bluuebunny/crossref_metadata_2025 huggingface dataset:
Creating science and technology information databases for developing and sustaining sub-Saharan Africa's indigenous knowledge
Authors: Ezinwa Nwagwu Williams
Published: June 2007

In this article, indigenous knowledge is defined as holistic of all forms of knowledge emanating from an indigenous community. The critical relevance of local science and technology information (STI) databases in the development and sustainability of Africa's indigenous knowledge is discussed. It is advocated that local African STI databases should be considered required development infrastructures because they will provide information resources that are more adequate for national planning and management than their international counterparts. Furthermore, the various stakeholders and their roles are identified and the policy environment of STI databases in Africa examined. Constraints notwithstanding, local databases for African STI resources are envisaged to enhance global distribution and sharing of Africa's indigenous knowledge.
The effect of vocal hygiene and behavior modification instruction on the self-reported vocal health habits of public school music teachers
Authors: Hackworth Rhonda S.
Published: June 2007

This study examined the effects of vocal hygiene and behavior modification instruction on self-reported behaviors of music teachers. Subjects ( N = 76) reported daily behaviors for eight weeks: water consumption, warm-up, talking over music/noise, vocal rest, nonverbal commands, and vocal problems. Subjects were in experimental group 1 or 2, or the control group. Both experimental groups received vocal hygiene instruction. Experimental group 2 also received behavior modification information designed to help teachers individually identify and correct their vocal problems. Results showed experimental group 2 significantly increased vocal rest and significantly decreased reports of vocal problems in the weeks closest to treatment. Although differences provide limited information, the indications stress the importance of behavior modification's inclusion in vocal hygiene programs. Individual variance implies that some subjects have difficulty managing vocal hygiene routines. Additional study of effects of multiple, varied treatment sessions may clarify the impact of treatments over extended periods of time.
Students' experience of music learning in Hong Kong's secondary schools
Authors: Ho Wai-Chung
Published: June 2007

An important aim of this article is to show that, although Hong Kong's overall education system has encouraged an integration of global, national and local cultures, there are barriers and difficulties in achieving this goal beyond the implementation of school music education. Data are drawn from a questionnaire with 1806 students (880 boys and 926 girls) attending grades 7—9 in 16 Hong Kong secondary schools. This article elucidates students' experiences of school music and interprets their musical and other experiences. It is argued that the Hong Kong music curriculum does not have the flexibility to be able to adapt to global, national and local cultures.
Entrepreneurship and Social Capital
Authors: Casson Mark , Giusta Marina Della
Published: June 2007

Governments have invested heavily in building local and regional entrepreneurial networks in order improve economic performance and regeneration. However, there are many types of network, and different types of network are appropriate for different purposes. Some types of network are most useful in the early stages of entrepreneurial activity and others at later stages. Careful definitions are necessary in order to analyse the role of networks in generating interpersonal and inter-organizational trust, and hence in augmenting the stock of social capital. Effective networks are normally intermediated by reputable trust-brokers. The reputation of government gives it a significant role as a trust-broker, but there is a danger that its reputation may be undermined when it extends its activities into areas where it lacks the competence to intervene effectively.
Why People Refuse to Make Tradeoffs in Person Tradeoff Elicitations: A Matter of Perspective?
Authors: Damschroder Laura J. , Roberts Todd R. , Zikmund-Fisher Brian J. , Ubel Peter A.
Published: June 2007

Objective. Person tradeoff (PTO) elicitations assess people's values for health states by asking them to compare the value of treatment programs. For example, people might be asked how many patients need to be cured of health condition X to equal the benefit of curing 100 people of condition Y. However, when faced with PTO elicitations, people frequently refuse to make quantifiable tradeoffs, exhibiting 2 kinds of refusals: 1) They say that 2 treatment programs have equal value, that curing 100 of X is just as good as curing 100 of Y, even if X is a less serious condition than Y, or 2) they say that the 2 programs are incomparable, that millions of people need to be cured of X to be as good as curing 100 of Y. The authors explore whether people would be more willing to make tradeoffs if the focus was changed from trading off groups of patients to choosing the best decision or evaluating treatment benefits. Design. Two randomized trials used diverse samples (N=2400) via the Internet to test for the effect of perspective on refusal rates. The authors predicted that perspectives that removed people from decision-making roles would increase their willingness make tradeoffs. Results. Contrary to expectations, refusal rates increased when people were removed from decision-making roles. In fact, the more pressure put on people to make a decision, the less likely they were to refuse to make tradeoffs. Conclusion. To reduce PTO refusals, it is best to adopt a decision-maker perspective.
Do Risk Attitudes Differ across Domains and Respondent Types?
Authors: Prosser Lisa A. , Wittenberg Eve
Published: June 2007

