bluuebunny/crossref_metadata_2025_split huggingface dataset:
School-based strategies to prevent violence, trauma, and psychopathology: The challenges of going to scale
Authors: Aber Lawrence , Brown Joshua L. , Jones Stephanie M. , Berg Juliette , Torrente Catalina 
Published: April 2011

AbstractChildren's trauma-related mental health problems are widespread, largely untreated and constitute significant barriers to academic achievement and attainment. Translational research has begun to identify school-based interventions to prevent violence, trauma and psychopathology. We describe in detail the findings to date on research evaluating one such intervention, the Reading, Writing, Respect, and Resolution (4Rs) Program. The 4Rs Program has led to modest positive impacts on both classrooms and children after 1 year that appear to cascade to more impacts in other domains of children's development after 2 years. This research strives not only to translate research into practice but also translate practice into research. However, considerable challenges must be met for such research to inform prevention strategies at population scale.
Language and cognitive outcomes in internationally adopted children
Authors: Eigsti Inge-Marie , Weitzman Carol , Schuh Jillian , de Marchena Ashley , Casey B. J. 
Published: April 2011

AbstractThis study focuses on the association between language skills and core cognitive processes relative to the duration of institutionalization in children adopted from orphanages abroad. Participants in the adoptive group (n = 46) had arrived in the United States between the ages of 2 and 84 months (mean = 24 months), and had been living in the United States for 1–9 years. Drawing on both experimental and standardized assessments, language skills of the international adoptees differed as a function of length of time spent in an institution and from those of 24 nonadopted controls. Top-down cognitive assessments including measures of explicit memory and cognitive control differed between adopted and nonadopted children, yet differences between groups in bottom-up implicit learning processes were unremarkable. Based on the present findings, we propose a speculative model linking language and cognitive changes to underlying neural circuitry alterations that reflect the impact of chronic stress, due to adoptees' experience of noncontingent, nonindividualized caregiving. Thus, the present study provides support for a relationship between domain-general cognitive processes and language acquisition, and describes a potential mechanism by which language skills are affected by institutionalization.
Dynamical Diffraction Simulations in FePt—I
Authors: Torres Karen L. , Vanfleet Richard R. , Thompson Gregory B. 
Published: April 2011

AbstractA series of multislice simulations to quantify the effect of various degrees of order, composition, and thickness on the electron diffracted intensities were performed using the L10 FePt system as the case study. The dynamical diffraction studies were done in both a convergent electron beam diffraction and selected area electron diffraction condition. The L10 symmetry demonstrated some peculiar challenges in the simulation, in particular between the {111} plane normal and the ⟨111⟩ direction, which are not equivalent because of tetragonality. A hybrid weighting function atom of Fe-Pt was constructed to account for S < 1 or nonequiatomic compositions. This statistical approach reduced the complexity of constructing a crystal with the probability that a particular atom was at a particular lattice site for a given order parameter and composition. Considerations of accelerating voltage, convergent angle, and thermal effects are discussed. The simulations revealed significant differences in intensity ratios between films of various compositions but equivalent unit cell numbers and degree of order.
INCARCERATION AND THE HEALTH OF THE AFRICAN AMERICAN COMMUNITY
Authors: Schnittker Jason , Massoglia Michael , Uggen Christopher 
Published: April 2011

AbstractThis article reviews evidence linking incarceration and health, with a particular focus on African Americans, who are disproportionately affected by the incarceration system. Although inmates generally suffer from worse health than comparable, non-institutionalized adults, this comparison is not uniformly the case, and some of the strongest negative effects of incarceration emerge after release, suggesting that the struggles of reintegration into society are as important as the conditions of incarceration. We review evidence for the basic relationship between incarceration and health from individual-level and aggregate-level studies, as well as from evidence and speculation regarding potential mediating mechanisms. Many questions remain regarding these mechanisms and, by extension, which policies are most promising for reducing incarceration's impact on health. Among other issues, the incarceration-health connection also raises fundamental questions regarding the level of harm society is willing to accept as part of routine punishment for criminal behavior.
ADDRESSING RACIAL DISPARITIES IN HEALTH USING LIFE COURSE PERSPECTIVES
Authors: Colen Cynthia G. 
Published: April 2011

