bluuebunny/crossref_metadata_2025_split huggingface dataset:
Looking for the Origin of Modernity
Authors: Kozlowski Janusz K. , Sacchi Dominique 
Published: June 2007

AbstractThere is no direct, constant relationship between the anthropological and cultural aspects of modernity. Anthropologically modern peoples display a certain heterogeneity that is not unconnected with earlier peoples, and the culture produced by modern humans, which is also heterogeneous, is differentiated diachronically and according to territory. Though paleogenetic research seems to point us to a single, African source for modern peoples, who had replaced the pre-sapiens populations in Eurasia, this view is not completely proven or accepted. On the other hand, paleo-genetic research has contributed to our relinquishing the hypothesis of a multiregional ‘total continuity’ of local pre-modern populations in the Old World. Indeed the theory of a partial replacement, by a migration ‘out of Africa’, appears to be getting increasingly plausible. This article deals with the problems of the origins of modern man from the points of view of anthropological, paleogenetic, paleoenvironmental and cultural approaches.
Richness and Diversity of Burial Rituals in the Upper Paleolithic
Authors: Giacobini Giacomo 
Published: June 2007

AbstractAmong the cultural innovations by which the Upper Palaeolithic period is characterized, those relating to burial practices furnish the possibility of evaluating the profound changes which differentiated this era from the Middle Palaeolithic. The graves of the Upper Palaeolithic offer us a sometimes very compelling glimpse of the complexity of the symbolic, cognitive and social environment of those peoples, as well as of the evolution and diversification over time and space of their rituals associated with death. This article considers the set of burials discovered to date within the boundaries of Italy as particularly representative of these features. Numerous, diverse and well-endowed, they provide important information about the peoples of the Upper Palaeolithic and of the way they responded to death. These graves also represent a significant body of evidence for the debate on the degree to which Palaeolithic man can be considered culturally fully human and the extent to which he intentionally buried his dead.
The Origins of Language: Material Sources
Authors: Otte Marcel 
Published: June 2007

AbstractThis article seeks to show the interaction between cultural and anatomic evolution in the birth and differentiation of cultures and languages. The diversity which characterizes our world does not preclude logical regularities due to the coherence of the human mind, which evolved slowly through the paleontological phases of its emergence over millions of years. The anatomical retroaction of the hominids is analyzed to show that, in the long run, anatomy reflected ‘cultural selection’. With the anatomic evolution of man, culture became a crucial component for all human beings and their anatomy simply adapted progressively to this fact.
Language and Communication among Hominids
Authors: Jucquois Guy 
Published: June 2007

AbstractThe question of the origin of ‘natural’ human language has fascinated the scientific world for a very long time and seems to be generating a renewed level of interest. This paper will show that all elements converge to indicate a long and slow process of separation by which the hominids very progressively became distinguished from the other higher primates and more generally from other animal species. Biological and neurological developments created favourable structures for the future emergence of human languages. These developments were further potentialized by the appearance of new forms of co-operation within human communities. Such anthropological, socio-cultural and ‘political’ elements were determinant in allowing the transition to the specifically human functions of language. If these elements are not taken into consideration, researchers are reduced to imaging the appearance of a mutation from which solely Homo sapiens would have benefited and from which Homo neanderthalensis would have been excluded, as must equally be excluded any intermingling between the various varieties of hominids.
Negative regulation of the SH2-homology–containing protein-tyrosine phosphatase-1 (SHP-1) P2 promoter by the HTLV-1 Tax oncoprotein
Authors: Cheng Jihua , Kydd Andre R. , Nakase Koichi , Noonan Kristin M. , Murakami Akikazu , Tao Hong , Dwyer Markryan , Xu Chen , Zhu Quan , Marasco Wayne A. 
Published: June 2007

