bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glucocorticoid Receptor Phosphorylation Differentially Affects Target Gene Expression
Authors: Chen Weiwei , Dang Thoa , Blind Raymond D. , Wang Zhen , Cavasotto Claudio N. , Hittelman Adam B. , Rogatsky Inez , Logan Susan K. , Garabedian Michael J. 
Published: May 2008

AbstractThe glucocorticoid receptor (GR) is phosphorylated at multiple sites within its N terminus (S203, S211, S226), yet the role of phosphorylation in receptor function is not understood. Using a range of agonists and GR phosphorylation site-specific antibodies, we demonstrated that GR transcriptional activation is greatest when the relative phosphorylation of S211 exceeds that of S226. Consistent with this finding, a replacement of S226 with an alanine enhances GR transcriptional response. Using a battery of compounds that perturb different signaling pathways, we found that BAPTA-AM, a chelator of intracellular divalent cations, and curcumin, a natural product with antiinflammatory properties, reduced hormone-dependent phosphorylation at S211. This change in GR phosphorylation was associated with its decreased nuclear retention and transcriptional activation. Molecular modeling suggests that GR S211 phosphorylation promotes a conformational change, which exposes a novel surface potentially facilitating cofactor interaction. Indeed, S211 phosphorylation enhances GR interaction with MED14 (vitamin D receptor interacting protein 150). Interestingly, in U2OS cells expressing a nonphosphorylated GR mutant S211A, the expression of IGF-binding protein 1 and interferon regulatory factor 8, both MED14-dependent GR target genes, was reduced relative to cells expressing wild-type receptor across a broad range of hormone concentrations. In contrast, the induction of glucocorticoid-induced leucine zipper, a MED14-independent GR target, was similar in S211A- and wild-type GR-expressing cells at high hormone levels, but was reduced in S211A cells at low hormone concentrations, suggesting a link between GR phosphorylation, MED14 involvement, and receptor occupancy. Phosphorylation also affected the magnitude of repression by GR in a gene-selective manner. Thus, GR phosphorylation at S211 and S226 determines GR transcriptional response by modifying cofactor interaction. Furthermore, the effect of GR S211 phosphorylation is gene specific and, in some cases, dependent upon the amount of activated receptor.
Anointing with Rubble: Ruins in the Lebanese War Novel
Authors: Seigneurie Ken 
Published: May 2008

When the Lebanese civil war officially broke out in 1975, the conflict looked a lot like one of the numerous proxy wars that hitched local animosities to the East-West ideological struggle. Within a year, however, the cart began pulling the horse as ethnic-sectarian struggle preempted secular and Cold War imperatives. For literature, wartime chaos punctured the myth of progress and along with it realist literature predicated on a knowable world. After a half century of serving the Arab cause, realism became an overnight anachronism and from its grip emerged the Lebanese war novel.
The result is a retooled modernist literature that stresses the ideological preconditions for renewal in a new notion of human dignity. Hassan Daoud's 1983 Binayat Mathilde (The House of Mathilde), Hoda Barakat's 1990 Hajar al-dahik (The Stone of Laughter), and Rashid al-Daif's 1995 'Azizi al-sayyid Kawabata (Dear Mr Kawabata) show how violence and coercion infuse the city and humiliate the self during war. Human dignity emerges in these novels only as a longed-for memory or vision of what was or ought to be. In Arabic literature nothing is more redolent of memory and longing than the medieval literary motif of “stopping before the ruins” (wuquf 'ala al-atlal), to remember former people and places. Hilary Kilpatrick's pioneering work has revealed how the motif can be reappropriated to probe “deeper layers of consciousness,” and is “connected with the role of memory in literature today as a device for structuring experience.”
This essay argues that the Lebanese war novel has also quietly incorporated “stopping before the ruins” into a modernist idiom. This is not simply to state that the abandoned campsite has now become the burned-out home and that the ex-lover has become one's family, neighbors or associates. In these novels the ruins motif sets in motion the mental processes that condition the conviction that human life is possessed of innate dignity regardless of how history and war may compromise it. I argue in a final section of this essay that this socio-literary practice corresponds closely to Julia Kristeva's account of psychosexual trauma in her theory of infantile abjection.
Detection of APC Gene Deletions Using Quantitative Multiplex PCR of Short Fluorescent Fragments
Authors: Castellsagué Ester , González Sara , Nadal Marga , Campos Olga , Guinó Elisabet , Urioste Miguel , Blanco Ignacio , Frebourg Thierry , Capellá Gabriel 
Published: May 2008

