bluuebunny/crossref_metadata_2025_split huggingface dataset:
POVERTY, FAMILIES AND THE INVESTMENT STATE
Authors: Nygård Mikael , Krüger Nicole 
Published: October 2012

ABSTRACT
Finland and Germany are traditionally seen as members of different welfare regimes with rather different approaches to family policies. During the last decade or so, poverty concerns have received an increasingly prominent position within family policy in both countries. The objects for these concerns have been different constellations of ‘poor’ families, and the policies pursued to counteract poverty have ranged from targeted measures to investments in childcare services. It has been suggested that the motivation behind recent social policy developments in Europe is a stronger accentuation of so-called social investment ideas calling for more activation, targeting and higher future returns through investments in human capital. This article explores the impact of social investment ideas on policy discourses about family-related poverty in Finland and Germany since the late-1980s by analysing poverty constructions and anti-poverty policy recommendations in government and party programs. The findings suggest a stronger focus on social investment ideas in the German discourse in terms of higher accentuation of ideas relating to equal opportunities, activation and prevention of poverty in a life-cycle perspective, whereas targeting have become a main topic in Finnish elite discourses. Furthermore, while being conditioned by institutional factors and historical policy legacies, social investment ideas have largely been adopted in an incremental way parallel to path-dependent national policy legacies.
The relationship of supervisor and trainee gender match and gender attitude match to supervisory style and the supervisory working alliance
Authors: Rarick Susan L. , Ladany Nicholas 
Published: October 2012

AbstractBackground: Gender‐related events have the potential to impact the supervisory relationship. Gender events might be related to the match between supervisors and supervisees on variables such as gender or gender attitudes. Method: In this study, we sought to determine whether gender match and gender attitude match were related to supervisory style and the supervisory working alliance in 94 supervisory dyads using four instruments: the Gender Attitude Inventory; Operationalisation of Gender Match; Supervisory Styles Inventory; and the Working Alliance Inventory/Supervision. Results: Progressive dyads (in which supervisors have more liberal attitudes about societal issues and culturally defined roles for women than their supervisees) were perceived by supervisors as more task‐oriented than parallel‐high dyads (in which supervisors and supervisees both had liberal attitudes). Implications for counselling supervision are discussed.
Bayesian correlated clustering to integrate multiple datasets
Authors: Kirk Paul , Griffin Jim E. , Savage Richard S. , Ghahramani Zoubin , Wild David L. 
Published: October 2012

AbstractMotivation: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct—but often complementary—information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured through parameters that describe the agreement among the datasets.Results: Using a set of six artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real Saccharomyces cerevisiae datasets. In the two-dataset case, we show that MDI’s performance is comparable with the present state-of-the-art. We then move beyond the capabilities of current approaches and integrate gene expression, chromatin immunoprecipitation–chip and protein–protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques—as well as to non-integrative approaches—demonstrate that MDI is competitive, while also providing information that would be difficult or impossible to extract using other methods.Availability: A Matlab implementation of MDI is available from http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/.Contact: D.L.Wild@warwick.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
KASpOD—a web service for highly specific and explorative oligonucleotide design
Authors: Parisot Nicolas , Denonfoux Jérémie , Dugat-Bony Eric , Peyret Pierre , Peyretaillade Eric 
Published: October 2012

Abstract
Summary: KASpOD is a web service dedicated to the design of signature sequences using a k-mer–based algorithm. Such highly specific and explorative oligonucleotides are then suitable for various goals, including Phylogenetic Oligonucleotide Arrays.
Availability: http://g2im.u-clermont1.fr/kaspod.
Contact: eric.peyretaillade@udamail.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Predicting protein residue–residue contacts using deep networks and boosting
Authors: Eickholt Jesse , Cheng Jianlin 
Published: October 2012

