bluuebunny/crossref_metadata_2025_split huggingface dataset:
‘I am living a peaceful life with my grandchildren. Nothing else.’ Stories of adversity and ‘resilience’ of older women caring for children in the context of HIV/AIDS and other stressors
Authors: CASALE MARISA 
Published: February 2011

ABSTRACTWhile the adverse effects of HIV and AIDS on female care-givers in southern Africa have been well documented, there are too few examples of more nuanced analyses, which reflect not only adversity and challenges, but also positive responses, perspectives and experiences. By discussing findings of qualitative research conducted with nine female carers of children in South Africa's Kwazulu-Natal province, one of the world's most HIV-affected regions, this paper explores two themes, focusing mainly on older (grandmother) carers: (a) their strength and resourcefulness in responding to adversity to ensure their families' survival and (b) their leadership role in affronting HIV and related stigma within their own families. These two themes unfold through insights provided by the stories of two study participants, which are discussed in the context of the broader study findings and literature. The aim of this research is both to add to experiential data on the much-debated notion of ‘resilience’ and further challenge the stereotype of older carers or ‘rural African grandmothers’ as passive victims of a changing world, rather than key agents of change. While terms such as ‘coping strategies’ and ‘resilience’ should be used cautiously, it is important to consider carers' short-term responses to the many challenges faced, with a view to constructively informing interventions.
Robotics competitions as benchmarks for AI research
Authors: Anderson John , Baltes Jacky , Cheng Chi Tai 
Published: February 2011

AbstractIn the last two decades various intelligent robotics competitions have become very popular. Arguably the most well-known of these are the robotic soccer competitions. In addition to their value in attracting media and capturing the minds of the general public, these competitions also provide benchmark problems for various robotics and artificial intelligence (AI) technologies. As with any benchmark, care must be taken that the benchmark does not introduce unwarranted biases. This paper critically evaluates the AI contributions made by various robotic competitions on AI research.
Ayurveda for agents: an attempt to bring the sciences of natural and artificial intelligence closer together
Authors: van Eijk Rogier M. 
Published: February 2011

AbstractThis paper advocates a new science of intelligence, one that is holistic, multi-disciplinary, oriented to crucial values as health and well-being and able to contribute to the solution of real-world problems. As a starting point we study the interplay between two research disciplines that until now have been hardly related to each other: Ayurveda and multi-agent systems. We consider some possible results of the cross fertilisation like for instance the application of ayurvedic knowledge to improve the skills of practical reasoning agents.
The impact of mobility on HIV control: a modelling study
Authors: VISSERS D. C. J. , DE VLAS S. J. , BAKKER R. , URASSA M. , VOETEN H. A. C. M. , HABBEMA J. D. F. 
Published: February 2011

SUMMARYMobility is associated with HIV due to more risky sexual behaviour of mobile groups such as travellers and migrants. Limited participation of such groups may reduce the effectiveness of HIV interventions disproportionally. The established STDSIM model, which simulates transmission and control of HIV and STD, was extended to simulate mobility patterns based on data from Tanzania. We explored the impact of non-participation of mobile groups (travellers and recent migrants) on the effectiveness of two interventions: condom promotion and health education aiming at partner reduction. If mobile groups do not participate, the effectiveness of both interventions could be reduced by 40%. The impact of targeting travellers with a combined HIV campaign is close to that of a general population intervention. In conclusion, it is important to account for possible non-participation of migrants and travellers. If non-participation is substantial, impact of interventions can be greatly improved by actively approaching these people.
Dietary patterns, food and macronutrient intakes among adults in three ethnic groups in rural Kenya
Authors: Hansen Andreas W , Christensen Dirk L , Larsson Melanie W , Eis Jeannette , Christensen Tue , Friis Henrik , Mwaniki David L , Kilonzo Beatrice , Boit Michael K , Borch-Johnsen Knut , Tetens Inge 
Published: February 2011