Objective . To evaluate differences in risk attitude across the domains of health and money for 2 types of respondents, patients and community members. Methods . Two groups of respondents, patients with multiple sclerosis (n = 56) and members of the general community (n = 57), completed a survey that collected information on risk attitudes and socioeconomic and clinical variables (e.g., disability level). Risk attitude was measured using 2 standard-gamble questions on money and 1 standard-gamble question on health outcomes. Multivariate regression was used to evaluate the relationship between risk attitude and respondent type (patient v. community), adjusting for covariates that could affect risk attitude. Results . The median certainty equivalents for money gambles were significantly different from and less than the expected value of the gamble for both types of respondents. Median certainty equivalents for the health gamble were not significantly different from the expected value for either group of respondents. For all 3 gambles, there was no difference in median certainty equivalents between the 2 types of respondents in both unadjusted and adjusted analyses. Conclusions . Risk attitude varied across domains but not by respondent type. Patients and community members were predominantly risk neutral with respect to health outcomes and risk averse with respect to money. Research on risk preferences on money outcomes may not be an appropriate proxy for risk preferences regarding health outcomes. Risk preferences may depend more on characteristics of the choice than on respondent type.
Structure of Art, Structure of Mind
Authors: Anati Emmanuel
Published: June 2007

This paper sketches a comprehensive methodology to analyse the elementary structures of prehistoric art. A formal analysis of art is proposed through the distinction between pictograms, ideograms and psychograms. The dynamic between these elements and the thematic contents of the represented scenes is related to the four main types of social organization: early hunters, early gatherers, late hunters, pastoralists and complex economy societies. Cultural patterns of these societies and formal elements of art may appear as sharing the same elementary structures.
Looking for the Origin of Modernity
Authors: Kozlowski Janusz K. , Sacchi Dominique
Published: June 2007

There 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

Among 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

This 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

The 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.
Exploring New Directions for Research in the Radical Political Economy of Consumption
Authors: Pietrykowski Bruce
Published: June 2007

The sphere of consumption and the behavior of consumers has been a neglected area of investigation by radical political economists. The production/consumption duality is examined with special reference to Marx. Postmodern Marxism is offered as an alternative with which to examine consumer activities. Furthermore, insights and methods of analysis from the social construction of technology (SCOT) and feminist theory are investigated. These approaches can help to reclaim the terrain of consumer behavior for heterodox economics.
Racial Profiling and the Political Demand for Data
Authors: Liederbach John , Trulson Chad R. , Fritsch Eric J. , Caeti Tory J. , Taylor Robert W.
Published: June 2007

We are currently witnessing a large-scale, national movement toward the mandated collection of traffic stop data by police. The intended goal of mandated data collection is the identification and elimination of racial profiling by police. However, problems related to this trend are beginning to emerge, especially in states that have initiated required data collection in the absence of rigorous and standardized methodologies. The present study describes the results of a pilot project that was designed to develop and implement improved strategies for the collection and analysis of racial profiling data in Texas and elsewhere. The article includes an overview of the national trend toward racial profiling data collection as well as a discussion of the primary problems related to the study of racial profiling during traffic stops.
The Politics of the Body in Pain: Reading the Ethics of Imagery
Authors: Dauphinée Elizabeth
Published: June 2007

Images of the body in pain are the primary medium through which we come to know war, torture and other pain-producing activities. The Cartesian paradigm of subjectivity suggests that pain is an interior event that can only be imperfectly expressed through language or visuality. This creates a significant disjuncture between the body that experiences pain and the one who observes this body through the technologies of visual culture. The imperative to make pain visible is driven by the desire to access the pain of the other; but, in the context of the Cartesian subject, this access is simultaneously impossible. This article explores the ethics of using such imagery for projects that seek to resist or oppose war and torture, and suggests alternative ways of understanding and responding to bodies in pain.
Benevolent Patriotism: Art, Dissent and The American Effect
Authors: Lisle Debbie
Published: June 2007