Abstract
Background: Approximately 20% of classic familial adenomatous polyposis (FAP) cases and 70% to 80% of attenuated FAP (AFAP) cases are negative for the APC/MUTYH point mutation. Quantitative multiplex PCR of short fluorescent fragments (QMPSF), a technique for detecting copy number alterations, has been successfully applied to several cancer syndrome genes. We used QMPSF for the APC gene to screen FAP APC/MUTYH mutation-negative families to improve their diagnostic surveillance.
Methods: We set up and validated APC-gene QMPSF using 23 negative and 1 positive control and examined 45 (13 FAP and 32 AFAP) unrelated members of APC/MUTYH mutation-negative families for copy number alterations. We confirmed the results using multiplex ligation-dependent probe amplification (MLPA). We used different approaches such as sequencing, quantitative real time-PCR (QRT-PCR), and fluorescence in situ hybridization (FISH) to further characterize the identified deletions.
Results: APC QMPSF was capable of detecting deletions with an acceptable variability, as shown by mean values (SD) of allele dosage for the deleted control obtained from intra- and interexperimental replicates [0.52 (0.05) and 0.45 (0.10)]. We detected 3 gross deletions in 13 (23%) of the classic FAP cases analyzed (1 complete gene deletion and 2 partial deletions encompassing exons 9 and 10 and exons 11–15, respectively). No rearrangements were detected in the 32 AFAP cases.
Conclusions: QMPSF is able to detect rearrangements of the APC gene. Our findings highlight the importance of using a copy number alteration methodology as a first step in the routine genetic testing of FAP families in the clinical setting.
Tcf3 Functions as a Steady-State Limiter of Transcriptional Programs of Mouse Embryonic Stem Cell Self-Renewal
Authors: Yi Fei , Pereira Laura , Merrill Bradley James 
Published: May 2008

Abstract
Elucidating the underlying transcriptional control of pluripotent cells is necessary for the development of new methods of inducing and maintaining pluripotent cells in vitro. Three transcription factors, Nanog, Oct4, and Sox2, have been reported to form a feedforward circuit promoting pluripotent cell self-renewal in embryonic stem cells (ESC). Previously, we found that a transcriptional repressor activity of Tcf3, a DNA-binding effector of Wnt signaling, reduced Nanog promoter activity and Nanog levels in mouse embryonic stem cells (mESC). The objective of this study was to determine the scope of Tcf3 effects on gene expression and self-renewal beyond the regulation of Nanog levels. We show that Tcf3 acts broadly on a genome-wide scale to reduce the levels of several promoters of self-renewal (Nanog, Tcl1, Tbx3, Esrrb) while not affecting other ESC genes (Oct4, Sox2, Fgf4). Comparing effects of Tcf3 ablation with Oct4 or Nanog knockdown revealed that Tcf3 counteracted effects of both Nanog and Oct4. Interestingly, the effects of Tcf3 were more strongly correlated with Oct4 than with Nanog, despite the normal levels of Oct4 in TCF3−/− mESC. The deranged gene expression allowed TCF3−/− mESC self-renewal even in the absence of leukemia inhibitory factor and delayed differentiation in embryoid bodies. These findings identify Tcf3 as a cell-intrinsic inhibitor of pluripotent cell self-renewal that functions by limiting steady-state levels of self-renewal factors.
Disclosure of potential conflicts of interest is found at the end of this article.
Relationships between soil seed bank, vegetation and soil fertility along an urbanisation gradient
Authors: Pellissier Vincent , Rozé Françoise , Aguejdad Rahim , Quénol Hervé , Clergeau Philippe 
Published: May 2008