AbstractObjectiveTo compare dietary patterns and food and macronutrient intakes among adults in three ethnic groups in rural Kenya.DesignIn the present cross-sectional study, dietary intake was estimated in adult volunteers using two non-consecutive interactive 24 h recalls. Dietary patterns were assessed from the number of meals and snacks per day and from the food items and major food groups registered, and their contribution to energy intake (EI) was calculated. Anthropometric values were measured and sociodemographic data obtained using a questionnaire.SettingA cross-sectional study was conducted in the Bondo, Kitui and Transmara districts of rural Kenya. A high prevalence of food insecurity in Kenya underlines the importance of describing the dietary patterns and intakes in different Kenyan ethnic groups.SubjectsA total of 1163 (61 % women) adult Luo, Kamba and Maasai, with a mean age of 38·6 (range: 18–68) years, volunteered to participate.ResultsDietary patterns and food groups contributing to EI differed significantly among the ethnic groups. Mean EI ranged from 5·8 to 8·6 MJ/d among women and from 7·2 to 10·5 MJ/d among men, with carbohydrates contributing between 55·7 % and 74·2 % and fat contributing between 14·5 % and 30·2 % of total EI. Mean protein intake ranged from 0·72 to 1·3 g/kg per d, and EI:BMR ratio ranged between 1·1 and 1·6 in both sexes, and was highest among the Luo. Prevalence of underweight (BMI < 18·5 kg/m2) was 13·7 %, 20·5 % and 24·2 % in the Luo, Kamba and Maasai, respectively.ConclusionsThe degree of food insecurity measured as a degree of undernutrition and as dietary patterns differed considerably among the ethnic groups. The Maasai and Kamba in particular were exposed to food insecurity.
AUTOMORPHISMS OF THE UHF ALGEBRA THAT DO NOT EXTEND TO THE CUNTZ ALGEBRA
Authors: CONTI ROBERTO 
Published: February 2011

AbstractThe automorphisms of the canonical core UHF subalgebra ℱnof the Cuntz algebra 𝒪ndo not necessarily extend to automorphisms of 𝒪n. Simple examples are discussed within the family of infinite tensor products of (inner) automorphisms of the matrix algebrasMn. In that case, necessary and sufficient conditions for the extension property are presented. Also addressed is the problem of extending to 𝒪nthe automorphisms of the diagonal 𝒟n, which is a regular maximal abelian subalgebra with Cantor spectrum. In particular, it is shown that there exist product-type automorphisms of 𝒟nthat do not extend to (possibly proper) endomorphisms of 𝒪n.
Vowel Identification by Listeners With Hearing Impairment in Response to Variation in Formant Frequencies
Authors: Molis Michelle R. , Leek Marjorie R. 
Published: February 2011

Purpose
This study examined the influence of presentation level and mild-to-moderate hearing loss on the identification of a set of vowel tokens systematically varying in the frequency locations of their second and third formants.

Method

Five listeners with normal hearing (NH listeners) and five listeners with hearing impairment (HI listeners) identified synthesized vowels that represented both highly identifiable and ambiguous examples of /
i
/, /ʊ/, and /ɝ/.

Results
Response patterns of NH listeners showed significant changes, with an increase in presentation level from 75 dB SPL to 95 dB SPL, including increased category overlap. HI listeners, listening only at the higher level, showed greater category overlap than normal and overall identification patterns that differed significantly from those of NH listeners. Excitation patterns based on estimates of auditory filters suggested smoothing of the internal representations, resulting in impaired formant resolution.

Conclusions
Both increased presentation level for NH listeners and the presence of hearing loss produced a significant change in vowel identification for this stimulus set. Major differences were observed between NH listeners and HI listeners in vowel category overlap and in the sharpness of boundaries between vowel tokens. It is likely that these findings reflect imprecise internal spectral representations due to reduced frequency selectivity.
Evidence for Preserved Novel Word Learning in Down Syndrome Suggests Multiple Routes to Vocabulary Acquisition
Authors: Mosse Emma K. , Jarrold Christopher 
Published: February 2011

Purpose
Three studies investigated novel word learning, some requiring phonological production, each involving between 11 and 17 individuals with Down syndrome, and between 15 and 24 typically developing individuals matched for receptive vocabulary. The effect of stimuli wordlikeness and incidental procedure-based memory demands were examined to see whether these may account for an apparent impairment in word learning in Down syndrome demonstrated in earlier research.