Abstract
Motivation: Protein residue–residue contacts continue to play a larger and larger role in protein tertiary structure modeling and evaluation. Yet, while the importance of contact information increases, the performance of sequence-based contact predictors has improved slowly. New approaches and methods are needed to spur further development and progress in the field.
Results: Here we present DNCON, a new sequence-based residue–residue contact predictor using deep networks and boosting techniques. Making use of graphical processing units and CUDA parallel computing technology, we are able to train large boosted ensembles of residue–residue contact predictors achieving state-of-the-art performance.
Availability: The web server of the prediction method (DNCON) is available at http://iris.rnet.missouri.edu/dncon/.
Contact: chengji@missouri.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Real Time Metagenomics: Using k-mers to annotate metagenomes
Authors: Edwards Robert A. , Olson Robert , Disz Terry , Pusch Gordon D. , Vonstein Veronika , Stevens Rick , Overbeek Ross 
Published: October 2012

Abstract
Summary: Annotation of metagenomes involves comparing the individual sequence reads with a database of known sequences and assigning a unique function to each read. This is a time-consuming task that is computationally intensive (though not computationally complex). Here we present a novel approach to annotate metagenomes using unique k-mer oligopeptide sequences from 7 to 12 amino acids long. We demonstrate that k-mer-based annotations are faster and approach the sensitivity and precision of blastx-based annotations without loosing accuracy. A last-common ancestor approach was also developed to describe the members of the community.
Availability and implementation: This open-source application was implemented in Perl and can be accessed via a user-friendly website at http://edwards.sdsu.edu/rtmg. In addition, code to access the annotation servers is available for download from http://www.theseed.org/. FIGfams and k-mers are available for download from ftp://ftp.theseed.org/FIGfams/.
Contact: redwards@mail.sdsu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A universal measure of chaotropicity and kosmotropicity
Authors: Cray Jonathan A. , Russell John T. , Timson David J. , Singhal Rekha S. , Hallsworth John E. 
Published: October 2012

SummaryDiverse parameters, including chaotropicity, can limit the function of cellular systems and thereby determine the extent of Earth's biosphere. Whereas parameters such as temperature, hydrophobicity, pressure, pH, Hofmeister effects, and water activity can be quantified via standard scales of measurement, the chao‐/kosmotropic activities of environmentally ubiquitous substances have no widely accepted, universal scale. We developed an assay to determine and quantify chao‐/kosmotropicity for 97 chemically diverse substances that can be universally applied to all solutes. This scale is numerically continuous for the solutes assayed (from +361 kJ kg−1 mol−1 for chaotropes to −659 kJ kg−1 mol−1 for kosmotropes) but there are key points that delineate (i) chaotropic from kosmotropic substances (i.e. chaotropes ≥ +4; kosmotropes ≤ −4 kJ kg−1 mol−1); and (ii) chaotropic solutes that are readily water‐soluble (log P < 1.9) from hydrophobic substances that exert their chaotropic activity, by proxy, from within the hydrophobic domains of macromolecular systems (log P > 1.9). Examples of chao‐/kosmotropicity values are, for chaotropes: phenol +143, CaCl2 +92.2, MgCl2 +54.0, butanol +37.4, guanidine hydrochloride +31.9, urea +16.6, glycerol [> 6.5 M] +6.34, ethanol +5.93, fructose +4.56; for kosmotropes: proline −5.76, sucrose −6.92, dimethylsulphoxide (DMSO) −9.72, mannitol −6.69, trehalose −10.6, NaCl −11.0, glycine −14.2, ammonium sulfate −66.9, polyethylene glycol‐ (PEG‐)1000 −126; and for relatively neutral solutes: methanol, +3.12, ethylene glycol +1.66, glucose +1.19, glycerol [< 5 M] +1.06, maltose −1.43 (kJ kg−1 mol−1). The data obtained correlate with solute interactions with, and structure–function changes in, enzymes and membranes. We discuss the implications for diverse fields including microbial ecology, biotechnology and astrobiology.
Carbohydrate utilization by enterohaemorrhagic Escherichia coliO157:H7 in bovine intestinal content
Authors: Bertin Yolande , Chaucheyras‐Durand Frédérique , Robbe‐Masselot Catherine , Durand Alexandra , de la Foye Anne , Harel Josée , Cohen Paul S. , Conway Tyrell , Forano Evelyne , Martin Christine 
Published: October 2012

