bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lexical Plasticity in Early Bilinguals Does Not Alter Phoneme Categories: II. Experimental Evidence
Authors: Sebastián-Gallés Núria , Vera-Constán Fátima , Larsson Johan P. , Costa Albert , Deco Gustavo 
Published: October 2008

Abstract
When listening to modified speech, either naturally or artificially altered, the human perceptual system rapidly adapts to it. There is some debate about the nature of the mechanisms underlying this adaptation. Although some authors propose that listeners modify their prelexical representations, others assume changes at the lexical level. Recently, Larsson, Vera, Sebastian-Galles, and Deco [Lexical plasticity in early bilinguals does not alter phoneme categories: I. Neurodynamical modelling. Journal of Cognitive Neuroscience, 20, 76–94, 2008] proposed a biologically plausible computational model to account for some existing data, one which successfully modeled how long-term exposure to a dialect triggers the creation of new lexical entries. One specific prediction of the model was that prelexical (phoneme) representations should not be affected by dialectal exposure (as long as the listener is exposed to both standard and dialectal pronunciations). Here we present a series of experiments testing the predictions of the model. Native listeners of Catalan, with extended exposure to Spanish-accented Catalan, were tested on different auditory lexical decision tasks and phoneme discrimination tasks. Behavioral and electrophysiological recordings were obtained. The results supported the predictions of our model. On the one hand, both error rates and N400 measurements indicated the existence of alternative lexical entries for dialectal varieties. On the other hand, no evidence of alterations at the phoneme level, either in the behavioral discrimination task or in the electrophysiological measurement (MMN), could be detected. The results of the present study are compared with those obtained in short-term laboratory exposures in an attempt to provide an integrative account.
Mismatch and Conflict: Neurophysiological and Behavioral Evidence for Conflict Priming
Authors: Mager Ralph , Meuth Sven G. , Kräuchi Kurt , Schmidlin Maria , Müller-Spahn Franz , Falkenstein Michael 
Published: October 2008

Abstract
Conflict-related cognitive processes are critical for adapting to sudden environmental changes that confront the individual with inconsistent or ambiguous information. Thus, these processes play a crucial role to cope with daily life. Generally, conflicts tend to accumulate especially in complex and threatening situations. Therefore, the question arises how conflict-related cognitive processes are modulated by the close succession of conflicts. In the present study, we investigated the effect of interactions between different types of conflict on performance as well as on electrophysiological parameters. A task-irrelevant auditory stimulus and a task-relevant visual stimulus were presented successively. The auditory stimulus consisted of a standard or deviant tone, followed by a congruent or incongruent Stroop stimulus. After standard prestimuli, performance deteriorated for incongruent compared to congruent Stroop stimuli, which were accompanied by a widespread negativity for incongruent versus congruent stimuli in the event-related potentials (ERPs). However, after deviant prestimuli, performance was better for incongruent than for congruent Stroop stimuli and an additional early negativity in the ERP emerged with a fronto-central maximum. Our data show that deviant auditory prestimuli facilitate specifically the processing of stimulus-related conflict, providing evidence for a conflict-priming effect.
Unconscious Learning versus Visual Perception: Dissociable Roles for Gamma Oscillations Revealed in MEG
Authors: Chaumon Maximilien , Schwartz Denis , Tallon-Baudry Catherine 
Published: October 2008

Abstract
Oscillatory synchrony in the gamma band (30–120 Hz) has been involved in various cognitive functions including conscious perception and learning. Explicit memory encoding, in particular, relies on enhanced gamma oscillations. Does this finding extend to unconscious memory encoding? Can we dissociate gamma oscillations related to unconscious learning and to conscious perception? We investigate these issues in a magnetoencephalographic experiment using a modified version of the contextual cueing paradigm. In this visual search task, repeated presentation of search arrays triggers an unconscious spatial learning process that speeds reaction times but leaves conscious perception unaffected. In addition to a high-frequency perceptual gamma activity present throughout the experiment, we reveal the existence of a fronto-occipital network synchronized in the low gamma range specifically engaged in unconscious learning. This network shows up as soon as a display is searched for the second time and disappears as behavior gets affected. We suggest that oscillations in this network shape neural processing to build an efficient neural route for learned displays. Accordingly, in the last part of the experiment, evoked responses dissociate learned images at early latencies, suggesting that a sharpened representation is activated without resort on learning gamma oscillations, whereas perceptual gamma oscillations remain unaffected.
‘Doing Family’: Two Cases in Contemporary Syria
Authors: Rabo Annika 
Published: October 2008