Method
Paired associate word and nonword learning tasks were presented, requiring participants to learn the names of novel characters. The nonword stimuli varied in the degree of wordlikeness in 2 studies. A third study investigated extraneous task demand.

Results

Across 3 studies, there was no suggestion of a word learning deficit associated with Down syndrome (η
2
p
for the main effect of group of .03, .11, and .03, respectively), despite the level of phonological representation required. There was evidence that novel word learning by participants with Down syndrome exceeded that which their verbal short-term memory capacity would predict.

Conclusions
Vocabulary acquisition in Down syndrome may not rely on verbal short-term memory to the same extent as in typically developing children, lending support to the suggestion that new word learning may be underpinned by an additional memory process.
How Well Do Children Who Are Internationally Adopted Acquire Language? A Meta-Analysis
Authors: Scott Kathleen A. , Roberts Jenny A. , Glennen Sharon 
Published: February 2011

Purpose
In this article, the authors present the results of a systematic and meta-analytic examination of the language outcomes of children who are internationally adopted. The study examined the questions of whether the early life experiences of children who are internationally adopted and the language switch that occurs after adoption hinder the acquisition of language skills.

Method
The authors selected available studies on the language acquisition of internationally adopted children using search strategies from both a comprehensive set of databases and manual searching of selected studies. Study eligibility criteria included (a) participants clearly identified as being internationally adopted, (b) measurable language outcomes were reported, (c) a control group or normative measure was used in the design of the study, and (d) effect size was reported, or data were provided to calculate effect size.

Results
The meta-analysis found that as a group, the children expressed great variability in their language skills. Overall, they were more likely to have poorer language outcomes than comparison children, but several moderating variables were found.

Conclusions
The results of the meta-analysis have direct clinical application regarding the assessment and treatment of language skills of internationally adopted children. The study also has implications for future studies of the language development of internationally adopted children.
Sortase-catalyzed transformations that improve the properties of cytokines
Authors: Popp Maximilian W. , Dougan Stephanie K. , Chuang Tzu-Ying , Spooner Eric , Ploegh Hidde L. 
Published: February 2011

Recombinant protein therapeutics often suffer from short circulating half-life and poor stability, necessitating multiple injections and resulting in limited shelf-life. Conjugation to polyethylene glycol chains (PEG) extends the circulatory half-life of many proteins, but the methods for attachment often lack specificity, resulting in loss of biological activity. Using four-helix bundle cytokines as an example, we present a general platform that uses sortase-mediated transpeptidation to facilitate site-specific attachment of PEG to extend cytokine half-life with full retention of biological activity. Covalently joining the N and C termini of proteins to obtain circular polypeptides, again executed using sortase, increases thermal stability. We combined both PEGylation and circularization by exploiting two distinct sortase enzymes and the use of a molecular suture that allows both site-specific PEGylation and covalent closure. The method developed is general, uses a set of easily accessible reagents, and should be applicable to a wide variety of proteins, provided that their termini are not involved in receptor binding or function.
LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data
Authors: Yang Rendong , Zhang Chen , Su Zhen 
Published: February 2011

Abstract
Summary: We propose a three-step periodicity detection algorithm named LSPR. Our method first preprocesses the raw time-series by removing the linear trend and filtering noise. In the second step, LSPR employs a Lomb–Scargle periodogram to estimate the periodicity in the time-series. Finally, harmonic regression is applied to model the cyclic components. Inferred periodic transcripts are selected by a false discovery rate procedure. We have applied LSPR to unevenly sampled synthetic data and two Arabidopsis diurnal expression datasets, and compared its performance with the existing well-established algorithms. Results show that LSPR is capable of identifying periodic transcripts more accurately than existing algorithms.
Availability: LSPR algorithm is implemented as MATLAB software and is available at http://bioinformatics.cau.edu.cn/LSPR
Contact: zhensu@cau.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
GOSSIP: a method for fast and accurate global alignment of protein structures
Authors: Kifer I. , Nussinov R. , Wolfson H. J. 
Published: February 2011