AbstractIn the United States, African Americans face stark inequalities in health. The life course perspective offers a unique viewpoint through which racial disparities in morbidity and mortality may be understood as the result of repeated exposures to risk factors during both childhood and adulthood. However, the utility of this approach is limited by its failure to investigate the degree to which racial/ethnic minorities are able to translate gains in socioeconomic status into favorable health outcomes, both for themselves and for their children. In order to adequately reflect the realities of marginalized groups, life course models must explore the interactive nature of linkages across lifecourse stages, pay particular attention to the unique processes that create and maintain health disparities over time, and consider the specific contexts in which these processes occur. To this end, I examine the ways in which exclusionary forces and discriminatory conditions are likely to prevent African American women and their children from reaping the health benefits typically associated with upward socioeconomic mobility.
The forgotten face of regular physical exercise: a ‘natural’ anti-atherogenic activity
Authors: Szostak Justyna , Laurant Pascal 
Published: April 2011

Humans are not programmed to be inactive. The combination of both accelerated sedentary lifestyle and constant food availability disturbs ancient metabolic processes leading to excessive storage of energy in tissue, dyslipidaemia and insulin resistance. As a consequence, the prevalence of Type 2 diabetes, obesity and the metabolic syndrome has increased significantly over the last 30 years. A low level of physical activity and decreased daily energy expenditure contribute to the increased risk of cardiovascular morbidity and mortality following atherosclerotic vascular damage. Physical inactivity leads to the accumulation of visceral fat and consequently the activation of the oxidative stress/inflammation cascade, which promotes the development of atherosclerosis. Considering physical activity as a ‘natural’ programmed state, it is assumed that it possesses atheroprotective properties. Exercise prevents plaque development and induces the regression of coronary stenosis. Furthermore, experimental studies have revealed that exercise prevents the conversion of plaques into a vulnerable phenotype, thus preventing the appearance of fatal lesions. Exercise promotes atheroprotection possibly by reducing or preventing oxidative stress and inflammation through at least two distinct pathways. Exercise, through laminar shear stress activation, down-regulates endothelial AT1R (angiotensin II type 1 receptor) expression, leading to decreases in NADPH oxidase activity and superoxide anion production, which in turn decreases ROS (reactive oxygen species) generation, and preserves endothelial NO bioavailability and its protective anti-atherogenic effects. Contracting skeletal muscle now emerges as a new organ that releases anti-inflammatory cytokines, such as IL-6 (interleukin-6). IL-6 inhibits TNF-α (tumour necrosis factor-α) production in adipose tissue and macrophages. The down-regulation of TNF-α induced by skeletal-muscle-derived IL-6 may also participate in mediating the atheroprotective effect of physical activity.
Proteins without 3D structure: definition, detection and beyond
Authors: Orosz Ferenc , Ovádi Judit 
Published: April 2011

Abstract
Motivation: Predictions, and experiments to a lesser extent, following the decoding of the human genome showed that a significant fraction of gene products do not have well-defined 3D structures. While the presence of structured domains traditionally suggested function, it was not clear what the absence of structure implied. These and many other findings initiated the extensive theoretical and experimental research into these types of proteins, commonly known as intrinsically disordered proteins (IDPs). Crucial to understanding IDPs is the evaluation of structural predictors based on different principles and trained on various datasets, which is currently the subject of active research. The view is emerging that structural disorder can be considered as a separate structural category and not simply as absence of secondary and/or tertiary structure. IDPs perform essential functions and their improper functioning is responsible for human diseases such as neurodegenerative disorders.
Contact: ovadi@enzim.hu
Supplementary information: Supplementary data are available at Bioinformatics online.
An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure
Authors: Kim Seongho , Fang Aiqin , Wang Bing , Jeong Jaesik , Zhang Xiang 
Published: April 2011

Abstract
Motivation: Comprehensive two-dimensional gas chromatography mass spectrometry (GC × GC–MS) brings much increased separation capacity, chemical selectivity and sensitivity for metabolomics and provides more accurate information about metabolite retention times and mass spectra. However, there is always a shift of retention times in the two columns that makes it difficult to compare metabolic profiles obtained from multiple samples exposed to different experimental conditions.
Results: The existing peak alignment algorithms for GC × GC–MS data use the peak distance and the spectra similarity sequentially and require predefined either distance-based window and/or spectral similarity-based window. To overcome the limitations of the current alignment methods, we developed an optimal peak alignment using a novel mixture similarity by employing the peak distance and the spectral similarity measures simultaneously without any variation windows. In addition, we examined the effect of the four different distance measures such as Euclidean, Maximum, Manhattan and Canberra distances on the peak alignment. The performance of our proposed peak alignment algorithm was compared with the existing alignment methods on the two sets of GC × GC–MS data. Our analysis showed that Canberra distance performed better than other distances and the proposed mixture similarity peak alignment algorithm prevailed against all literature reported methods.
Availability: The data and software mSPA are available at http://stage.louisville.edu/faculty/x0zhan17/software/software-development.
Contact: s0kim023@louisville.edu; xiang.zhang@louisville.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Services for prediction of drug susceptibility for HIV proteases and reverse transcriptases at the HIV drug research centre
Authors: Spjuth Ola , Eklund Martin , Lapins Maris , Junaid Muhammad , Wikberg Jarl E. S. 
Published: April 2011