AbstractFamily and household compositions are highly varied in contemporary Syria. The variation is to a large extent related to rural-urban habitation, class background, and ethnic or religious affiliation. Rural, poor, and Sunni Muslim Syrians, for example, tend to have larger families and economic interdependencies, while urban, better off, and minorities tend to have smaller and more independent family and household units. But despite such differences there's a general understanding and acceptance that marriage and parenthood is how women and men become adults. Many Syrian families and households do not, however, conform to these norms. In this article empirical material collected in northeast Syria since the late 1970s will illustrate the differences between an urban and a rural family. The case of each family illustrates the great heterogeneity of doing and talking family in contemporary Syria but also shows how local family ideals are reaffirmed.
Loss of Mll5 results in pleiotropic hematopoietic defects, reduced neutrophil immune function, and extreme sensitivity to DNA demethylation
Authors: Heuser Michael , Yap Damian B. , Leung Malina , de Algara Teresa Ruiz , Tafech Alaeddin , McKinney Steven , Dixon John , Thresher Rosemary , Colledge Bill , Carlton Mark , Humphries R. Keith , Aparicio Samuel A. 
Published: October 2008

Abstract
MLL5 is a divergent member of the Drosophila Trithorax-related (SET) domain and plant homeodomain (PHD) domain-containing chromatin regulators that are involved in the regulation of transcriptional “memory” during differentiation. Human MLL5 is located on chromosome 7q22, which frequently is deleted in myeloid leukemias, suggesting a possible role in hemopoiesis. To address this question, we generated a loss-of-function allele (Mll5tm1Apa) in the murine Mll5 locus. Unlike other Mll genes, Mll5tm1Apa homozygous mice are viable but display defects in immunity and hematopoiesis. First, Mll5tm1Apa homozygous mice show increased susceptibility to spontaneous eye infections, associated with a cell-autonomous impairment of neutrophil function. Second, Mll5tm1Apa/tm1Apa mice exhibit a mild impairment of erythropoiesis. Third, Mll5tm1Apa/tm1Apa hematopoietic stem cells (HSCs) have impaired competitive repopulating capacity both under normal conditions and when subjected to self-renewal stimulation by NUP98-HOXA10. Fourth, Mll5tm1Apa homozygous HSCs show a dramatic sensitivity to DNA demethylation–induced differentiation (5-azadeoxycytidine). Taken together, our data show that MLL5 is involved in terminal myeloid differentiation and the regulation of HSC self-renewal by a mechanism that involves DNA methylation. These data warrant investigation of MLL5 expression levels as a predictive marker of demethylating-agent response in patients with myelodysplastic syndromes and leukemias and identify MLL5 as a key regulator of normal hematopoiesis.
Transcriptional regulation of mouse alpha A-crystallin gene in a 148kb Cryaa BAC and its derivates
Authors: Wolf Louise , Yang Ying , Wawrousek Eric , Cvekl Ales 
Published: October 2008

Abstract

Background
αA-crystallin is highly expressed in the embryonic, neonatal and adult mouse lens. Previously, we identified two novel distal control regions, DCR1 and DCR3. DCR1 was required for transgenic expression of enhanced green fluorescent protein, EGFP, in lens epithelium, whereas DCR3 was active during "late" stages of lens primary fiber cell differentiation. However, the onset of transgenic EGFP expression was delayed by 12–24 hours, compared to the expression of the endogenous Cryaa gene.