SummaryThe bovine gastrointestinal (GI) tract is the main reservoir for enterohaemorrhagic Escherichia coli (EHEC) responsible for food‐borne infections. Characterization of nutrients preferentially used by EHEC in the bovine intestine would help to develop ecological strategies to reduce EHEC carriage. However, the carbon sources that support the growth of EHEC in the bovine intestine are poorly documented. In this study, a very low concentration of glucose, the most abundant monomer included in the cattle dietary polysaccharides, was detected in bovine small intestine contents (BSIC) collected from healthy cows at the slaughterhouse. Six carbohydrates reported to be included in the mucus layer covering the enterocytes [galactose, N‐acetyl‐glucosamine (GlcNAc), N‐acetyl‐ galactosamine (GalNAc), fucose, mannose and N‐acetyl neuraminic acid (Neu5Ac)] have been quantified for the first time in BSIC and accounted for a total concentration of 4.2 mM carbohydrates. The genes required for enzymatic degradation of the six mucus‐derived carbohydrates are highly expressed during the exponential growth of the EHEC strain O157:H7 EDL933 in BSIC and are more strongly induced in EHEC than in bovine commensal E. coli. In addition, EDL933 consumed the free monosaccharides present in the BSIC more rapidly than the resident microbiota and commensal E. coli, indicating a competitive ability of EHEC to catabolize mucus‐derived carbohydrates in the bovine gut. Mutations of EDL933 genes required for the catabolism of each of these sugars have been constructed, and growth competitions of the mutants with the wild‐type strain clearly demonstrated that mannose, GlcNAc, Neu5Ac and galactose catabolism confers a high competitive growth advantage to EHEC in BSIC and probably represents an ecological niche for EHEC strains in the bovine small intestine. The utilization of these mucus‐derived monosaccharides by EDL933 is apparently required for rapid growth of EHEC in BSIC, and for maintaining a competitive growth rate as compared with that of commensal E. coli. The results suggest a strategy for O157:H7 E. coli survival in the bovine intestine, whereby EHEC rapidly consumes mucus‐derived carbohydrates that are poorly consumed by bacteria belonging to the resident intestinal microbiota, including commensal E. coli.
Residential care: an effective response to out‐of‐home children and young people?
Authors: Carrà Elisabetta 
Published: October 2012

AbstractThe ever‐growing number of out‐of‐home children in Italy over the last decade has urged an assessment of the available care services. Although foster care is spreading rapidly, many young people are still housed in residential facilities. Reflection on residential care quality has intensified at both a national and an international level. This paper presents the results of a study on residential care facilities for children and young people in the region of Northern Italy (Lombardy). Four dimensions of ‘quality’ are considered: efficiency, effectiveness, participation in planning and intervention, and empowerment of children and their family relationships. The combined effects of these dimensions are defined as ‘relational quality’. The results show that residential care facilities are generally good, while Social Services resources often appear inadequate for interventions aimed at birth families (efficiency). The well‐being of children in residential care facilities is high, even if they tend to move from one facility to another, rarely returning to their birth family (effectiveness). The involvement of children and their families at different stages of the care path is limited (participative approach). Finally, the most critical element is the failure to properly involve birth families (empowerment).
Riparian ecosystems in human cancers
Authors: Alfarouk Khalid O. , Ibrahim Muntaser E. , Gatenby Robert A. , Brown Joel S. 
Published: October 2012

