bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased Tissue Factor Expression Is Associated with Reduced Survival in Non–Small Cell Lung Cancer and with Mutations of TP53 and PTEN
Authors: Regina Sandra , Valentin Jean-Baptiste , Lachot Sébastien , Lemarié Etienne , Rollin Jérôme , Gruel Yves 
Published: August 2009

Abstract
Background: Tissue factor (TF), the main initiator of blood coagulation, is also a signaling protein that regulates cancer progression. TF synthesis was recently shown to be affected by tumor suppressor genes (TSGs) in tumor cell lines. We therefore studied TF gene (F3) expression and the status of genes coding for tumor protein p53 (TP53), phosphatase and tensin homolog (PTEN), and serine/threonine kinase 11 (STK11) in non–small cell lung cancer (NSCLC). Heparanase (HPSE) gene expression was also measured because this endo-β-D-glucuronidase was recently shown to enhance TF gene expression.
Methods: TF and heparanase mRNA expression was measured by real-time PCR in 53 NSCLC tumors. Exons 5–8 of TP53 were sequenced from genomic DNA. Mutations of PTEN and STK11 were screened by multiplex ligation-dependent probe amplification.
Results: TF mRNA levels were significantly higher in T3–T4 tumors (P = 0.04) and in stages III–IV of NSCLC (P = 0.03). Mutations of TP53, STK11, and PTEN were identified in 20 (37.7%), 21 (39%), and 20 (37.7%) of tumors, respectively. TF expression was higher in mutated TP53 (TP53Mut) (P = 0.02) and PTENMut (P = 0.03) samples. Moreover, TF mRNA increased from 2700 copies (no mutation) to 11 6415 when 3 TSG were mutated. Heparanase gene expression did not differ according to TF gene (F3) expression or TSG mutation. The median survival time was shorter in patients with tumor TF mRNA levels above median values (relative risk 2.2; P = 0.03, multivariate analysis) and when TP53 was mutated (relative risk 1.8; P = 0.02).
Conclusions: These results provide clear evidence that combined oncogene events affecting TSG dramatically increase TF gene expression in lung tumors. Moreover, this study suggests that TF gene expression could be used as a prognostic marker in NSCLC. .
Marine benthic algae of the South Kamchatka state wildlife sanctuary (Kamchatka, Russia)
Authors: Selivanova Olga N. , Zhigadlova Galina G. 
Published: August 2009

Abstract
We present new data on marine algae of the South Kamchatka state wildlife sanctuary (Yuzhno-Kamchatskii Zakaznik, Russia), a protected natural area of federal significance. The species list of macrophytic marine algae is accompanied by information on their reproduction and distribution. This list updates the taxonomy and expands a previous list, with many new species, including 2 species previously unknown from the Pacific coasts of Russia (Colaconema endophyticum, Acrochaetium plumosum), 2 species new to the coasts of Kamchatka (Colaconema daviesii and Acrochaete geniculata), and 11 species recorded for the first time from the area studied (Erythrocladia irregularis, Palmaria hecatensis, Palmaria mollis, Meiodiscus concrescens, Crossocarpus lamuticus, Cirrulicarpus ruprechtianum, Rhodomela sibirica, Urospora elongata, Zygomitus reticulatus, Acrochaete ramosa, Acrochaete pterosiphoniae) (Nagai) Zhigadlova, comb. nov. (=Entocladia pterosiphoniae). The importance of the wildlife sanctuary for the conservation of biodiversity in Kamchatka is noted.
Composition and annual cycle of phytoplankton assemblages in the northeastern Adriatic Sea
Authors: Viličić Damir , Djakovac Tamara , Burić Zrinka , Bosak Sunčica 
Published: August 2009