Results
Here, we used bacterial artificial chromosome (BAC) and standard transgenic approaches to examine temporal and spatial regulation of the mouse Cryaa gene. Two BAC transgenes, with EGFP insertions into the third coding exon of Cryaa gene, were created: the intact αA-crystallin 148 kb BAC (αA-BAC) and αA-BAC(ΔDCR3), which lacks approximately 1.0 kb of genomic DNA including DCR3. Expression of EGFP in the majority of both BAC transgenics nearly recapitulated the endogenous expression pattern of the Cryaa gene in lens, but not outside of the lens. The number of cells expressing αA-crystallin in the lens pit was higher compared to the number of cells expressing EGFP. Next, we generated additional lines using a 15 kb fragment of αA-crystallin locus derived from αA-BAC(ΔDCR3), 15 kb Cryaa/EGFP. A 15 kb region of Cryaa/EGFP supported the expression pattern of EGFP also in the lens pit. However, co-localization studies of αA-crystallin and EGFP indicated that the number of cells that showed transgenic expression was higher compared to cells expressing αA-crystallin in the lens pit.

Conclusion
We conclude that a 148 kb αA-BAC likely contains all of the regulatory regions required for αA-crystallin expression in the lens, but not in retina, spleen and thymus. In addition, while the 15 kb Cryaa/EGFP region also supported the expression of EGFP in the lens pit, expression in regions such as the hindbrain, indicate that additional genomic regions may play modulatory functions in regulating extralenticular αA-crystallin expression. Finally, deletion of DCR3 in either αA-BAC(ΔDCR3) or Cryaa (15 kb) transgenic mice result in EGFP expression patterns that are consistent with DCR's previously established role as a distal enhancer active in "late" primary lens fiber cells.
Evolutionary analysis of the highly dynamic CHEK2duplicon in anthropoids
Authors: Münch Claudia , Kirsch Stefan , Fernandes António MG , Schempp Werner 
Published: October 2008

Abstract

Background
Segmental duplications (SDs) are euchromatic portions of genomic DNA (≥ 1 kb) that occur at more than one site within the genome, and typically share a high level of sequence identity (>90%). Approximately 5% of the human genome is composed of such duplicated sequences. Here we report the detailed investigation of CHEK2 duplications. CHEK2 is a multiorgan cancer susceptibility gene encoding a cell cycle checkpoint kinase acting in the DNA-damage response signalling pathway. The continuous presence of the CHEK2 gene in all eukaryotes and its important role in maintaining genome stability prompted us to investigate the duplicative evolution and phylogeny of CHEK2 and its paralogs during anthropoid evolution.

Results
To study CHEK2 duplicon evolution in anthropoids we applied a combination of comparative FISH and in silico analyses. Our comparative FISH results with a CHEK2 fosmid probe revealed the single-copy status of CHEK2 in New World monkeys, Old World monkeys and gibbons. Whereas a single CHEK2 duplication was detected in orangutan, a multi-site signal pattern indicated a burst of duplication in African great apes and human. Phylogenetic analysis of paralogous and ancestral CHEK2 sequences in human, chimpanzee and rhesus macaque confirmed this burst of duplication, which occurred after the radiation of orangutan and African great apes. In addition, we used inter-species quantitative PCR to determine CHEK2 copy numbers. An amplification of CHEK2 was detected in African great apes and the highest CHEK2 copy number of all analysed species was observed in the human genome. Furthermore, we detected variation in CHEK2 copy numbers within the analysed set of human samples.

