bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early onset MSI-H colon cancer with MLH1 promoter methylation, is there a genetic predisposition?
Authors: van Roon Eddy HJ , van Puijenbroek Marjo , Middeldorp Anneke , van Eijk Ronald , de Meijer Emile J , Erasmus Dianhdra , Wouters Kim AD , van Engeland Manon , Oosting Jan , Hes Frederik J , Tops Carli MJ , van Wezel Tom , Boer Judith M , Morreau Hans 
Published: May 2010

Abstract

Background
To investigate the etiology of MLH1 promoter methylation in mismatch repair (MMR) mutation-negative early onset MSI-H colon cancer. As this type of colon cancer is associated with high ages, young patients bearing this type of malignancy are rare and could provide additional insight into the etiology of sporadic MSI-H colon cancer.

Methods
We studied a set of 46 MSI-H colon tumors cases with MLH1 promoter methylation which was enriched for patients with an age of onset below 50 years (n = 13). Tumors were tested for CIMP marker methylation and mutations linked to methylation: BRAF, KRAS, GADD45A and the MLH1 -93G>A polymorphism. When available, normal colon and leukocyte DNA was tested for GADD45A mutations and germline MLH1 methylation. SNP array analysis was performed on a subset of tumors.

Results
We identified two cases (33 and 60 years) with MLH1 germline promoter methylation. BRAF mutations were less frequent in colon cancer patients below 50 years relative to patients above 50 years (p-value: 0.044). CIMP-high was infrequent and related to BRAF mutations in patients below 50 years. In comparison with published controls the G>A polymorphism was associated with our cohort. Although similar distribution of the pathogenic A allele was observed in the patients with an age of onset above and below 50 years, the significance for the association was lost for the group under 50 years. GADD45A sequencing yielded an unclassified variant. Tumors from both age groups showed infrequent copy number changes and loss-of-heterozygosity.

Conclusion
Somatic or germline GADD45A mutations did not explain sporadic MSI-H colon cancer. Although germline MLH1 methylation was found in two individuals, locus-specific somatic MLH1 hypermethylation explained the majority of sporadic early onset MSI-H colon cancer cases. Our data do not suggest an intrinsic tendency for CpG island hypermethylation in these early onset MSI-H tumors other than through somatic mutation of BRAF.
Xenon Inhibits Excitatory but Not Inhibitory Transmission in Rat Spinal Cord Dorsal Horn Neurons
Authors: Georgiev Stefan K , Furue Hidemasa , Baba Hiroshi , Kohno Tatsuro 
Published: May 2010

Background: The molecular targets for the promising gaseous anaesthetic xenon are still under investigation. Most studies identify N-methyl-D-aspartate (NMDA) receptors as the primary molecular target for xenon, but the role of α-amino-3-hydroxy-5-methyl-4-isoxazole-4-propionic acid (AMPA) receptors is less clear. In this study we evaluated the effect of xenon on excitatory and inhibitory synaptic transmission in the superficial dorsal horn of the spinal cord using in vitro patch-clamp recordings from rat spinal cord slices. We further evaluated the effects of xenon on innocuous and noxious stimuli using in vivo patch-clamp method. Results: In vitro, xenon decreased the amplitude and area under the curve of currents induced by exogenous NMDA and AMPA and inhibited dorsal root stimulation-evoked excitatory postsynaptic currents. Xenon decreased the amplitude, but not the frequency, of miniature excitatory postsynaptic currents. There was no discernible effect on miniature or evoked inhibitory postsynaptic currents or on the current induced by inhibitory neurotransmitters. In vivo, xenon inhibited responses to tactile and painful stimuli even in the presence of NMDA receptor antagonist. Conclusions: Xenon inhibits glutamatergic excitatory transmission in the superficial dorsal horn via a postsynaptic mechanism. There is no substantial effect on inhibitory synaptic transmission at the concentration we used. The blunting of excitation in the dorsal horn lamina II neurons could underlie the analgesic effect of xenon.
Peripheral blood gene expression patterns discriminate among chronic inflammatory diseases and healthy controls and identify novel targets
Authors: Mesko Bertalan , Poliskal Szilard , Szegedi Andrea , Szekanecz Zoltan , Palatka Karoly , Papp Maria , Nagy Laszlo 
Published: May 2010

Abstract

Background
Chronic inflammatory diseases including inflammatory bowel disease (IBD; Crohn's disease and ulcerative colitis), psoriasis and rheumatoid arthritis (RA) afflict millions of people worldwide, but their pathogenesis is still not well understood.
It is also not well known if distinct changes in gene expression characterize these diseases and if these patterns can discriminate between diseased and control patients and/or stratify the disease. The main focus of our work was the identification of novel markers that overlap among the 3 diseases or discriminate them from each other.