Abstract.Questions: How does urbanisation influence soil mineral nitrogen stocks (nitrate and ammonium stocks) and what are the consequences of these modifications on the functional diversity of the herbaceous vegetation (vascular plants) and the seed bank?Location: Nine study sites were located on an urbanisation gradient in the city of Rennes, France.Methods: Three urbanisation levels were defined: urban areas (high grey/green ratio), suburban (medium grey/green ratio) and periurban (low grey/green ratio). For each urbanisation level, nitrates and ammonium stocks were quantified; the herbaceous vegetation was surveyed as well as the soil seed bank (using the seedling emergence method).Results: Nitrate concentration increased with urbanisation (the nitrate level in urban plots was twice the concentration in periurban ones) whereas the ammonium level was higher in periurban areas than in urban areas. In urban plots, the vegetation and the seed bank were more nitrophilous, whereas the nitrogen requirement was lower for periurban species. The relationship between the seed bank and the above‐ground vegetation was not significant.Conclusions: The higher nitrate concentration in the urban area appeared to be related to higher concentrations of atmospheric pollutants found in this area and lower ammonium levels may be related to the higher temperature in urban areas (leading to higher nitrification rates). The shift in the composition of the seed bank and vegetation appeared to be a consequence of higher nitrate stocks. The dissimilarity between the seed bank and vegetation may be caused by enhanced emergence of nitrophilous species in urban areas.
Importance of soils, topography and geographic distance in structuring central Amazonian tree communities
Authors: Bohlman Stephanie A. , Laurance William F. , Laurance Susan G. , Nascimento Henrique E.M. , Fearnside Philip M. , Andrade Ana 
Published: May 2008

AbstractQuestion:What is the relative contribution of geographic distance, soil and topographic variables in determining the community floristic patterns and individual tree species abundances in the nutrient‐poor soils of central Amazonia?Location:Central Amazonia near Manaus, Brazil.Methods:Our analysis was based on data for 1105 tree species (≥ 10 cm dbh) within 40 1‐ha plots over a ca. 1000‐km2 area. Slope and 26 soil‐surface parameters were measured for each plot. A main soil‐fertility gradient (encompassing soil texture, cation content, nitrogen and carbon) and five other uncorrelated soil and topographic variables were used as potential predictors of plant‐community composition. Mantel tests and multiple regressions on distance matrices were used to detect relationships at the community level, and ordinary least square (OLS) and conditional autoregressive (CAR) models were used to detect relationships for individual species abundances.Results:Floristic similarity declined rapidly with distance over small spatial scales (0–5 km), but remained constant (ca. 44%) over distances of 5 to 30 km, which indicates lower beta diversity than in western Amazonian forests. Distance explained 1/3 to 1/2 more variance in floristics measures than environmental variables. Community composition was most strongly related to the main soil‐fertility gradient and C:N ratio. The main fertility gradient and pH had the greatest impact of species abundances. About 30% of individual tree species were significantly related to one or more soil/topographic parameters.Conclusions:Geographic distance and the main fertility gradient are the best predictors of community floristic composition, but other soil variables, particularly C:N ratio, pH, and slope, have strong relationships with a significant portion of the tree community.
Aerobic Alcohol Oxidation by Ruthenium Species Stabilized on Nanocrystalline Magnesium Oxide by Basic Ionic Liquids
Authors: Kantam M. Lakshmi , Pal Ujjwal , Sreedhar B. , Bhargava Suresh , Iwasawa Yasuhiro , Tada Mizuki , Choudary B. M. 
Published: May 2008

AbstractThe selective oxidation of various alcohols into their corresponding aldehydes and ketones was achieved by ruthenium species stabilized on the nanocrystalline magnesium oxide (NAP‐MgO) by the incorporation of choline hydroxide, a basic ionic liquid, in excellent yields. The procedure is simple, efficient and environmentally benign. The catalyst can be used for four cycles with almost consistent activity.
Novel Prolinamide‐Supported Polystyrene as Highly Stereoselective and Recyclable Organocatalyst for the Aldol Reaction
Authors: Gruttadauria Michelangelo , Giacalone Francesco , Marculescu Adriana Mossuto , Noto Renato 
Published: May 2008

AbstractA new prolinamide derivative anchored to a polystyrene support has been straightforwardly prepared and employed as heterogeneous catalyst in the direct asymmetric aldol reaction with good results in terms of yield and stereoselectivity. The optimal reaction conditions were found when a 1:2 (v/v) water/chloroform mixture was used. This mixture was the best compromise between the good swelling properties of chloroform and the formation of a concentrated organic phase due to the presence of water. Noticeably, the enantioselectivities obtained employing acetone as ketone were, to the best of our knowledge, the highest achieved with a supported proline derivative. This catalyst can be easily recovered, regenerated and recycled, without loss of activity, at least for twelve cycles.
Organocatalytic Asymmetric syn‐Aldol Reactions of Aldehydes with Long‐Chain Aliphatic Ketones on Water and with Dihydroxyacetone in Organic Solvents
Authors: Zhu Ming‐Kui , Xu Xiao‐Ying , Gong Liu‐Zhu 
Published: May 2008