Abstract
Motivation: The database of known protein structures (PDB) is increasing rapidly. This results in a growing need for methods that can cope with the vast amount of structural data. To analyze the accumulating data, it is important to have a fast tool for identifying similar structures and clustering them by structural resemblance. Several excellent tools have been developed for the comparison of protein structures. These usually address the task of local structure alignment, an important yet computationally intensive problem due to its complexity. It is difficult to use such tools for comparing a large number of structures to each other at a reasonable time.
Results: Here we present GOSSIP, a novel method for a global all-against-all alignment of any set of protein structures. The method detects similarities between structures down to a certain cutoff (a parameter of the program), hence allowing it to detect similar structures at a much higher speed than local structure alignment methods. GOSSIP compares many structures in times which are several orders of magnitude faster than well-known available structure alignment servers, and it is also faster than a database scanning method. We evaluate GOSSIP both on a dataset of short structural fragments and on two large sequence-diverse structural benchmarks. Our conclusions are that for a threshold of 0.6 and above, the speed of GOSSIP is obtained with no compromise of the accuracy of the alignments or of the number of detected global similarities.
Availability: A server, as well as an executable for download, are available at http://bioinfo3d.cs.tau.ac.il/gossip/.
Contact: wolfson@tau.ac.il; ilonak@post.tau.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
Model annotation for synthetic biology: automating model to nucleotide sequence conversion
Authors: Misirli Goksel , Hallinan Jennifer S. , Yu Tommy , Lawson James R. , Wimalaratne Sarala M. , Cooling Michael T. , Wipat Anil 
Published: February 2011

Abstract
Motivation: The need for the automated computational design of genetic circuits is becoming increasingly apparent with the advent of ever more complex and ambitious synthetic biology projects. Currently, most circuits are designed through the assembly of models of individual parts such as promoters, ribosome binding sites and coding sequences. These low level models are combined to produce a dynamic model of a larger device that exhibits a desired behaviour. The larger model then acts as a blueprint for physical implementation at the DNA level. However, the conversion of models of complex genetic circuits into DNA sequences is a non-trivial undertaking due to the complexity of mapping the model parts to their physical manifestation. Automating this process is further hampered by the lack of computationally tractable information in most models.
Results: We describe a method for automatically generating DNA sequences from dynamic models implemented in CellML and Systems Biology Markup Language (SBML). We also identify the metadata needed to annotate models to facilitate automated conversion, and propose and demonstrate a method for the markup of these models using RDF. Our algorithm has been implemented in a software tool called MoSeC.
Availability: The software is available from the authors' web site http://research.ncl.ac.uk/synthetic_biology/downloads.html.
Contact: anil.wipat@ncl.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists
Authors: Voss Björn , Hanselmann Michael , Renard Bernhard Y. , Lindner Martin S. , Köthe Ullrich , Kirchner Marc , Hamprecht Fred A. 
Published: February 2011

Abstract
Motivation: Alignment of multiple liquid chromatography/mass spectrometry (LC/MS) experiments is a necessity today, which arises from the need for biological and technical repeats. Due to limits in sampling frequency and poor reproducibility of retention times, current LC systems suffer from missing observations and non-linear distortions of the retention times across runs. Existing approaches for peak correspondence estimation focus almost exclusively on solving the pairwise alignment problem, yielding straightforward but suboptimal results for multiple alignment problems.
Results: We propose SIMA, a novel automated procedure for alignment of peak lists from multiple LC/MS runs. SIMA combines hierarchical pairwise correspondence estimation with simultaneous alignment and global retention time correction. It employs a tailored multidimensional kernel function and a procedure based on maximum likelihood estimation to find the retention time distortion function that best fits the observed data. SIMA does not require a dedicated reference spectrum, is robust with regard to outliers, needs only two intuitive parameters and naturally incorporates incomplete correspondence information. In a comparison with seven alternative methods on four different datasets, we show that SIMA yields competitive and superior performance on real-world data.
Availability: A C++ implementation of the SIMA algorithm is available from http://hci.iwr.uni-heidelberg.de/MIP/Software.
Contact: fred.hamprecht@iwr.uni-heidelberg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
DDN: a caBIG® analytical tool for differential network analysis
Authors: Zhang Bai , Tian Ye , Jin Lu , Li Huai , Shih Ie-Ming , Madhavan Subha , Clarke Robert , Hoffman Eric P. , Xuan Jianhua , Hilakivi-Clarke Leena , Wang Yue 
Published: February 2011