Methods
Diseased (n = 13, n = 15 and n = 12 in IBD, psoriasis and RA respectively) and healthy patients (n = 18) were recruited based on strict inclusion and exclusion criteria; peripheral blood samples were collected by clinicians (30 ml) in Venous Blood Vacuum Collection Tubes containing EDTA and peripheral blood mononuclear cells were separated by Ficoll gradient centrifugation. RNA was extracted using Trizol reagent. Gene expression data was obtained using TaqMan Low Density Array (TLDA) containing 96 genes that were selected by an algorithm and the statistical analyses were performed in Prism by using non-parametric Mann-Whitney U test (P-values < 0.05).

Results
Here we show that using a panel of 96 disease associated genes and measuring mRNA expression levels in peripheral blood derived mononuclear cells; we could identify disease-specific gene panels that separate each disease from healthy controls. In addition, a panel of five genes such as ADM, AQP9, CXCL2, IL10 and NAMPT discriminates between all samples from patients with chronic inflammation and healthy controls. We also found genes that stratify the diseases and separate different subtypes or different states of prognosis in each condition.

Conclusions
These findings and the identification of five universal markers of chronic inflammation suggest that these diseases have a common background in pathomechanism, but still can be separated by peripheral blood gene expression. Importantly, the identified genes can be associated with overlapping biological processes including changed inflammatory response. Gene panels based on such markers can play a major role in the development of personalized medicine, in monitoring disease progression and can lead to the identification of new potential drug targets in chronic inflammation.
Two-hybrid analysis of Ty3 capsid subdomain interactions
Authors: Zhang Min , Larsen Liza SZ , Irwin Becky , Bilanchone Virginia , Sandmeyer Suzanne 
Published: May 2010

Abstract

Background
The yeast retrotransposon Ty3 forms stable virus-like particles. Gag3, the major structural protein, is composed of capsid, spacer and nucleocapsid domains. The capsid domain of Gag3 was previously modeled as a structure similar to retrovirus capsid.

Findings
Two-hybrid analysis was used to understand the interactions that contribute to particle assembly. Gag3 interacted with itself as predicted based on its role as the major structural protein. The N-terminal subdomain (NTD) of the capsid was able to interact with itself and with the C-terminal subdomain (CTD) of the capsid, but interacted less well with intact Gag3. Mutations previously shown to block particle assembly disrupted Gag3 interactions more than subdomain interactions.

Conclusions
The findings that the NTD interacts with itself and with the CTD are consistent with previous modeling and a role similar to that of the capsid in retrovirus particle structure. These results are consistent with a model in which the Gag3-Gag3 interactions that initiate assembly differ from the subdomain interactions that potentially underlie particle stability.
Antimicrobial anxiety: the impact of stress on antimicrobial immunity
Authors: Radek Katherine A 
Published: May 2010

AbstractReview on the mechanisms behind stress-induced immune modulation of antimicrobial responses.Leukocytes and epithelial cells are fundamental to antimicrobial immunity. Their antimicrobial responses are an evolutionarily conserved component of the innate immune system and are influenced by the host's response to external stimuli. The efficacy of host defense via antimicrobial responses derives from the ability of AMPs to rapidly identify and eradicate foreign microbes and activate proinflammatory pathways, and from the capacity of later innate and adaptive immune responses to amplify protection through distinct biochemical mechanisms. Recent advances in neuroimmunology have identified a direct link between the neuroendocrine and immune systems, where environmental stimuli are generally believed to promote a transient effect on the immune system in response to environmental challenges and are presumably brought back to baseline levels via neuroendocrine pathways. Stress is an environmental stimulus that flares from a variety of circumstances and has become engrained in human society. Small bouts of stress are believed to enhance the host's immune response; however, prolonged periods of stress can be detrimental through excess production of neuroendocrine-derived mediators that dampen immune responses to invasive pathogens. Elucidation of the mechanisms behind stress-induced immune modulation of antimicrobial responses will ultimately lead to the development of more effective therapeutic interventions for pathologic conditions. It is the intent of this review to broaden the existing paradigm of how stress-related molecules dampen immune responses through suppression of antimicrobial mechanisms, and to emphasize that bacteria can use these factors to enhance microbial pathogenesis during stress.
Synthesis of brushite nanoparticles at different temperatures
Authors: Singh Sujata , Singh Vaishali , Aggarwal Saroj , Mandal Uttam 
Published: May 2010