AbstractAn on‐water, asymmetric, and direct syn‐aldol reaction of aliphatic ketones with aromatic aldehydes catalyzed by a primary amino acid‐based organocatalyst afforded the syn‐aldol adducts in high yields with excellent diastereo‐ and enantioselectivities (up to > 20/1 dr, >99% ee), and a highly enantioselective syn‐aldol reaction of dihydroxyacetone with a variety of aldehydes in THF proceeded with 14/1 to >20/1 dr and 92 to >99% ee. Water not only accelerated the reaction, but also enhanced the enantioselectivity. This positive water effect might arise from the hydrogen bond formed between a pendant hydroxy group of surface water molecules at the hydrophobic interface with the amide oxygen of the organocatalyst, which increases the acidity of the amide NH and thereby strengthens the related hydrogen bond formed with the aldehyde.
Practical implications of liver and heart iron load assessment by T2*‐MRI in children and adults with transfusion‐dependent anemias
Authors: Deborah Chirnomas Sarah , Geukes‐Foppen Marnix , Barry Kristen , Braunstein Jennifer , Kalish Leslie A. , Neufeld Ellis J. , Powell Andrew J. 
Published: May 2008

AbstractThis study examined the relationship between hepatic and myocardial iron concentration, assessed by T2*‐MRI in 66 patients (3–82 years) with transfusion‐dependent anemias and thalassemia intermedia, to determine whether hepatic iron levels alone suffice for chelation adjustments. We found a poor correlation between hepatic and myocardial iron (r = 0.10, P = 0.43) and identified a subgroup (14%) with increased myocardial iron without a matched degree of hepatic hemosiderosis. Left ventricular ejection fraction was insensitive for detecting elevated myocardial iron. These findings were present in both adult and pediatric patients. We recommend therapeutic monitoring of iron burden by evaluation of both liver and myocardial iron with T2*‐MRI. Am. J. Hematol., 2008. © 2008 Wiley‐Liss, Inc.
Geographic variation in loud calls of sportive lemurs (Lepilemur ssp.) and their implications for conservation
Authors: Méndez‐Cárdenas Maria , Randrianambinina Blanchard , Rabesandratana Andriatahiana , Rasoloharijaona Solofonirina , Zimmermann Elke 
Published: May 2008

AbstractBioacoustical studies in nonhuman primates have shown that loud calls can be reliably used as a noninvasive diagnostic tool for discriminating cryptic taxa, for their monitoring in the field as well as for the reconstruction of their phylogeny. To date, it is unknown, whether loud calls can be used for these purposes in sportive lemurs, for which current genetic studies suggest the existence of at least 24 cryptic species. The aim of this study was to compare the structure of loud calls of populations of sportive lemurs to characterize informative acoustic traits for taxa discrimination and to establish a phylogenetic tree based on acoustic structure. We have based our study on Inter‐River‐Systems (IRSs) as operational taxonomic units. Samples were collected from nine different localities of four IRSs along a transect from northwestern to northern Madagascar. Two call types, the ouah and the high‐pitched call, were present in almost all IRSs. Six temporal and eight spectral parameters were measured in 196 calls of the best quality given by 21 different males. Variation within and between IRSs was assessed by multivariate statistics. Loud calls differed significantly among the different IRSs. The IRSs varied most in spectral parameters, whereas temporal parameters were less variable. Phylogenetic analysis using parsimony yielded 11 out of 17 acoustic characters as phylogenetically informative. The acoustic tree had an average branch support of 78%. Its topology coincided less with geographic distances than with genetic tree topology. Altogether our findings revealed that loud calls separated geographically isolated populations of sportive lemurs specifically. Based on these results, noninvasive tools for diagnosis and monitoring of cryptic species in nature can be developed for conservation management. Am. J. Primatol. 70:828–838, 2008. © 2008 Wiley‐Liss, Inc.
Variation in limb proportions between Jomon foragers and Yayoi agriculturalists from prehistoric Japan
Authors: Temple Daniel H. , Auerbach Benjamin M. , Nakatsukasa Masato , Sciulli Paul W. , Larsen Clark Spencer 
Published: May 2008