This article examines the role of contemporary art in a post-9/11 context through The American Effect exhibition at the Whitney Museum of American Art in New York in 2003. This exhibition displayed a range of artworks from around the world that specifically engaged with, commented upon and interrogated the USA's pre-eminent position as a global superpower. In the politically charged climate after 9/11, the exhibition offered itself as a critical voice amid the more obvious patriotic clamour: it was one of the places where Americans could ask (and answer) the question, `Why do they hate us so much?' Although The American Effect claimed to be a space of dissent, it ultimately failed to question, let alone challenge, US global hegemony. Instead, the exhibition articulated a benevolent patriotism that forced artwork from other nations into supplicating and abject positions, and it obscured the complex discursive networks that connect artists, curators, critics, audiences and art museums.
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

Expression 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

The 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

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

Background

The 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.

Results

Sixty-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.

Conclusion

Together, 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

Background

The 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.

Results

Here 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.

Conclusion

These 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

Background

Chemokines 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).

Methods

We 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.

Results

RANTES-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).

Conclusion

RANTES-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

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

Population 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

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

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.
A Splicing Variant of the Androgen Receptor Detected in a Metastatic Prostate Cancer Exhibits Exclusively Cytoplasmic Actions
Authors: Jagla Monika , Fève Marie , Kessler Pascal , Lapouge Gaëlle , Erdmann Eva , Serra Sebastian , Bergerat Jean-Pierre , Céraline Jocelyn
Published: June 2007

The androgen receptor (AR) is a ligand-activated transcription factor that displays genomic actions characterized by binding to androgen-response elements in the promoter of target genes as well as nongenomic actions that do not require nuclear translocation and DNA binding. In this study, we report exclusive cytoplasmic actions of a splicing variant of the AR detected in a metastatic prostate cancer. This AR variant, named AR23, results from an aberrant splicing of intron 2, wherein the last 69 nucleotides of the intronic sequence are retained, leading to the insertion of 23 amino acids between the two zinc fingers in the DNA-binding domain. We show that the nuclear entry of AR23 upon dihydrotestosterone (DHT) stimulation is impaired. Alternatively, DHT-activated AR23 forms cytoplasmic and perinuclear aggregates that partially colocalize with the endoplasmic reticulum and are devoid of genomic actions. However, in LNCaP cells, this cytoplasmic DHT-activated AR23 remains partially active as evidenced by the activation of transcription from androgen-responsive promoters, the stimulation of NF-κB transcriptional activity and by the decrease of AP-1 transcriptional activity. Our data reveal novel cytoplasmic actions for this splicing AR variant, suggesting a contribution in prostate cancer progression.
Vascular Calcification in Middle Age and Long-Term Risk of Hip Fracture: The Framingham Study
Authors: Samelson Elizabeth J , Cupples L Adrienne , Broe Kerry E , Hannan Marian T , O'Donnell Christopher J , Kiel Douglas P
Published: June 2007

Osteoporosis and atherosclerosis frequently occur in the same individuals and may share similar pathogenic mechanisms. This study examined the relation between severity of aortic calcification in middle-age years and subsequent risk of hip fracture in women and men in the population-based Framingham Study.

Introduction: We assessed vascular calcification in women and men in middle age and risk of hip fracture at advanced age.

Materials and Methods: Participants included 2499 Framingham cohort members (mean age, 61 yr; range, 47–80 yr). Semiquantitative methods were used to determine severity of abdominal aortic calcification on baseline radiographs. Information on potential confounding factors was obtained from study examinations conducted at, or before, baseline radiography. Hip fractures were ascertained by active surveillance and confirmed by medical records.