AbstractPhase pure, stable nanocrystalline brushite particles with average diameter in the range of 23–87 nm were obtained by the reverse microemulsion technique employing a mixture of surfactants (Aliquat 336 & Tween 80) as template directing agents, and calcium nitrate tetrahydrate and biammonium hydrogen phosphate as precursors. Particle sizes and morphologies were tuned by adjusting the reaction parameters, precursor concentration and temperature. FTIR, TEM, and XRD were used to characterize morphological changes of as synthesized nanoparticles. FTIR and XRD analyses confirmed the formation of brushite nanoparticles. Variations in the reaction temperature resulted in changes in the particle morphology and distribution. At high temperatures (60°C), the sample exhibited high monodispersity and spherical morphology with the average grain size of 42 nm. At low temperatures (6°C), nanoflakes were formed. The results suggest that a reverse microemulsion system provides facile media for control of the phase and morphology of nanoscale calcium phosphate biominerals. A mechanism providing an insight into the formation of brushite particles has also been proposed.
An analysis of tree stand stability relative to Institute of Meteorology and Water Management (IMGW) classification of maximum wind velocities
Authors: Kałuża Tomasz , Leśny Jacek 
Published: May 2010

An analysis of tree stand stability relative to Institute of Meteorology and Water Management (IMGW) classification of maximum wind velocities
Analysing tree susceptibility to uprooting one has to compare external power acting on a tree with its resistance to uprooting (critical moment). The critical uprooting moment for a tree depends on both plant parameters and substratum. Results of an assessment of critical moments of studied pine and black alder tree stands are presented in this paper. Field studies consisted of uprooting trees with parallel measurements of critical moments. Results were compared with the moments of uprooting power of extreme winds. These moments were related to classification of maximum wind velocities proposed by the Institute of Meteorology and Water Management (IMGW).
The impact of beaver ponds on tree stand in a river valley
Authors: Boczoń Andrzej , Wróbel Michał , Syniaiev Valentyn 
Published: May 2010

The impact of beaver ponds on tree stand in a river valley
The number of beavers in Poland rapidly increases which may result in conflicts between man and beavers. Despite the fact that beaver ponds play important role in increasing of biodiversity, water retention and soil moisture, they may also cause the die out of tree stands in river valleys and lead consequently to disappearance of typical riparian forest communities. Field studies demonstrated that long term flooding inhibited tree growth. Many trees died after 2 years of flooding. Long flooding caused the death of 80% of trees.
A multidisciplinary approach to reveal the Sicily Climate and Environment over the last 20 000 years
Authors: Incarbona Alessandro , Zarcone Giuseppe , Agate Mauro , Bonomo Sergio , Stefano Enrico , Masini Federico , Russo Fabio , Sineo Luca 
Published: May 2010