AbstractIntratumoral evolution produces extensive genetic heterogeneity in clinical cancers. This is generally attributed to an increased mutation rate that continually produces new genetically defined clonal lineages. Equally important are the interactions between the heritable traits of cancer cells and their microenvironment that produces natural selection favoring some clonal ‘species’ over others. That is, while mutations produce the heritable variation, environmental selection and cellular adaptation govern the strategies (and genotypes) that can proliferate within the tumor ecosystem. Here we ask: What are the dominant evolutionary forces in the cancer ecosystem? We propose that the tumor vascular network is a common and primary cause of intratumoral heterogeneity. Specifically, variations in blood flow result in variability in substrate, such as oxygen, and metabolites, such as acid, that serve as critical, but predictable, environmental selection forces. We examine the evolutionary and ecological consequences of variable blood flow by drawing an analogy to riparian habitats within desert landscapes. We propose that the phenotypic properties of cancer cells will exhibit predictable spatial variation within tumor phenotypes as a result of proximity to blood flow. Just as rivers in the desert create an abrupt shift from the lush, mesic riparian vegetation along the banks to sparser, xeric and dry‐adapted plant species in the adjacent drylands, we expect blood vessels within tumors to promote similarly distinct communities of cancer cells that change abruptly with distance from the blood vessel. We propose vascular density and blood flow within a tumor as a primary evolutionary force governing variations in the phenotypic properties of cancer cells thus providing a unifying ecological framework for understanding intratumoral heterogeneity.
Structural and dynamic determinants of type I interferon receptor assembly and their functional interpretation
Authors: Piehler Jacob , Thomas Christoph , Garcia K.Christopher , Schreiber Gideon 
Published: October 2012

SummaryType I interferons (IFNs) form a network of homologous cytokines that bind to a shared, heterodimeric cell surface receptor and engage signaling pathways that activate innate and adaptive immune responses. The ability of IFNs to mediate differential responses through the same cell surface receptor has been subject of a controversial debate and has important medical implications. During the past decade, a comprehensive insight into the structure, energetics, and dynamics of IFN recognition by its two‐receptor subunits, as well as detailed correlations with their functional properties on the level of signal activation, gene expression, and biological responses were obtained. All type I IFNs bind the two‐receptor subunits at the same sites and form structurally very similar ternary complexes. Differential IFN activities were found to be determined by different lifetimes and ligand affinities toward the receptor subunits, which dictate assembly and dynamics of the signaling complex in the plasma membrane. We present a simple model, which explains differential IFN activities based on rapid endocytosis of signaling complexes and negative feedback mechanisms interfering with ternary complex assembly. More insight into signaling pathways as well as endosomal signaling and trafficking will be required for a comprehensive understanding, which will eventually lead to therapeutic applications of IFNs with increased efficacy.
Structural basis for self‐recognition by autoimmune T‐cell receptors
Authors: Yin Yiyuan , Li Yili , Mariuzza Roy A. 
Published: October 2012

SummaryT‐cell receptors (TCRs) recognize peptides presented by major histocompatibility complex molecules (pMHC) to discriminate between foreign and self‐antigens. Whereas T‐cell recognition of foreign peptides is essential for protection against microbial pathogens, recognition of self‐peptides by T cells that have escaped negative selection in the thymus can lead to autoimmune disease. Structural studies of autoimmune TCR–pMHC complexes have provided insights into the mechanisms underlying self‐recognition and escape from thymic deletion. Two broad categories of self‐reactive TCRs can be clearly distinguished: (i) TCRs with altered binding topologies to self‐pMHC and (ii) TCRs that bind self‐pMHC in the canonical diagonal orientation, but where there are structural defects or suboptimal anchors in the self‐ligand. For both categories, however, the overall stability of the autoimmune TCR–pMHC complex is markedly reduced compared to anti‐microbial complexes, allowing the autoreactive T cells to evade negative selection, yet retain the ability to be activated by self‐antigens in target organs. Additionally, the structures provide insights into TCR cross‐reactivity, which can contribute to autoimmunity by increasing the likelihood of self‐pMHC recognition. Efforts are now underway to understand the impact of structural alterations in autoimmune TCR–pMHC complexes on higher order assemblies involved in TCR signaling, as well as on immunological synapse formation.
Conformational variation in structures of classical and non‐classical MHCII proteins and functional implications
Authors: Painter Corrie A. , Stern Lawrence J. 
Published: October 2012