AbstractExpression of SH2-homology–containing protein-tyrosine phosphatase-1 (SHP-1), a candidate tumor suppressor, is repressed in human T-cell leukemia virus type-1 (HTLV-1)–transformed lymphocyte cell lines, adult T-cell leukemia (ATL) cells, and in other hematologic malignancies. However, the mechanisms underlying regulation and repression of SHP-1 remain unclear. Herein, we cloned the putative full-length, hematopoietic cell–specific SHP-1 P2 promoter and identified the “core” promoter regions. HTLV-1 Tax profoundly represses P2 promoter activity and histone deacetylase-1 (HDAC1) potentiates such inhibition. NF-κB was implicated as both a rate-limiting factor for basal P2 promoter activity and important for Tax-induced promoter silencing (TIPS). Chromatin immunoprecipitation studies demonstrated that NF-κB dissociates from the SHP-1 P2 promoter following the binding of Tax and HDAC1. This is in agreement with coimmunoprecipitation studies where NF-κB competed with HDAC1 for association with Tax protein. We propose that in TIPS, Tax recruits HDAC1 to the SHP-1 P2 promoter and forms an inhibitory complex that results in deacetylation and dissociation of NF-κB from the promoter and attenuation of SHP-1 expression. TIPS provides a possible first step toward HTLV-1 leukemogenesis through its down-modulation of this key immediate early negative regulator of IL-2 signaling.
Revisions to the staging and classification of mycosis fungoides and Sézary syndrome: a proposal of the International Society for Cutaneous Lymphomas (ISCL) and the cutaneous lymphoma task force of the European Organization of Research and Treatment of Cancer (EORTC)
Authors: Olsen Elise , Vonderheid Eric , Pimpinelli Nicola , Willemze Rein , Kim Youn , Knobler Robert , Zackheim Herschel , Duvic Madeleine , Estrach Teresa , Lamberg Stanford , Wood Gary , Dummer Reinhard , Ranki Annamari , Burg Gunter , Heald Peter , Pittelkow Mark , Bernengo Maria-Grazia , Sterry Wolfram , Laroche Liliane , Trautinger Franz , Whittaker Sean 
Published: June 2007

AbstractThe ISCL/EORTC recommends revisions to the Mycosis Fungoides Cooperative Group classification and staging system for cutaneous T-cell lymphoma (CTCL). These revisions are made to incorporate advances related to tumor cell biology and diagnostic techniques as pertains to mycosis fungoides (MF) and Sézary syndrome (SS) since the 1979 publication of the original guidelines, to clarify certain variables that currently impede effective interinstitution and interinvestigator communication and/or the development of standardized clinical trials in MF and SS, and to provide a platform for tracking other variables of potential prognostic significance. Moreover, given the difference in prognosis and clinical characteristics of the non-MF/non-SS subtypes of cutaneous lymphoma, this revision pertains specifically to MF and SS. The evidence supporting the revisions is discussed as well as recommendations for evaluation and staging procedures based on these revisions.
Hook2 contributes to aggresome formation
Authors: Szebenyi Györgyi , Wigley W Christian , Hall Branden , Didier Aaron , Yu Michelle , Thomas Philip , Krämer Helmut 
Published: June 2007

Abstract

Background
Aggresomes are pericentrosomal accumulations of misfolded proteins, chaperones and proteasomes. Their positioning near the centrosome, like that of other organelles, requires active, microtubule-dependent transport. Linker proteins that can associate with the motor protein dynein, organelles, and microtubules are thought to contribute to the active maintenance of the juxtanuclear localization of many membrane bound organelles and aggresomes. Hook proteins have been proposed to serve as adaptors for the association of cargos with dynein for transport on microtubules. Hook2 was shown to localize to the centrosome, bind centriolin, and contribute to centrosomal function.

Results
Here we show that overexpression of hook2 promotes the accumulation of the cystic fibrosis transmembrane regulator in aggresomes without altering its biochemical properties or its steady state level. A dominant negatively acting form of hook2 that lacks the centriolin binding C-terminal inhibits aggresome formation.