Abstract
Summary: The HIV Drug Research Centre (HIVDRC) has established Web services for prediction of drug susceptibility for HIV proteases and reverse transcriptases. The services are based on two proteochemometric models which accepts a protease or reverse transcriptase sequence in amino acid form, and outputs the predicted drug susceptibility values. The predictions are based on a comprehensive analysis where all the relevant inhibitors are included, resulting in models with excellent predictive capabilities.
Availability and Implementation: The services are implemented as interoperable Web services (REST and XMPP), with supporting web pages to allow for individual analyses. A set of plugins were also developed which make the services available from the Bioclipse workbench for life science. Services are available at http://www.hivdrc.org/services.
Contact: ola.spjuth@farmbio.uu.se
RuleBender: a visual interface for rule-based modeling
Authors: Xu Wen , Smith Adam M. , Faeder James R. , Marai G. Elisabeta 
Published: April 2011

Abstract
Summary: Rule-based modeling (RBM) is a powerful and increasingly popular approach to modeling intracellular biochemistry. Current interfaces for RBM are predominantly text-based and command-line driven. Better visual tools are needed to make RBM accessible to a broad range of users, to make specification of models less error prone and to improve workflows. We present RULEBENDER, an open-source visual interface that facilitates interactive debugging, simulation and analysis of RBMs.
Availability: RULEBENDER is freely available for Mac, Windows and Linux at http://rulebender.org.
Contact: faeder@pitt.edu; marai@cs.pitt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Multicentre phase II study of the CyclOBEAP regimen for patients with peripheral T‐cell lymphoma with analysis of biomarkers
Authors: Niitsu Nozomi , Hayama Miyuki , Yoshino Tadashi , Nakamura Shigeo , Tamaru Jun‐Ichi , Nakamine Hirokazu , Okamoto Masataka 
Published: April 2011

SummaryPeripheral T‐cell lymphoma (PTCL) has a poorer prognosis than diffuse large B‐cell lymphoma (DLBCL). We administered the CyclOBEAP regimen (cyclophosphamide, vincristine, bleomycin, etoposide, doxorubicin, prednisolone) to patients with DLBCL, and reported its safety and efficacy. Here, we report the results of a multicentre phase II study of the CyclOBEAP regimen in patients with PTCL. In addition, NME1 remained a prognostic factor for survival, as shown in patients who were treated with CyclOBEAP. There were 84 eligible patients and the median age was 54 years. The 5‐year overall survival (OS) rate was 72% and progression‐free survival (PFS) rate was 61%. The 5‐year OS was 93% among the anaplastic large‐cell lymphoma cases, 74% among the angioimmunoblastic T‐cell lymphoma cases, and 63% among the cases of PTCL‐not otherwise specified. When the patients were divided according to the International Prognostic Index or Prognostic Index for PTCL, the 5‐year OS and PFS rates did not significantly differ among the risk groups. Positivity for NME1 was found to be a significant independent prognostic factor. Grade 4 neutropenia was observed in 80 patients and thrombocytopenia in nine patients. Our results suggest that the CyclOBEAP therapy is safe and effective for PTCLs. Furthermore, the NME1 protein may be an important prognostic factor in PTCL.
Direct activation of STAT5 by ETV6‐LYN fusion protein promotes induction of myeloproliferative neoplasm with myelofibrosis
Authors: Takeda Yusuke , Nakaseko Chiaki , Tanaka Hiroaki , Takeuchi Masahiro , Yui Makiko , Saraya Atsunori , Miyagi Satoru , Wang Changshan , Tanaka Satomi , Ohwada Chikako , Sakaida Emiko , Yamaguchi Naoto , Yokote Koutaro , Hennighausen Lothar , Iwama Atsushi 
Published: April 2011

