotland seafloor pressures and temperatures are suitable for hydrate formation. In addition to the possibility of natural methane hydrate being present in this region, conditions may also be favourable for carbon dioxide storage as a liquid and hydrate. A computer program has been developed to calculate the depth to the base of the carbon dioxide and methane hydrate stability zones in two offshore regions: the Faeroe–Shetland Channel and the northern Rockall Trough. Results predict that methane hydrate remains stable to a maximum depth of 650 m below the seabed in the Faeroe–Shetland Channel, and 600 m below the seabed in the northern Rockall Trough; the carbon dioxide hydrate stability zone extends below the seabed to a depth of 345 and 280 m, respectively. No physical evidence for the existence of natural hydrate in these regions has been confirmed. Suitable conditions for carbon dioxide storage as a liquid and hydrate exist, and should this storage method be developed further, a more refined program and greater offshore investigations to improve data sets would be necessary to scope the full potential.
Regional versus detailed velocity analysis to quantify hydrate and free gas in marine sediments: the South Shetland Margin case study
Authors: Tinivella Umberta , Loreto Maria Filomena , Accaino Flavio 
Published: July 2009

Abstract
The presence of gas hydrate and free gas within marine sediments deposited along the South Shetland margin, offshore the Antarctic Peninsula, was confirmed by low and high resolution geophysical data, acquired during three research cruises. Seismic data analysis has revealed the presence of a bottom-simulating reflector that is very strong and continuous in the eastern part of the margin. This area can be considered as a useful site to study the seismic characteristics of sediments containing gas hydrate, with a particular focus on the estimation of gas hydrate and free gas amounts in the pore space. Pre-stack depth migration and tomographic inversion were performed to produce a regional velocity field of gas-phase bearing sediments and to obtain information about the average thickness of gas hydrate and free gas layers. Using these data and theoretical models, the gas hydrate and free gas concentrations can be estimated. Moreover, the common image gather semblance analysis revealed the presence of detailed features, such as layers with small thickness characterized by low velocity alternating with high velocity layers, below and above the bottom-simulating reflector. These layers are associated with free gas trapped within the hydrate stability zone and deeper sediments. Thus, the use of the detailed and the regional velocity field analysis is important to give a more reliable estimate of gas content in the marine sediments.
Bilateral Investment Treaties and the European Union. Recent Developments in Arbitration and Before the ECJ
Authors: Potestà Michele 
Published: July 2009

AbstractThe issue of the relationship between Bilateral Investment Treaties (BITs) and the EU legal order has recently attracted attention amongst scholars and practitioners in the field of international investment arbitration. Under a first perspective of the problem, the Arbitral Tribunal in Eastern Sugar B.V. v. The Czech Republic was confronted with the question of whether there was any room left for BITs between EU Member States. The Tribunal discussed the legal arguments advanced for and against the applicability of such "intra-EU BITs" between Member States. The issue, which is particularly relevant considering that there are currently more than 190 BITs concluded between EU Member States, will be analysed in the first part of this article. Under a second point of view of the problem, the European Court of Justice (ECJ) handed down two judgments on 3 March 2009 addressing incompatibilities with EC Law resulting from certain BITs entered into by Sweden and Austria with third countries. The second part of this article will deal with the consequences arising out of the Court's rulings with regard to existing and future BITs entered into by Member States with third countries.
Identification and molecular characterization of recurrent genomic deletions on 7p12 in the IKZF1 gene in a large cohort of BCR-ABL1–positive acute lymphoblastic leukemia patients: on behalf of Gruppo Italiano Malattie Ematologiche dell'Adulto Acute Leukemia Working Party (GIMEMA AL WP)
Authors: Iacobucci Ilaria , Storlazzi Clelia Tiziana , Cilloni Daniela , Lonetti Annalisa , Ottaviani Emanuela , Soverini Simona , Astolfi Annalisa , Chiaretti Sabina , Vitale Antonella , Messa Francesca , Impera Luciana , Baldazzi Carmen , D'Addabbo Pietro , Papayannidis Cristina , Lonoce Angelo , Colarossi Sabrina , Vignetti Marco , Piccaluga Pier Paolo , Paolini Stefania , Russo Domenico , Pane Fabrizio , Saglio Giuseppe , Baccarani Michele , Foà Robin , Martinelli Giovanni 
Published: July 2009

AbstractThe BCR-ABL1 fusion gene defines the subgroup of acute lymphoblastic leukemia (ALL) with the worst clinical prognosis. To identify oncogenic lesions that combine with BCR-ABL1 to cause ALL, we used Affymetrix Genome-Wide Human SNP arrays (250K NspI and SNP 6.0), fluorescence in situ hybridization, and genomic polymerase chain reaction to study 106 cases of adult BCR-ABL1–positive ALL. The most frequent somatic copy number alteration was a focal deletion on 7p12 of IKZF1, which encodes the transcription factor Ikaros and was identified in 80 (75%) of 106 patients. Different patterns of deletions occurred, but the most frequent were those characterized by a loss of exons 4 through 7 (Δ4-7) and by removal of exons 2 through 7 (Δ2-7). A variable number of nucleotides (patient specific) were inserted at the conjunction and maintained with fidelity at the time of relapse. The extent of the Δ4-7 deletion correlated with the expression of a dominant-negative isoform with cytoplasmic localization and oncogenic activity, whereas the Δ2-7 deletion resulted in a transcript lacking the translation start site. The IKZF1 deletion also was identified in the progression of chronic myeloid leukemia to lymphoid blast crisis (66%) but never in myeloid blast crisis or chronic-phase chronic myeloid leukemia or in patients with acute myeloid leukemia. Known DNA sequences and structural features were mapped along the breakpoint cluster regions, including heptamer recombination signal sequences recognized by RAG enzymes during V(D)J recombination, suggesting that IKZF1 deletions could arise from aberrant RAG-mediated recombination.
A comparison of random forest and its Gini importance with standard chemometric methods for the feature selection and classification of spectral data
Authors: Menze Bjoern H , Kelm B Michael , Masuch Ralf , Himmelreich Uwe , Bachert Peter , Petrich Wolfgang , Hamprecht Fred A 
Published: July 2009

AbstractBackgroundRegularized regression methods such as principal component or partial least squares regression perform well in learning tasks on high dimensional spectral data, but cannot explicitly eliminate irrelevant features. The random forest classifier with its associated Gini feature importance, on the other hand, allows for an explicit feature elimination, but may not be optimally adapted to spectral data due to the topology of its constituent classification trees which are based on orthogonal splits in feature space.ResultsWe propose to combine the best of both approaches, and evaluated the joint use of a feature selection based on a recursive feature elimination using the Gini importance of random forests' together with regularized classification methods on spectral data sets from medical diagnostics, chemotaxonomy, biomedical analytics, food science, and synthetically modified spectral data. Here, a feature selection using the Gini feature importance with a regularized classification by discriminant partial least squares regression performed as well as or better than a filtering according to different univariate statistical tests, or using regression coefficients in a backward feature elimination. It outperformed the direct application of the random forest classifier, or the direct application of the regularized classifiers on the full set of features.ConclusionThe Gini importance of the random forest provided superior means for measuring feature relevance on spectral data, but – on an optimal subset of features – the regularized classifiers might be preferable over the random forest classifier, in spite of their limitation to model linear dependencies only. A feature selection based on Gini importance, however, may precede a regularized linear classification to identify this optimal subset of features, and to earn a double benefit of both dimensionality reduction and the elimination of noise from the classification task.