Results: Thirty-five-year cumulative incidence of hip fracture was 16% in women and 5% in men with prevalent aortic calcification at baseline (score 1+) and 14% in women and 4% in men without aortic calcification (score 0). Hazard ratios (HRs) and 95% CIs for hip fracture did not increase from the lowest to the highest category of aortic calcification. HRs were 1.0, 1.2 (95% CI, 0.9–1.8), 1.2 (95% CI, 0.7–1.9), 1.1 (95% CI, 0.7–1.7), and 1.4 (95% CI, 0.8–2.3) in women (p for trend = 0.44) and 1.0, 1.8 (95% CI, 0.8–3.8), 1.8 (95% CI, 0.7–4.6), 1.5 (95% CI, 0.6–3.9), and 1.2 (95% CI, 0.2–5.7) in men (p for trend = 0.29) for aortic calcification scores 0 (reference), 1–4, 4–5, 6–10, and 11+, respectively. However, aortic calcification score was strongly associated with increased risk of death (p for trend < 0.0001 in women and men). HRs (95% CIs) for mortality from the lowest to highest aortic calcification score were 1.0, 1.6 (1.4–1.9), 1.7 (1.4–2.1), 1.8 (1.5–2.2), and 2.1 (1.7–2.6) for women, and for men were 1.0, 1.4 (1.1–1.6), 1.4 (1.2–1.8), 1.6 (1.3–2.0), and 1.9 (1.5–2.5).

Conclusions: Vascular calcification in middle-aged adults does not increase long-term hip fracture risk.
Abortion Among Young Women and Subsequent Life Outcomes
Authors: Fergusson David M. , Boden Joseph M. , Horwood L. John
Published: June 2007

CONTEXT:  Young women frequently cite concerns about the effects of unplanned pregnancies on future life course outcomes, including education, employment and relationships, as reasons for seeking abortion. There is relatively little evidence as to whether abortion leads to improved life course outcomes for young women who choose this option.

METHODS:  Data from 492 women participating in a 25‐year longitudinal study of a New Zealand birth cohort were used in regression models that examined the relationship between pregnancy and abortion history prior to age 21 and selected social and economic outcomes at ages 21–25.

RESULTS:  Compared with young women who became pregnant before age 21 but did not seek an abortion, young women who had an abortion had significantly better outcomes on six out of 10 measures spanning education, income, welfare dependence and domestic violence. Adjustment for confounding factors indicated that most of these differences were explained by family, social and educational characteristics that were present prior to pregnancy. Nonetheless, even after adjustment for confounding factors, young women who had abortions had higher levels of subsequent educational achievement than those who became pregnant but did not have abortions.

CONCLUSIONS:  Abortion may mitigate some effects of early unplanned pregnancy. However, further study of its potential risks and benefits is needed so that women can make fully informed decisions as to whether to terminate unintended pregnancies.
Identifying Barriers to Emergency Contraception Use Among Young Women from Various Sociocultural Groups in British Columbia, Canada
Authors: Shoveller Jean , Chabot Cathy , Soon Judith A. , Levine Marc
Published: June 2007

CONTEXT:  Despite advances related to the provision of emergency contraception in Canada, particularly the granting of independent prescriptive authority to pharmacists in 2000, little is known about the ways in which women perceive potential barriers to using it.

METHODS:  In 2004, an ethnically diverse sample of 52 women living in Greater Vancouver participated in interviews that were analyzed for an assessment of women’s knowledge, attitudes and experiences related to emergency contraception, with particular attention to the ways in which ethnicity affected their stories.

RESULTS:  Participants generally misperceived emergency contraception as an abortifacient, and often mistakenly thought that it has long‐term effects on health and fertility. Knowledge gaps regarding reproductive physiology impeded clear understanding of when it is most effective. Participants also reported receiving subtle and sometimes overtly stigmatizing messages from providers when they sought emergency contraception. Asian and South Asian women were particularly concerned about negative interactions with providers; for example, they feared that female providers from their sociocultural community might recognize, chastise or gossip about them. Institutional policies (e.g., a Catholic hospital’s refusal to provide the method), coupled with low awareness of pharmacists’ prescriptive authority, also created barriers to use.

CONCLUSIONS:  Women’s ability to benefit from emergency contraception is hampered by lack of knowledge and conservative cultural or social mores. Serious contextual and structural shifts are required before woman‐centered approaches to provision of the method become the norm.
Multipartnered Fertility Among Young Women with a Nonmarital First Birth: Prevalence and Risk Factors
Authors: Benjamin Guzzo Karen , Furstenberg Frank F.
Published: June 2007

CONTEXT:  Although early nonmarital fertility has been well studied, less attention has been paid to the subsequent fertility of young unwed mothers. In particular, the frequency with which these young women have subsequent births with a new partner (multipartnered fertility) and the risk factors associated with doing so are unknown.