AbstractVariation in limb proportions between prehistoric Jomon and Yayoi people of Japan are explored by this study. Jomon people were the descendents of Pleistocene nomads who migrated to the Japanese Islands around 30,000 yBP. Phenotypic and genotypic evidence indicates that Yayoi people were recent migrants to Japan from continental Northeast Asia who likely interbred with Jomon foragers. Limb proportions of Jomon and Yayoi people were compared using RMA regression and “Quick‐Test” calculations to investigate relative variability between these two groups. Cluster and principal components analyses were performed on size‐standardized limb lengths and used to compare Jomon and Yayoi people with other groups from various climatic zones. Elongated distal relative to proximal limb lengths were observed among Jomon compared to Yayoi people. Jomon limb proportions were similar to human groups from temperate/tropical climates at lower latitudes, while Yayoi limb proportions more closely resemble groups from colder climates at higher latitudes. Limb proportional similarities with groups from warmer environments among Jomon foragers likely reflect morphological changes following Pleistocene colonization of the Japanese Islands. Cold‐derived limb proportions among the Yayoi people likely indicate retention of these traits following comparatively recent migrations to the Japanese Islands. Changes in limb proportions experienced by Jomon foragers and retention of cold‐derived limb proportions among Yayoi people conform to previous findings that report changes in these proportions following long‐standing evolution in a specific environment. Am J Phys Anthropol, 2008. © 2008 Wiley‐Liss, Inc.
Portal Venous Territories Within the Human Liver: An Anatomical Reappraisal
Authors: Fasel Jean H.D. 
Published: May 2008

AbstractSubdivision of the human liver into eight portal venous segments (according to Couinaud) is largely established in the anatomical and clinical community. However, this concept is challenged by an increasing number of surgical and radiological reports. We reexamined the intrahepatic portal venous architecture to understand the inconsistencies published. For this purpose, we studied the livers of 20 deceased who had donated their body to the Anatomy Department. The organs were investigated by portal venous injection, subsequent liver corrosion, and analysis of the branching pattern. After a usual bifurcation of the portal vein (order 0 vessel) into a right and left branch (first order vessels), the number of second order branches observed was between 9 and 44, with an average of 20. This seemingly trivial matter of fact suggests that the human liver does not consist of the eight segments presumed, but of many more. Supposedly contradictory observations turn out to be explainable by differing combinations of this large number of territories, and not simply by anatomical variability. For practical surgical purposes, we conclude that the useful eight‐segment scheme needs conceptual reappraisal when a more realistic approach to the individual hepatic territoriality in the patients under consideration is demanded. We submit a “1‐2‐20‐concept” as a possible key. Anat Rec, 291:636–642, 2008. © 2008 Wiley‐Liss, Inc.
Vascular Changes in Hepatocellular Carcinoma
Authors: Yang Zhen Fan , Poon Ronnie T.P. 
Published: May 2008

AbstractHepatocellular carcinoma (HCC) is one of the most vascular solid tumors, in which angiogenesis plays an important role. The status of angiogenesis in HCC correlates with the disease progression and prognosis, and thus provides a potential therapeutic target. This review summarizes the vascular changes and molecular and cellular basis of angiogenesis in HCC. Development of HCC is characterized by arterialization of its blood supply and sinusoidal capillarization. Vascular endothelial growth factor (VEGF) is a potent angiogenic factor that plays a critical role in mediating angiogenesis in HCC. The VEGF can function on various types of cells, such as endothelial cells, hepatic stellate cells, endothelial progenitor cells and hemangiocytes, to induce vascular changes in HCC. Therefore, blockade of VEGF‐mediated pathways, either by anti‐VEGF neutralizing antibody or tyrosine kinase inhibitors that target VEGF receptors, suppresses carcinogenesis and angiogenesis in HCC. In addition to VEGF, several other angiogenic factors in HCC have recently been identified. These factors can also regulate angiogenic processes through interaction with VEGF or VEGF‐independent pathways. Despite the fact that treatment of HCC remains a tough task due to lack of effective systemic therapy, antiangiogenic therapy has already entered clinical trials in HCC patients and sheds light on a promising novel treatment for this disease. Anat Rec, 291:721–734, 2008. © 2008 Wiley‐Liss, Inc.