Abstract
Summary: Differential dependency network (DDN) is a caBIG® (cancer Biomedical Informatics Grid) analytical tool for detecting and visualizing statistically significant topological changes in transcriptional networks representing two biological conditions. Developed under caBIG® 's In Silico Research Centers of Excellence (ISRCE) Program, DDN enables differential network analysis and provides an alternative way for defining network biomarkers predictive of phenotypes. DDN also serves as a useful systems biology tool for users across biomedical research communities to infer how genetic, epigenetic or environment variables may affect biological networks and clinical phenotypes. Besides the standalone Java application, we have also developed a Cytoscape plug-in, CytoDDN, to integrate network analysis and visualization seamlessly.
Availability: The Java and MATLAB source code can be downloaded at the authors' web site http://www.cbil.ece.vt.edu/software.htm
Contact: yuewang@vt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Gobe: an interactive, web-based tool for comparative genomic visualization
Authors: Pedersen Brent S. , Tang Haibao , Freeling Michael 
Published: February 2011

Abstract
Summary: Gobe is a web-based tool for viewing comparative genomic data. It supports viewing multiple genomic regions simultaneously. Its simple text format and flash-based rendering make it an interactive, exploratory research tool. Gobe can be used without installation through our web service, or downloaded and customized with stylesheets and javascript callback functions.
Availability: Gobe is a flash application that runs in all modern web-browsers. The full source-code, including that for the online web application is available under the MIT license at: http://github.com/brentp/gobe. Sample applications are hosted at http://try-gobe.appspot.com/ and http://synteny.cnr.berkeley.edu/gobe-app/.
Contact: bpederse@berkeley.edu
Projected expansion of the subtropical biome and contraction of the temperate and equatorial upwelling biomes in the North Pacific under global warming
Authors: Polovina Jeffrey J. , Dunne John P. , Woodworth Phoebe A. , Howell Evan A. 
Published: February 2011

Abstract
Polovina, J. J., Dunne, J. P., Woodworth, P. A., and Howell, E. A. 2011. Projected expansion of the subtropical biome and contraction of the temperate and equatorial upwelling biomes in the North Pacific under global warming. – ICES Journal of Marine Science, 68: 986–995. A climate model that includes a coupled ocean biogeochemistry model is used to define large oceanic biomes in the North Pacific Ocean and describe their changes over the 21st century in response to the IPCC Special Report on Emission Scenario A2 future atmospheric CO2 emissions scenario. Driven by enhanced stratification and a northward shift in the mid-latitude westerlies under climate change, model projections demonstrated that between 2000 and 2100, the area of the subtropical biome expands by ∼30% by 2100, whereas the area of temperate and equatorial upwelling (EU) biomes decreases by ∼34 and 28%, respectively, by 2100. Over the century, the total biome primary production and fish catch is projected to increase by 26% in the subtropical biome and decrease by 38 and 15% in the temperate and the equatorial biomes, respectively. Although the primary production per unit area declines slightly in the subtropical and the temperate biomes, it increases 17% in the EU biome. Two areas where the subtropical biome boundary exhibits the greatest movement is in the northeast Pacific, where it moves northwards by as much as 1000 km per 100 years and at the equator in the central Pacific, where it moves eastwards by 2000 km per 100 years. Lastly, by the end of the century, there are projected to be more than 25 million km2 of water with a mean sea surface temperature of 31°C in the subtropical and EU biomes, representing a new thermal habitat. The projected trends in biome carrying capacity and fish catch suggest resource managers might have to address long-term trends in fishing capacity and quota levels.