Conclusion
We propose that hook2 contributes to the establishment and maintenance of the pericentrosomal localization of aggresomes by promoting the microtubule-based delivery of protein aggregates to pericentriolar aggresomes.
Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme
Authors: Su Li-Jen , Chang Ching-Wei , Wu Yu-Chung , Chen Kuang-Chi , Lin Chien-Ju , Liang Shu-Ching , Lin Chi-Hung , Whang-Peng Jacqueline , Hsu Shih-Lan , Chen Chen-Hsin , Huang Chi-Ying F 
Published: June 2007

AbstractBackgroundThe development of microarrays permits us to monitor transcriptomes on a genome-wide scale. To validate microarray measurements, quantitative-real time-reverse transcription PCR (Q-RT-PCR) is one of the most robust and commonly used approaches. The new challenge in gene quantification analysis is how to explicitly incorporate statistical estimation in such studies. In the realm of statistical analysis, the various available methods of the probe level normalization for microarray analysis may result in distinctly different target selections and variation in the scores for the correlation between microarray and Q-RT-PCR. Moreover, it remains a major challenge to identify a proper internal control for Q-RT-PCR when confirming microarray measurements.ResultsSixty-six Affymetrix microarray slides using lung adenocarcinoma tissue RNAs were analyzed by a statistical re-sampling method in order to detect genes with minimal variation in gene expression. By this approach, we identifiedDDX5as a novel internal control for Q-RT-PCR. Twenty-three genes, which were differentially expressed between adjacent normal and tumor samples, were selected and analyzed using 24 paired lung adenocarcinoma samples by Q-RT-PCR using two internal controls,DDX5andGAPDH. The percentage correlation between Q-RT-PCR and microarray were 70% and 48% by usingDDX5andGAPDHas internal controls, respectively.ConclusionTogether, these quantification strategies for Q-RT-PCR data processing procedure, which focused on minimal variation, ought to significantly facilitate internal control evaluation and selection for Q-RT-PCR when corroborating microarray data.
Saccharomyces cerevisiae FKBP12 binds Arabidopsis thaliana TOR and its expression in plants leads to rapamycin susceptibility
Authors: Sormani Rodnay , Yao Lei , Menand Benoît , Ennar Najla , Lecampion Cécile , Meyer Christian , Robaglia Christophe 
Published: June 2007

AbstractBackgroundThe eukaryotic TOR pathway controls translation, growth and the cell cycle in response to environmental signals such as nutrients or growth-stimulating factors. The TOR protein kinase can be inactivated by the antibiotic rapamycin following the formation of a ternary complex between TOR, rapamycin and FKBP12 proteins. The TOR protein is also found in higher plants despite the fact that they are rapamycin insensitive. Previous findings using the yeast two hybrid system suggest that the FKBP12 plant homolog is unable to form a complex with rapamycin and TOR, while the FRB domain of plant TOR is still able to bind to heterologous FKBP12 in the presence of rapamycin. The resistance to rapamycin is therefore limiting the molecular dissection of the TOR pathway in higher plants.ResultsHere we show that none of the FKBPs from the model plant Arabidopsis (AtFKBPs) is able to form a ternary complex with the FRB domain of AtTOR in the presence of rapamycin in a two hybrid system. An antibody has been raised against the AtTOR protein and binding of recombinant yeast ScFKBP12 to native Arabidopsis TOR in the presence of rapamycin was demonstrated in pull-down experiments. Transgenic lines expressing ScFKBP12 were produced and were found to display a rapamycin-dependent reduction of the primary root growth and a lowered accumulation of high molecular weight polysomes.ConclusionThese results further strengthen the idea that plant resistance to rapamycin evolved as a consequence of mutations in plant FKBP proteins. The production of rapamycin-sensitive plants through the expression of the ScFKBP12 protein illustrates the conservation of the TOR pathway in eukaryotes. Since AtTOR null mutants were found to be embryo lethal [1], transgenic ScFKBP12 plants will provide an useful tool for the post-embryonic study of plant TOR functions. This work also establish for the first time a link between TOR activity and translation in plant cells
The association of RANTES polymorphism with severe acute respiratory syndrome in Hong Kong and Beijing Chinese
Authors: Ng Man Wai , Zhou Gangqiao , Chong Wai Po , Lee Loretta Wing Yan , Law Helen Ka Wai , Zhang Hongxing , Wong Wilfred Hing Sang , Fok Susanna Fung Shan , Zhai Yun , Yung Raymond WH , Chow Eudora Y , Au Ka Leung , Chan Eric YT , Lim Wilina , Peiris JS Malik , He Fuchu , Lau Yu Lung 
Published: June 2007