AbstractPhytoplankton abundance and seasonality in the northeastern Adriatic Sea were directly related to the annual regime of the Po River discharge in the period 2002–2007. In 2005, 2006, and 2007, there was a shift in the timing of the annual Po River maximum discharge and of phytoplankton maxima from spring to autumn. In addition, the eastern coastal area was greatly influenced by oligotrophic karstic rivers and the Eastern Adriatic Current. Dominant phytoplankton taxa were defined on the basis of abundance and frequency of appearance. Such an approach may help in the comparison of phytoplankton communities within different environments. The dominant taxa were the diatomsCerataulina pelagica,Chaetoceros socialis,Chaetoceros vixvisibilisandPseudo-nitzschiaspp., which appeared at maximum abundances >106cells l-1in more than 20% of samples. Among other phytoplankton, the most common was the coccolithophoridEmiliania huxleyi(maximum abundance of 2×105cells l-1in 50% of samples), and the dinoflagellateProrocentrum minimum(maximum abundance of 3×105cells l-1in 12% of samples). The present state of the phytoplankton community may provide valuable information for evaluation of possible future environmental changes in the shallow Mediterranean ecosystem.
Phylogenetic position of freshwater and marine Sigmoidea species: introducing a marine hyphomycete Halosigmoidea gen. nov. (Halosphaeriales)
Authors: Jones E.B. Gareth , Zuccaro Alga , Mitchell Julian , Nakagiri Akira , Chatmala Ittichai , Pang Ka-Lai 
Published: August 2009

Abstract
The aquatic hyphomycete genus Sigmoidea, with freshwater and marine representatives, is re-examined at the morphological and molecular levels. Currently six species are accepted, four from freshwater habitats (S. prolifera, S. aurantiaca, S. contorta, S. praelonga) and two marine species (S. marina, S. luteola). Phylogenetic analyses of the ribosomal small subunit rRNA gene sequences of freshwater and marine Sigmoidea species indicate that the marine species are distantly placed from the freshwater species, S. prolifera and Pseudosigmoidea cranei. The latter species are placed in the Dothideomycetes, in sister clades, with 81% bootstrap support. The phylogenetic placement of both marine Sigmoidea species, inferred from large subunit rRNA gene sequences, was within the genus Corollospora (Halosphaeriales, Sordariomycetes, Pezizomycotina). An undescribed Sigmoidea species isolated from the Baltic Sea and one previously incorrectly identified as S. marina from Japan (S. parvula sp. nov.) formed a clade together with Corollospora quinqueseptata and Varicosporina ramulosa, and were located in a sister group to S. luteola and S. marina. Based on morphological and phylogenetic evidence, Halosigmoidea gen. nov. is proposed to accommodate the three marine Sigmoidea species (S. luteola, S. marina, S. parvula sp. nov.). Identification keys to the genera Halosigmoidea, Pseudosigmoidea and Sigmoidea, and Halosigmoidea species are provided.
Proline metabolism in response to salt stress in common reed [Phragmites australis (Cav.) Trin. ex Steud]
Authors: Zhen Wei-Bo , Ma Qing-Hu 
Published: August 2009

Abstract
We studied effects of salt stress on proline accumulation and the activities of proline metabolic enzymes in reed, a salt-tolerant, cosmopolitan, aquatic grass. A concentration-dependent inhibition of plant growth occurred in the presence of NaCl, which was accompanied by high amounts of proline accumulation. Reed tolerance of salt stress reaches a limit at approximately 200 mm NaCl. Free proline content and pyrroline-5-carboxylate synthetase (P5CS) activity both increased with salt stress treatment, while ornithine aminotransferase (OAT) activity appeared to be unaffected, suggesting that the glutamate pathway, rather than the ornithine pathway, plays a vital role in proline accumulation during osmotic regulation. The activity of the proline degrading enzyme, proline dehydrogenase (PDH), decreased under salt stress, indicating that proline catabolism may also be responsible for proline accumulation in response to salt stress. Furthermore, high salinity ≥250 mm NaCl, which stops growth of reed, decreases proline accumulation and P5CS, OAT, and PDH activities. This suggests that changes in enzyme activities of proline metabolism coupled with increased proline accumulation are involved in osmotic regulation of reed plants only when they are grown at salinities ≤200 mm NaCl.
Activation of thermomechanical pulp by laccases as studied by UV-Vis, UV resonance Raman and FTIR spectroscopy 10th EWLP, Stockholm, Sweden, August 25–28, 2008
Authors: Lähdetie Anni , Liitiä Tiina , Tamminen Tarja , Pere Jaakko , Jääskeläinen Anna-Stiina 
Published: August 2009

Abstract
The changes in lignin structure of spruce thermomechanical pulp (TMP), induced by treatment with laccase of Trametes hirsuta (ThL) and laccase of Melanocarpus albomyces (MaL), has been investigated by UV-Vis, UV resonance Raman (UVRR), and Fourier transform infrared (FTIR) spectroscopy. The spectroscopic results showed that the structural changes were small; however, the changes were slightly more pronounced in the case of MaL. Nevertheless, the brightness of the pulps remained higher after treatment with MaL than after treatment with ThL. Accordingly, MaL is a promising enzyme for fiber activation and functionalization.
Acute Care in Cervical Spinal Cord Trauma with Long-Term Benefit: A Review
Authors: Ashare Alan B. , Lyckman Alvin W. 
Published: August 2009