SummaryRecent structural characterizations of classical and non‐classical major histocompatibility complex class II (MHCII) proteins have provided a view into the dynamic nature of the MHCII–peptide binding groove and the role that structural changes play in peptide loading processes. Although there have been numerous reports of crystal structures for MHCII–peptide complexes, a detailed analysis comparing all the structures has not been reported, and subtle conformational variations present in these structures may not have been fully appreciated. We compared the 91 MHCII crystal structures reported in the PDB to date, including an HLA‐DR mutant particularly susceptible to DM‐mediated peptide exchange, and reviewed experimental and computational studies of the effect of peptide binding on MHCII structure. These studies provide evidence for conformational lability in and around the α‐subunit 3‐10 helix at residues α48‐51, a region known to be critical for HLA‐DM‐mediated peptide exchange. A biophysical study of MHC–peptide hydrogen bond strengths and a recent structure of the non‐classical MHCII protein HLA‐DO reveal changes in the same region. Conformational variability was observed also in the vicinity of a kink in the β‐subunit helical region near residue β66 and in the orientation and loop conformation in the β2 Ig domain. Here, we provide an overview of the regions within classical and non‐classical MHCII proteins that display conformational changes and the potential role that these changes may have in the peptide loading/exchange process.
Diversity‐oriented approaches for interrogating T‐cell receptor repertoire, ligand recognition, and function
Authors: Birnbaum Michael E. , Dong Shen , Garcia K. Christopher 
Published: October 2012

SummaryMolecular diversity lies at the heart of adaptive immunity. T‐cell receptors and peptide‐major histocompatibility complex molecules utilize and rely upon an enormous degree of diversity at the levels of genetics, chemistry, and structure to engage one another and carry out their functions. This high level of diversity complicates the systematic study of important aspects of T‐cell biology, but recent technical advances have allowed for the ability to study diversity in a comprehensive manner. In this review, we assess insights gained into T‐cell receptor function and biology from our increasingly precise ability to assess the T‐cell repertoire as a whole or to perturb individual receptors with engineered reagents. We conclude with a perspective on a new class of high‐affinity, non‐stimulatory peptide ligands we have recently discovered using diversity‐oriented techniques that challenges notions for how we think about T‐cell receptor signaling.
Latex C‐serum from Hevea brasiliensis induces non‐apoptotic cell death in hepatocellular carcinoma cell line (HepG2)
Authors: Lam K. L. , Yang K. L. , Sunderasan E. , Ong M. T. 
Published: October 2012

AbstractObjectivesLatex from Hevea brasiliensis (natural rubber tree primarily cultivated for its rubber particles) has no known primary metabolic function, although its biological role is as a plant defence system. The present study has evaluated specific anti‐proliferative effects of latex whole C‐serum and its subfractions, on human cancer cell lines.Materials and methodsCell viability assay using MTT, DNA fragmentation assay and real‐time PCR were used to evaluate the cytotoxic effects of latex whole C‐serum and its subfractions on the cell lines.ResultsMTT assay revealed very low LC50 values, 2.0 and 280 ng/ml, for DCS and DCP treatments, respectively. DCS was proven to be more potent compared to DCP, in conferring specific anti‐proliferative effects on the cancer cell lines. The study also indicated that anti‐proliferative activity of pre‐heated C‐serum fractions diminished significantly.ConclusionAlthough noteworthy cell death was reported, DNA fragmentation assay and real‐time PCR confirmed that that induced by latex C‐serum subfractions was not promoted via the classical apoptotic signalling pathway.