AbstractBackgroundChemokines play important roles in inflammation and antiviral action. We examined whether polymorphisms ofRANTES, IP-10andMigaffect the susceptibility to and outcome of severe acute respiratory syndrome (SARS).MethodsWe tested the polymorphisms ofRANTES, IP-10andMigfor their associations with SARS in 495 Hong Kong Chinese SARS patients and 578 controls. Then we tried to confirm the results in 356 Beijing Chinese SARS patients and 367 controls.ResultsRANTES-28 G allele was associated with SARS susceptibility in Hong Kong Chinese (P< 0.0001, OR = 2.80, 95%CI:2.11–3.71). Individuals withRANTES-28 CG and GG genotypes had a 3.28-fold (95%CI:2.32–4.64) and 3.06-fold (95%CI:1.47–6.39) increased risk of developing SARS respectively (P< 0.0001). This -28 G allele conferred risk of death in a gene-dosage dependent manner (P= 0.014) with CG and GG individuals having a 2.12-fold (95% CI: 1.11–4.06) and 4.01-fold (95% CI: 1.30–12.4) increased risk. For the replication ofRANTESdata in Beijing Chinese, the -28 G allele was not associated with susceptibility to SARS. However, -28 CG (OR = 4.27, 95%CI:1.64–11.1) and GG (OR = 3.34, 95%CI:0.37–30.7) were associated with admission to intensive care units or death due to SARS (P= 0.011).ConclusionRANTES-28 G allele plays a role in the pathogenesis of SARS.
Engineering of PA-IIL lectin from Pseudomonas aeruginosa – Unravelling the role of the specificity loop for sugar preference
Authors: Adam Jan , Pokorná Martina , Sabin Charles , Mitchell Edward P , Imberty Anne , Wimmerová Michaela 
Published: June 2007

Abstract

Background
Lectins are proteins of non-immune origin capable of binding saccharide structures with high specificity and affinity. Considering the high encoding capacity of oligosaccharides, this makes lectins important for adhesion and recognition. The present study is devoted to the PA-IIL lectin from Pseudomonas aeruginosa, an opportunistic human pathogen capable of causing lethal complications in cystic fibrosis patients. The lectin may play an important role in the process of virulence, recognizing specific saccharide structures and subsequently allowing the bacteria to adhere to the host cells. It displays high values of affinity towards monosaccharides, especially fucose – a feature caused by unusual binding mode, where two calcium ions participate in the interaction with saccharide. Investigating and understanding the nature of lectin-saccharide interactions holds a great potential of use in the field of drug design, namely the targeting and delivery of active compounds to the proper site of action.

Results

In vitro site-directed mutagenesis of the PA-IIL lectin yielded three single point mutants that were investigated both structurally (by X-ray crystallography) and functionally (by isothermal titration calorimetry). The mutated amino acids (22–23–24 triad) belong to the so-called specificity binding loop responsible for the monosaccharide specificity of the lectin. The mutation of the amino acids resulted in changes to the thermodynamic behaviour of the mutants and subsequently in their relative preference towards monosaccharides. Correlation of the measured data with X-ray structures provided the molecular basis for rationalizing the affinity changes. The mutations either prevent certain interactions to be formed or allow formation of new interactions – both of afore mentioned have strong effects on the saccharide preferences.