Abstract
We present a thorough review of the knowledge on the climate and environment in Sicily over the last 20 000 years, taking into account results of several studies carried using terrestrial and marine records. We obtain a coherent framework of the most important changes succeeded in the island, even if some points need further investigation.
All the reconstructions of surface temperatures of the seas and the air surrounding Sicily point out severe climatic conditions during the last glacial period. The steppe- and semisteppe-like vegetation pattern testifies, together with additional evidence from geochemical data of lacustrine evidence, markedly arid conditions. Fi-nally, significant episodes of sea level drop connected Sicily to the Italian Peninsula and favoured the dispersion of faunal elements from southern Italy.
The transition between the last glacial and the Holocene was not characterized by a gradual warming but was punctuated by two abrupt suborbital climatic fluctuations: Bølling-Allerød (warm) and Younger Dryas (cold), as recognized in the sediments recovered close to the northern and southern coast of Sicily. A denser arboreal cover is possibly indicated by the occurrence of dormouse and Arvicola remains.
Finally the sensitivity of Sicily to climate perturbations is demonstrated by the occurrence of repeated subtle climatic anomalies during the Holocene, including the Little Ice Age, also known from historical chronicles. Forests, woods and Mediterranean maquis developed in the early-middle Holocene. Thereafter was a general decline of arboreal vegetation, following a general aridification trend that seems to be a common feature in southern Europe and North Africa. Science Greek colonization (7th century before Christ), the landscape was intensively modelled for agriculture and breeding, leading to a significant loss of vegetation cover.
Alpine paleostress reconstruction and active faulting in Western Iberia
Authors: Antón Loreto , Muñoz-Martin Alfonso , Vicente Gerardo 
Published: May 2010

Abstract
The study of intraplate tectonics is crucial for understanding the deformation within plates, far from active plate boundaries and associated stress transmission to the plate interiors. This paper examines the tectonic evolution of the Variscan basement at the western margin of the Cenozoic Duero basin. Located east of the Vilariça Fault System in NW Iberia, this intraplate zone is a relatively flat but elevated area with an intense NNE-SSW trending fault system and associated moderate seismicity. Although the area has played an important role in the Duero basin configuration, its Alpine to present-day tectonic evolution has not been well constrained. In order to characterize the successive paleostress fields, 1428 pairs of fault-striae were measured at 56 sites and two focal mechanisms were used. Stress inversion methods have been applied to analyze paleostress regimes. Results show the existence of three dominant maximum horizontal stress (Shmax) trends: N-S, NE-SW and E-W. Relative and absolute dating of the activated faults for each Shmax shows that the clearly predominant N-S paleostress field in the zone has been active since the Oligocene up to the present day; while a NE-SW stress field is found to have been active during the Cretaceous and an older E-W paleostress field was active in the earlier Alpine cycle (Late Triassic).
Trace element behaviour during interaction between basalt and crustal rocks at 0.5–0.8 GPa: an experimental approach
Authors: Mollo Silvio , Misiti Valeria , Scarlato Piergiorgio 
Published: May 2010

Abstract
We experimentally investigate the major and trace elements behavior during the interaction between two partially molten crustal rocks (meta-anorthosite and metapelite) and a basaltic melt at 0.5–0.8 GPa. Results show that a hybrid melt is formed at the basalt-crust contact, where plagioclase crystallizes. This contact layer is enriched in trace elements which are incompatible with plagioclase crystals. Under these conditions, the trace element diffusion coefficients are one order of magnitude larger than those expected. Moreover, the HFSE diffusivity in the hybrid melt is surprisingly higher than the REE one. Such a feature is related to the plagioclase crystallization that changes the trace elements liquid-liquid partitioning (i.e. diffusivity) over a transient equilibrium that will persist as long as the crystal growth proceeds.
These experiments suggests that the behaviour of the trace elements is strongly dependent on the crystallization at the magma-crust interface. Diffusive processes like those investigated can be invoked to explain some unusual chemical features of contaminated magmatic suites.
Time series analysis (orbital cycles) of the uppermost Cenomanian-Lower Turonian sequence on the southern Tethyan margin using foraminifera
Authors: Soua Mohamed 
Published: May 2010

Time series analysis (orbital cycles) of the uppermost Cenomanian-Lower Turonian sequence on the southern Tethyan margin using foraminiferaTime series analysis has been performed for the first time on the Cenomanian-Turonian sequence in Central Tunisia in order to shed light on its Milankovitch-like cyclicity. This analysis was applied to two foraminiferal genera: the biserialHeterohelix, an oxygen-minimum zone (OMZ) dweller, and the triserialGuembelitria, a eutrophic surface dweller. Average sedimentary rates and the duration of the oceanic anoxic event (OAE2) in each studied section were estimated. The fluctuations in abundance of these two opportunistic species can be related mainly to both precessional (ca. 20 kyr) and eccentricity (100 and 400 kyr) cyclicity suggesting that changes in surface water fertility were linked to climate changes in the Milankovitch frequency band.
Organic-walled dinoflagellate cysts as a tool to recognize carbonate concretions: an example from Oligocene flysch deposits of the Western Carpathians
Authors: Barski Marcin , Bojanowski Maciej 
Published: May 2010