Abstract
Spinal cord injury involves three phases. In the first, trauma events deliver direct pressure to the cervical spine, which may compress, dislocate, or fracture the spine, and in turn compress, crush, or transect the spinal cord. In the process, local neurons are destroyed and sensory and motor pathways can be severed. In the second phase, acute tissue responses, bleeding, and inflammation rapidly and radically change the physical and chemical conditions at the wound site. Finally, days, weeks, and months after the initial trauma, chronic post-injury processes reform the wound site into a lasting scar that impedes regeneration of spinal cord pathways. A major goal of current spinal cord injury research should be rapid and lasting inhibition of acute and chronic tissue reactions in the spinal cord wound that lead to a growth-inhibiting environment and diverting these reactions toward conditions that favor regeneration of severed spinal pathways. Here, we consider experimental strategies that could form the basis for treatments that can be rapidly administered after trauma and provides lasting benefit to spinal cord regeneration and rehabilitation.
Rapid increases in mercury concentrations in the eggs of mallards fed methylmercury
Authors: Heinz Gary H. , Hoffman David J. , Klimstra Jon D. , Stebbins Katherine R. 
Published: August 2009

Abstract
To determine how quickly breeding birds would have to feed in a mercury-contaminated area before harmful concentrations of mercury, as methylmercury, built up in their eggs, we fed female mallards (Anas platyrhynchos) a control diet or diets containing 0.5, 1, 2, 4, or 8 μg/g mercury (on what was close to a dry weight basis) as methylmercury chloride for 23 d. After 18 d on their respective mercury diets, the eggs of mallards fed 0.5, 1, 2, 4, or 8 μg/g mercury contained 97.8, 86.0, 89.9, 88.9, and 85.9%, respectively, of the peak concentrations reached after 23 d. Depending on the dietary concentration of mercury, no more than approximately a week may be required for harmful concentrations (0.5–0.8 μg/g, wet weight) to be excreted into eggs.
Holistic Fracture Diagnostics: Consistent Interpretation of Prefrac Injection Tests Using Multiple Analysis Methods
Authors: Barree R. D. , Barree V. L. , Craig D. P. 
Published: August 2009

Summary
Since the introduction of the G-function derivative analysis, prefrac diagnostic injection tests have become a valuable and commonly used technique. Unfortunately, the technique is frequently misapplied or misinterpreted, leading to confusion and misdiagnosis of fracturing parameters. This paper presents a consistent method of analysis of the G-function, its derivatives, and its relationship to other diagnostic techniques including square-root(time) and log(∆pwf)-log(∆t) plots and their appropriate diagnostic derivatives.
Four field test examples are given for the most common diagnostic curve signatures. These show how multiple analysis methods can be applied to consistently interpret closure pressure and time, as well as pre- and post-closure flow regimes and reservoir properties from the test data. The cases include normal constant-area and constant permeability leakoff, pressure dependent fissure leakoff, fracture tip extension, and variable fracture storage. In some cases conventionally accepted analysis methods, such as the Sqrt(time) plot, can lead to misleading interpretations. A single consistent approach to analysis is described for each case. The example cases can be used to build a foundation for consistent and less ambiguous analysis of any complex fracture injection/falloff test.
Compositional Modeling of Two-Phase (Gas/Water) Flow in Pipes
Authors: Zaghloul Jose , Adewumi M. A. , Ityokumbul M. T. 
Published: August 2009

Summary
The current work presents a fully compositional tool for modeling systems exhibiting two-phase (gas/water) flow. The tool couples complex hydrodynamic and thermodynamic models to describe the behavior of fluids flowing in a pipe. The model described herein focuses on gas transmission with low-liquid loading conditions (hl/d &lt; 0.3).
Results show the model is capable of predicting the hydrodynamic behavior as well as the compositional profiles of gas and water flowing in a pipe. This is important in the light of compositional dependence of hydrate or acid formation. Compositional changes in the aqueous phase may create the conditions for forming hydrates or acids.
The model was benchmarked using several published works, details of which can be found in the work of Zaghloul (2006). In this paper, model performance is illustrated using a case study. The case study compares model calculations with an experimental data set obtained from Eaton et al. (1967). Model calculations predicted the observed flow pattern, pressure and liquid holdup profiles reported in the case study. Calculated pressures are within 2% of experimental values, while liquid holdup (approx 4%) is in agreement with the value predicted by Eaton's correlation (Eaton et al. 1967).
The model is capable of predicting the initial water condensation point in the pipeline and the concentration of different substances in the aqueous mixture. The tool gives production engineers important information on how much hydrate/corrosion inhibitors to inject and where, thus saving in the design, operation, and maintenance of pipeline systems.
Innovative Implementation of Compositional Delumping in Integrated Asset Modeling
Authors: Vignati E. , Cominelli A. , Rossi R. , Roscini P. 
Published: August 2009