METHODS:  The proportion of young women who had a first birth and the proportion who subsequently had a child with a new partner were determined among a sample of participants in Waves 1 (1995) and 3 (2001–2002) of the National Longitudinal Study of Adolescent Health. Multivariate analyses identified characteristics associated with multipartnered fertility.

RESULTS:  By Wave 3, when these young women were 19–25 years old, 29% had had a first birth, and 3% had had births with multiple partners. Among women with a nonmarital first birth, 14% subsequently had a birth with another partner, and 41% with two or more children had had multiple partners. The prevalence of multipartnered fertility differed sharply by race and ethnicity. Most new‐partner births occurred outside of marriage, especially among black women. Respondents who had no contact with their partner after informing him of their first pregnancy or who had not wanted to have a child with him had an increased likelihood of multipartnered fertility.

CONCLUSIONS:  The context in which first births occur sets the stage for subsequent childbearing. Programs that help women avoid having births in unfavorable circumstances, such as in early and unstable relationships, may reduce the prevalence of multipartnered fertility.
U.S. Women’s One‐Year Contraceptive Use Patterns, 2004
Authors: Frost Jennifer J. , Singh Susheela , Finer Lawrence B.
Published: June 2007

CONTEXT:  Unintended pregnancies occur far too often in the United States, and half occur when couples fail to practice contraception. Improved measures of the continuity of women’s contraceptive use, nonuse and switching patterns can help identify ways to reduce unintended pregnancy.

METHODS:  A nationally representative sample of 1,978 adult women at risk of unintended pregnancy was surveyed by telephone in 2004. Respondents provided detailed information about contraceptive use and periods of stopping or switching methods during the past year. A typology of patterns of contraceptive use was created, classifying women into mutually exclusive categories according to their exposure to pregnancy risk.

RESULTS:  Twenty‐three percent of women at risk of unintended pregnancy were exposed to a high risk of pregnancy because of gaps in contraceptive method use in the year prior to the survey—8% were consistent nonusers, and 15% experienced 1–11 months of nonuse while at risk. More than half of women used a method during each of the previous 12 months—38% used the same method or methods all year, and 24% switched methods. Fifteen percent of women had gaps in contraceptive use when they were not at risk. Women reported a variety of reasons for their gaps in contraceptive use, including method‐related difficulties and side effects, infrequent sex and being ambivalent about avoiding pregnancy.

CONCLUSIONS:  Strategies for reducing gaps in contraceptive use include improved counseling to help women both choose the right method and continue method use, especially when they have periods of infrequent sexual activity or are experiencing method‐related side effects or problems.
Visual Function at 11 Years of Age in Preterm-Born Children With and Without Fetal Brain Sparing
Authors: Kok Joke H. , Prick Liesbeth , Merckel Elly , Everhard Yolande , Verkerk Gijs J.Q. , Scherjon Sicco A.
Published: June 2007

OBJECTIVE. We have demonstrated earlier an accelerated maturation of the visual evoked potential in the first year of life in preterm infants with antenatal brain sparing. We have now assessed visual functioning at 11 years of age in the same cohort and compared the groups with and without brain sparing.

DESIGN/METHODS. One hundred sixteen survivors included in a study on the outcome of preterm infants born at <33 weeks' gestation with and without fetal brain sparing and admitted to the NICU were followed extensively. Ninety-eight infants (85%) were again assessed at 11 years of age. Data were available for fetal Doppler measurements indicating brain sparing, neonatal cerebral ultrasound scanning, and developmental outcome in the first 5 years. Mean birth weight was 1303 g; mean gestational age was 29.8 weeks. The infants were divided into 2 groups with and without brain sparing. Visual functioning was estimated by measuring visual acuity, visual fields, eye position, and binocular function and by visual motor tests.

RESULTS. Six percent of the children were found to have a visual acuity of <0.8, 12% had strabismus, and 14% to 46% showed abnormal results on the visual motor tests. No statistical differences were found between the 2 groups. However, children with severe cerebral ultrasound diagnoses in the neonatal period were found to have significantly more abnormalities on visual functioning and lower scores on visual motor tests than children without these morbidities.

CONCLUSIONS. Children with fetal brain sparing do not demonstrate a different development of their visual functioning at late school age. However, an abnormal cerebral ultrasound in the neonatal period is associated with impaired visual function in later life.