Conclusion
Our detailed analysis revealed the highly dynamic nature of CHEK2 duplication during anthropoid evolution. We determined a burst of CHEK2 duplication after the radiation of orangutan and African great apes and identified the highest CHEK2 copy number in human. In conclusion, our analysis of CHEK2 duplicon evolution revealed that SDs contribute to inter-species variation. Furthermore, our qPCR analysis led us to presume CHEK2 copy number variation in human, and molecular diagnostics of the cancer susceptibility gene CHEK2 inside the duplicated region might be hampered by the individual-specific set of duplicons.
Genomics and proteomics of immune modulatory effects of a butanol fraction of echinacea purpurea in human dendritic cells
Authors: Wang Chien-Yu , Staniforth Vanisree , Chiao Ming-Tsang , Hou Chia-Chung , Wu Han-Ming , Yeh Kuo-Chen , Chen Chun-Houh , Hwang Pei-Ing , Wen Tuan-Nan , Shyur Lie-Fen , Yang Ning-Sun 
Published: October 2008

AbstractBackgroundEchinaceaspp. extracts and the derived phytocompounds have been shown to induce specific immune cell activities and are popularly used as food supplements or nutraceuticals for immuno-modulatory functions. Dendritic cells (DCs), the most potent antigen presenting cells, play an important role in both innate and adaptive immunities. In this study, we investigated the specific and differential gene expression in human immature DCs (iDCs) in response to treatment with a butanol fraction containing defined bioactive phytocompounds extracted from stems and leaves ofEchinacea purpurea, that we denoted [BF/S+L/Ep].ResultsAffymetrix DNA microarray results showed significant up regulation of specific genes for cytokines (IL-8, IL-1β, and IL-18) and chemokines (CXCL 2, CCL 5, and CCL 2) within 4 h after [BF/S+L/Ep] treatment of iDCs. Bioinformatics analysis of genes expressed in [BF/S+L/Ep]-treated DCs revealed a key-signaling network involving a number of immune-modulatory molecules leading to the activation of a downstream molecule, adenylate cyclase 8. Proteomic analysis showed increased expression of antioxidant and cytoskeletal proteins after treatment with [BF/S+L/Ep] and cichoric acid.ConclusionThis study provides information on candidate target molecules and molecular signaling mechanisms for future systematic research into the immune-modulatory activities of an important traditional medicinal herb and its derived phytocompounds.
Improved coverage of cDNA-AFLP by sequential digestion of immobilized cDNA
Authors: Weiberg Arne , Pöhler Dirk , Morgenstern Burkhard , Karlovsky Petr 
Published: October 2008

AbstractBackgroundcDNA-AFLP is a transcriptomics technique which does not require prior sequence information and can therefore be used as a gene discovery tool. The method is based on selective amplification of cDNA fragments generated by restriction endonucleases, electrophoretic separation of the products and comparison of the band patterns between treated samples and controls. Unequal distribution of restriction sites used to generate cDNA fragments negatively affects the performance of cDNA-AFLP. Some transcripts are represented by more than one fragment while other escape detection, causing redundancy and reducing the coverage of the analysis, respectively.ResultsWith the goal of improving the coverage of cDNA-AFLP without increasing its redundancy, we designed a modified cDNA-AFLP protocol. Immobilized cDNA is sequentially digested with several restriction endonucleases and the released DNA fragments are collected in mutually exclusive pools. To investigate the performance of the protocol, software tool MECS (Multiple Enzyme cDNA-AFLP Simulation) was written in Perl. cDNA-AFLP protocols described in the literatur and the new sequential digestion protocol were simulated on sets of cDNA sequences from mouse, human andArabidopsis thaliana. The redundancy and coverage, the total number of PCR reactions, and the average fragment length were calculated for each protocol and cDNA set.ConclusionSimulation revealed that sequential digestion of immobilized cDNA followed by the partitioning of released fragments into mutually exclusive pools outperformed other cDNA-AFLP protocols in terms of coverage, redundancy, fragment length, and the total number of PCRs. Primers generating 30 to 70 amplicons per PCR provided the highest fraction of electrophoretically distinguishable fragments suitable for normalization. ForA. thaliana, human and mice transcriptome, the use of two marking enzymes and three sequentially applied releasing enzymes for each of the marking enzymes is recommended.
Prioritizing genes of potential relevance to diseases affected by sex hormones: an example of Myasthenia Gravis
Authors: Kaur Mandeep , Schmeier Sebastian , MacPherson Cameron R , Hofmann Oliver , Hide Winston A , Taylor Stephen , Willcox Nick , Bajic Vladimir B 
Published: October 2008