Summary
In reservoir simulations, it is common practice to use a limited number of components to describe the reservoir fluids, ranging from 2 (black-oil models) to 5–12 [compositional equation-of-state (EOS) based models]. On the opposite, surface models usually require a greater number of components, typically from 15 to 30. The hydrocarbon components used in surface models are usually lumped into pseudocomponents in reservoir simulations. This disparity in the description of the mixture may become an issue whenever integrated asset models are developed, with the aim of linking surface process and reservoir engineering.
In this paper we implemented a consistent integrated simulation workflow from reservoir to process. Process models with detailed compositional formulation were linked to compositionally simpler reservoir models, using Leibovic's delumping scheme (Leibovic et al. 1996, 2000) to convert fluid composition between EOSs with different component numbers.
The proposed workflow was applied to simulate two different recovery processes, namely a gas injection below the dewpoint in a sour gas/condensate reservoir; and a miscible gas injection in a near-critical volatile oil reservoir. Results of this implementation, in which detailed components are traced in reservoir model, are compared to integrated simulations in which all stages are modeled using detailed composition.
Modern Greek V V dvandva compounds: A linguistic innovation in the history of the Indo-European languages
Authors: Ralli Angela 
Published: August 2009

This paper deals with [V V] dvandva compounds, which are frequently used in East and Southeast Asian languages but also in Greek and its dialects: Greek is in this respect uncommon among Indo-European languages. It examines the appearance of this type of compounding in Greek by tracing its development in the late Medieval period, and detects a high rate of productivity in most Modern Greek dialects. It argues that the emergence of the [V V] dvandva pattern is not due to areal pressure or to a language-contact situation, but it is induced by a language internal change. It associates this change with the rise of productivity of compounding in general, and the expansion of verbal compounds in particular. It also suggests that the change contributes to making the compound-formation patterns of the language more uniform and systematic.Claims and proposals are illustrated with data from Standard Modern Greek and its dialects. It is shown that dialectal evidence is crucial for the study of the rise and productivity of [V V] dvandva compounds, since changes are not usually portrayed in the standard language.
Portuguese converted deverbal nouns: Constraints on their bases
Authors: Soares Rodrigues Alexandra 
Published: August 2009

The aim of this paper is to analyse the constraints that govern the formation of Portuguese converted deverbal nouns (‘CDNs’). To this end, we have analysed a total of 1323 converted deverbal nouns. The first type of constraints investigated are those found at the prosodic level: these deal with the configurational formatting of the minimal root. We will focus on the relationship between these constraints and the semantic and phonological identification of the lexical item in perceptual terms. The second level of constraints may be characterised as morphophonological-pragmatic. Many verbs contain morphological units that block the formation of CDNs because their [+Latinate] character has a certain stylistic effect in terms of pragmatic usage. The third level of constraints pertains to lexical-conceptual structure combined with argument structure.We will show that (i) the constraints on the bases of CDNs are not exclusively founded on morphological incompatibilities between derivational affixes and other morphological units with which they join. Thus, a derivational mechanism that does not involve affixation, such as conversion, is also ruled by restrictions on the bases. (ii) Structural constraints – based on argument structures and on prosodic, morphological and lexical-semantic structures – are interwoven with processing and pragmatic conditions. (iii) Word formation is organised in structures that have interfaces with each other.
How big can case systems get? Evidence from Scottish Gaelic
Authors: Stewart Thomas W. 
Published: August 2009