Conclusion
Mutagenesis of amino acids forming the specificity binding loop allowed identification of one amino acid that is crucial for definition of the lectin sugar preference. Altering specificity loop amino acids causes changes in saccharide-binding preferences of lectins derived from PA-IIL, via creation or blocking possible binding interactions. This finding opens a gate towards protein engineering and subsequent protein design to refine the desired binding properties and preferences, an approach that could have strong potential for drug design.
Optimisation of the T-square sampling method to estimate population sizes
Authors: Bostoen Kristof , Chalabi Zaid , Grais Rebecca F 
Published: June 2007

AbstractPopulation size and density estimates are needed to plan resource requirements and plan health related interventions. Sampling frames are not always available necessitating surveys using non-standard household sampling methods. These surveys are time-consuming, difficult to validate, and their implementation could be optimised. Here, we discuss an example of an optimisation procedure for rapid population estimation using T-Square sampling which has been used recently to estimate population sizes in emergencies. A two-stage process was proposed to optimise the T-Square method wherein the first stage optimises the sample size and the second stage optimises the pathway connecting the sampling points. The proposed procedure yields an optimal solution if the distribution of households is described by a spatially homogeneous Poisson process and can be sub-optimal otherwise. This research provides the first step in exploring how optimisation techniques could be applied to survey designs thereby providing more timely and accurate information for planning interventions.
nuID: a universal naming scheme of oligonucleotides for Illumina, Affymetrix, and other microarrays
Authors: Du Pan , Kibbe Warren A , Lin Simon M 
Published: June 2007

Abstract

Background
Oligonucleotide probes that are sequence identical may have different identifiers between manufacturers and even between different versions of the same company's microarray; and sometimes the same identifier is reused and represents a completely different oligonucleotide, resulting in ambiguity and potentially mis-identification of the genes hybridizing to that probe.

Results
We have devised a unique, non-degenerate encoding scheme that can be used as a universal representation to identify an oligonucleotide across manufacturers. We have named the encoded representation 'nuID', for nucleotide universal identifier. Inspired by the fact that the raw sequence of the oligonucleotide is the true definition of identity for a probe, the encoding algorithm uniquely and non-degenerately transforms the sequence itself into a compact identifier (a lossless compression). In addition, we added a redundancy check (checksum) to validate the integrity of the identifier. These two steps, encoding plus checksum, result in an nuID, which is a unique, non-degenerate, permanent, robust and efficient representation of the probe sequence. For commercial applications that require the sequence identity to be confidential, we have an encryption schema for nuID. We demonstrate the utility of nuIDs for the annotation of Illumina microarrays, and we believe it has universal applicability as a source-independent naming convention for oligomers.

Reviewers
This article was reviewed by Itai Yanai, Rong Chen (nominated by Mark Gerstein), and Gregory Schuler (nominated by David Lipman).
Cloning and characterization of microRNAs from wheat (Triticum aestivum L.)
Authors: Yao Yingyin , Guo Ganggang , Ni Zhongfu , Sunkar Ramanjulu , Du Jinkun , Zhu Jian-Kang , Sun Qixin 
Published: June 2007

Abstract
Background
MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition. So far, identification of miRNAs has been limited to a few model plant species, such as Arabidopsis, rice and Populus, whose genomes have been sequenced. Wheat is one of the most important cereal crops worldwide. To date, only a few conserved miRNAs have been predicted in wheat and the computational identification of wheat miRNAs requires the genome sequence, which is unknown.

Results
To identify novel as well as conserved miRNAs in wheat (Triticum aestivum L.), we constructed a small RNA library. High throughput sequencing of the library and subsequent analysis revealed the identification of 58 miRNAs, comprising 43 miRNA families. Of these, 35 miRNAs belong to 20 conserved miRNA families. The remaining 23 miRNAs are novel and form 23 miRNA families in wheat; more importantly, 4 of these new miRNAs (miR506, miR510, miR514 and miR516) appear to be monocot-specific. Northern blot analysis indicated that some of the new miRNAs are preferentially expressed in certain tissues. Based on sequence homology, we predicted 46 potential targets. Thus, we have identified a large number of monocot-specific and wheat-specific miRNAs. These results indicate that both conserved and wheat-specific miRNAs play important roles in wheat growth and development, stress responses and other physiological processes.

Conclusion
This study led to the discovery of 58 wheat miRNAs comprising 43 miRNA families; 20 of these families are conserved and 23 are novel in wheat. It provides a first large scale cloning and characterization of wheat miRNAs and their predicted targets.