AbstractBackgroundAbout 5% of western populations are afflicted by autoimmune diseases many of which are affected by sex hormones. Autoimmune diseases are complex and involve many genes. Identifying these disease-associated genes contributes to development of more effective therapies. Also, association studies frequently imply genomic regions that contain disease-associated genes but fall short of pinpointing these genes. The identification of disease-associated genes has always been challenging and to date there is no universal and effective method developed.ResultsWe have developed a method to prioritize disease-associated genes for diseases affected strongly by sex hormones. Our method uses various types of information available for the genes, but no information that directly links genes with the disease. It generates a score for each of the considered genes and ranks genes based on that score. We illustrate our method on early-onset myasthenia gravis (MG) using genes potentially controlled by estrogen and localized in a genomic segment (which contains the MHC and surrounding region) strongly associated with MG. Based on the considered genomic segment 283 genes are ranked for their relevance to MG and responsiveness to estrogen. The top three ranked genes, HLA-G, TAP2 and HLA-DRB1, are implicated in autoimmune diseases, while TAP2 is associated with SNPs characteristic for MG. Within the top 35 prioritized genes our method identifies 90% of the 10 already known MG-associated genes from the considered region without using any information that directly links genes to MG. Among the top eight genes we identified HLA-G and TUBB as new candidates. We show that ourab-initioapproach outperforms the other methods for prioritizing disease-associated genes.ConclusionWe have developed a method to prioritize disease-associated genes under the potential control of sex hormones. We demonstrate the success of this method by prioritizing the genes localized in the MHC and surrounding region and evaluating the role of these genes as potential candidates for estrogen control as well as MG. We show that our method outperforms the other methods. The method has a potential to be adapted to prioritize genes relevant to other diseases.
The dual transcriptional regulator CysR in Corynebacterium glutamicum ATCC 13032 controls a subset of genes of the McbR regulon in response to the availability of sulphide acceptor molecules
Authors: Rückert Christian , Milse Johanna , Albersmeier Andreas , Koch Daniel J , Pühler Alfred , Kalinowski Jörn 
Published: October 2008

Abstract

Background
Regulation of sulphur metabolism in Corynebacterium glutamicum ATCC 13032 has been studied intensively in the last few years, due to its industrial as well as scientific importance. Previously, the gene cg0156 was shown to belong to the regulon of McbR, a global transcriptional repressor of sulphur metabolism in C. glutamicum. This gene encodes a putative ROK-type regulator, a paralogue of the activator of sulphonate utilisation, SsuR. Therefore, it is an interesting candidate for study to further the understanding of the regulation of sulphur metabolism in C. glutamicum.

Results
Deletion of cg0156, now designated cysR, results in the inability of the mutant to utilise sulphate and aliphatic sulphonates. DNA microarray hybridisations revealed 49 genes with significantly increased and 48 with decreased transcript levels in presence of the native CysR compared to a cysR deletion mutant. Among the genes positively controlled by CysR were the gene cluster involved in sulphate reduction, fpr2 cysIXHDNYZ, and ssuR. Gel retardation experiments demonstrated that binding of CysR to DNA depends in vitro on the presence of either O-acetyl-L-serine or O-acetyl-L-homoserine. Mapping of the transcription start points of five transcription units helped to identify a 10 bp inverted repeat as the possible CysR binding site. Subsequent in vivo tests proved this motif to be necessary for CysR-dependent transcriptional regulation.

Conclusion
CysR acts as the functional analogue of the unrelated LysR-type regulator CysB from Escherichia coli, controlling sulphide production in response to acceptor availability. In both bacteria, gene duplication events seem to have taken place which resulted in the evolution of dedicated regulators for the control of sulphonate utilisation. The striking convergent evolution of network topology indicates the strong selective pressure to control the metabolism of the essential but often toxic sulphur-containing (bio-)molecules.