It is well known that case systems can be augmented by the accretion of adpositions to their objects. This paper documents and explores an extensive instance of such augmentation, far exceeding any studied to date, based on an analysis of a class of words in modern Scottish Gaelic (SG) the members of which have attributes of both prepositions and pronouns. Pedagogical materials tend to call these forms prepositional pronouns, yet present the forms in paradigms organized by prepositional element, as if they represented person-number inflections on prepositional bases. This approach does not translate well into a synchronic description, however, because deriving these forms from underlying sequences requires numerous ad hoc morphophonemic stipulations. Regardless of diachronic source(s), these forms are synchronically pronominal in distribution. Shifting to a whole-heartedly pronominal analysis entails a targeted expansion of pronominal paradigms, beyond the traditional 3 nominal cases to 14. Although a number of languages present a richer array of distinct pronominal case forms than those found among nouns (e.g. English, Spanish), SG is unique in the extent to which pronoun case forms exceed those of nouns. Moreover, English and Spanish pronouns show the remnants of a case system, whereas SG has created these distinctions.
Remote Laboratories Framework : Focus on Reusability and Security in m-Learning Situations
Authors: Fayolle Jacques , Gravier Christophe , Ates Mikael , Lardon Jeremy 
Published: August 2009

Remote laboratories is a spreading concept which allows the remote use of devices through Internet connexion. The paper deals with the providing of a framework which is reusable for many devices, from different end-user media such as phone, computer or TV and acceptable in industry, therefore taking into account multi information systems securities.
The problem is addressed through the point of view of m-learning situations which involves the lack of rich user interactions and the fact that the user belongs to external information systems when he interacts with the remote device.
The modelisation of the remote device with ontologies, the use of a central application server, message oriented middleware and standard web services (database, authentication) are the keys allowing the independence of the framework to the device.
The adaptation of the GUI to the end-user device is made through a proxy which refactor the requests and responses according to the capabilities of the end-user device (size of screen, interactions tools).
The use of a user-centric model of identities federation allows us to provide an efficient way to reach the goal of transparency to security constraints.
Secondary Lymphoid Organs: Responding to Genetic and Environmental Cues in Ontogeny and the Immune Response
Authors: Ruddle Nancy H. , Akirav Eitan M. 
Published: August 2009

Abstract
Secondary lymphoid organs (SLOs) include lymph nodes, spleen, Peyer’s patches, and mucosal tissues such as the nasal-associated lymphoid tissue, adenoids, and tonsils. Less discretely anatomically defined cellular accumulations include the bronchus-associated lymphoid tissue, cryptopatches, and isolated lymphoid follicles. All SLOs serve to generate immune responses and tolerance. SLO development depends on the precisely regulated expression of cooperating lymphoid chemokines and cytokines such as LTα, LTβ, RANKL, TNF, IL-7, and perhaps IL-17. The relative importance of these factors varies between the individual lymphoid organs. Participating in the process are lymphoid tissue initiator, lymphoid tissue inducer, and lymphoid tissue organizer cells. These cells and others that produce crucial cytokines maintain SLOs in the adult. Similar signals regulate the transition from inflammation to ectopic or tertiary lymphoid tissues.
Survival and Migration of Human Dendritic Cells Are Regulated by an IFN-α-Inducible Axl/Gas6 Pathway
Authors: Scutera Sara , Fraone Tiziana , Musso Tiziana , Cappello Paola , Rossi Silvia , Pierobon Daniele , Orinska Zane , Paus Ralf , Bulfone-Paus Silvia , Giovarelli Mirella 
Published: August 2009

Abstract
Axl, a prototypic member of the transmembrane tyrosine kinase receptor family, is known to regulate innate immunity. In this study, we show that Axl expression is induced by IFN-α during human dendritic cell (DC) differentiation from monocytes (IFN/DC) and that constitutively Axl-negative, IL-4-differentiated DC (IL-4/DC) can be induced to up-regulate Axl by IFN-α. This effect is inhibited by TLR-dependent maturation stimuli such as LPS, poly(I:C), TLR7/8 ligand, and CD40L. LPS-induced Axl down-regulation on the surface of human IFN-α-treated DC correlates with an increased proteolytic cleavage of Axl and with elevated levels of its soluble form. GM6001 and TAPI-1, general inhibitors of MMP and ADAM family proteases, restored Axl expression on the DC surface and diminished Axl shedding. Furthermore, stimulation of Axl by its ligand, Gas6, induced chemotaxis of human DC and rescued them from growth factor deprivation-induced apoptosis. Our study provides the first evidence that Gas6/Axl-mediated signaling regulates human DC activities, and identifies Gas6/Axl as a new DC chemotaxis pathway. This encourages one to explore whether dysregulation of this novel pathway in human DC biology is involved in autoimmunity characterized by high levels of IFN-α.