Organic-walled dinoflagellate cysts as a tool to recognize carbonate concretions: an example from Oligocene flysch deposits of the Western CarpathiansCarbonate concretions found within the Krosno shales (Polish Outer Carpathians) have formerly been interpreted as limestone exotics. Both the concretions and the host shales yield well preserved organic-walled dinoflagellate cysts. The dinoflagellate cyst assemblages provide valuable age-diagnostic information: they indicate a mid-Oligocene age and prove the concretionary origin of the carbonates. Detailed analysis of relative abundance, biodiversity and paleoecology of the dinoflagellates from concretions provides additional information on the sedimentary environment and the model of concretion formation.
Two Languages - One Annotation Scenario? Experience from the Prague Dependency Treebank
Authors: Cinková Silvie , Hajičová Eva , Panevová Jarmila , Sgall Petr 
Published: May 2010

Two Languages - One Annotation Scenario? Experience from the Prague Dependency Treebank
This paper compares the two FGD-based annotation scenarios for Czech and for English, with the Czech as the basis. We discuss the secondary predication expressed by infinitive and its functions in Czech and English, respectively. We give a few examples of English constructions that do not have direct counterparts in Czech (e.g., tough movement and causative constructions with make, get, and have), as well as some phenomena central in English but much less employed in Czech (object raising or control in adjectives as nominal predicates), and, last, structures more or less parallel both in their function and distribution, whose respective annotation differs due to significant differences in the respective linguistic traditions (verbs of perception).
Netgraph Query Language for the Prague Dependency Treebank 2.0
Authors: Mírovský Jiří 
Published: May 2010

Netgraph Query Language for the Prague Dependency Treebank 2.0
We study the annotation of the Prague Dependency Treebank 2.0 (PDT 2.0) and assemble a list of requirements on a query language that would allow searching for and studying all linguistic phenomena annotated in the treebank. We propose an extension to the query language of an existing search tool Netgraph 1.0 and show that the extended query language satisfies the list of requirements. We demonstrate how all principal linguistic phenomena annotated in the treebank can be searched for with the proposed query language and compare the query language to some other treebank search systems. The proposed query language has been implemented in the search tool Netgraph - we talk about features of a search tool that can simplify the searching and make it more powerful. We also present a table that shows the extent of usage of various features of the implemented query language by the users of Netgraph and mention several usages of Netgraph for other treebanks than PDT 2.0.
Czech Verbs of Communication with respect to the Types of Dependent Content Clauses
Authors: Kettnerová Václava 
Published: May 2010

Czech Verbs of Communication with respect to the Types of Dependent Content Clauses
The present paper describes a classification of Czech verbs of communication based on the information on the type of dependent content clauses which these verbs require to be complemented by. We distinguish assertive, interrogative and directive verbs of communication. Furthermore, we propose a method how to treat those verbs of communication which behave ‘neutrally’ with respect to the type of dependent content clauses.
Elastic Properties of La<sub>2-x</sub>Sr<sub>x</sub>CuO<sub>4</sub> (x=0.10-0.20)
Authors: Gupta S. , Tomar D. S. , Goyal S. C. 
Published: May 2010

The expressions for elastic constant for high temperature superconductors, derived using Mie-Grüneisen interaction potential, are used to analyze the elastic properties (bulk modulus, elastic wave velocity) of La2-xSrxCuO4 for x = 0.10 to 0.20. The Debye temperature θD has also been computed which is found to decrease with increasing Sr concentration. The value of bulk modulus in superconducting phase (Ks) is larger than the value in its normal phase (Kn=113.8 GPa) for x = 0.10 to 0.14. After this limit Ks decreases. A simple empirical relation between the difference in bulk moduli in the two phases (superconducting and normal) and Tc is proposed. The value of Tc for La1.85Sr0.15CuO4 obtained from the proposed relationship is in good agreement with the experimental value. Keywords: Phase transition temperature; Debye temperature; High-temperature superconductor. © 2010 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved. DOI: 10.3329/jsr.v2i2.2513 J. Sci. Res. 2 (2), 294-301 (2010)