SummaryMyeloproliferative neoplasms (MPN), a group of haematopoietic stem cell (HSC) disorders, are often accompanied by myelofibrosis. We previously identified the fusion of the ETV6 gene to the LYN gene (ETV6‐LYN) in idiopathic myelofibrosis with ins(12;8)(p13;q11q21). The introduction of ETV6‐LYN into HSCs resulted in fatal MPN with massive myelofibrosis in mice, implicating the rearranged LYN kinase in the pathogenesis of MPN with myelofibrosis. However, the signalling molecules directly downstream from and activated by ETV6‐LYN remain unknown. In this study, we demonstrated that the direct activation of STAT5 by ETV6‐LYN is crucial for the development of MPN. ETV6‐LYN was constitutively active as a kinase through autophosphorylation. ETV6‐LYN, but not its kinase‐dead mutant, supported cytokine‐free proliferation of haematopoietic cells. STAT5 was activated in a JAK2‐independent manner in ETV6‐LYN‐expressing cells. ETV6‐LYN interacted with STAT5 and directly activated STAT5 both in vitro and in vivo. Of note, ETV6‐LYN did not support the formation of colonies by Stat5‐deficient HSCs under cytokine‐free conditions and the capacity of ETV6‐LYN to induce MPN with myelofibrosis was profoundly attenuated in a Stat5‐null background. These findings define STAT5 as a direct target of ETV6‐LYN and unveil the LYN‐STAT5 axis as a novel pathway to augment proliferative signals in MPN and leukaemia.
Aberrantly activated anti‐apoptotic signalling mechanisms in chronic lymphocytic leukaemia cells: clues to the identification of novel therapeutic targets
Authors: Gitendra Wickremasinghe R. , Prentice Archibald G. , Steele Andrew J. 
Published: April 2011

SummaryChronic lymphocytic leukaemia (CLL) is the commonest haematological malignancy in the western world and is incurable by cytotoxic therapy. Considerable research effort has identified the signal transduction pathways in CLL cells that contribute to anti‐apoptotic signalling. Some pathways are constitutively activated in CLL cells but upregulated in normal cells only when protein tyrosine kinases (PTKs) are activated by ligands. This review describes which PTKs are aberrantly activated in CLL cells and are potential targets for inhibition. Additional potential targets within pathways downstream of these PTKs include Mek/Erk, mTorc1, protein kinase C, PI‐3 kinase/Akt, nuclear factor‐κB and cyclin‐dependent protein kinase. Numerous studies have identified chemical agents and antibodies that selectively kill CLL cells, irrespective of their genetic resistance to conventional chemotherapeutic agents, and which can overcome cytoprotective microenvironmental signalling. These studies have resulted in identification of novel therapies, some of which are currently undergoing clinical trials. In vitro and animal model studies and clinical trials could determine which inhibitors of which targets are the likely to be most effective and least toxic either singly or in combination.
Minimal disease assessment in the treatment of children and adolescents with intermediate‐risk (Stage III/IV) B‐cell non‐Hodgkin lymphoma: a children’s oncology group report
Authors: Shiramizu Bruce , Goldman Stanton , Kusao Ian , Agsalda Melissa , Lynch James , Smith Lynette , Harrison Lauren , Morris Erin , Gross Thomas G. , Sanger Warren , Perkins Sherrie , Cairo Mitchell S. 
Published: April 2011

SummaryChildren/adolescents with mature B‐cell non‐Hodgkin lymphoma (B‐NHL) have an excellent prognosis but relapses still occur. While chromosomal aberrations and/or clonal immunoglobulin (Ig) gene rearrangements may indicate risk of failure, a more universal approach was developed to detect minimal disease (MD). Children/adolescents with intermediate‐risk B‐NHL were treated with French‐British‐American/Lymphome Malins de Burkitt 96 (FAB/LMB96) B4 modified chemotherapy and rituximab. Specimens from diagnosis, end of induction (EOI), and end of therapy (EOT) were assayed for MD. Initial specimens were screened for IGHV family usage with primer pools followed by individual primers to identify MD. Thirty‐two diagnostic/staging specimens screened positive with primer pools and unique IGHV family primers were identified. Two patients relapsed; first relapse (4 months from diagnosis) was MD‐positive at EOI, the second (36 months from diagnosis) was MD‐positive at EOT. At EOI, recurrent rates were similar between the MRD‐positive and MRD‐negative patients (P = 0·40). At EOT, only 13/32 patients had MRD data available with one relapse in the MRD‐positive group and no recurrences in the MRD‐negative group (P = 0·077). The study demonstrated molecular‐disseminated disease in which IgIGHV primer pools could be used to assess MD. This feasibility study supports future investigations to assess the validity and significance of MD screening in a larger cohort of patients with intermediate‐risk mature B‐NHL.
Motivational interviewing: a useful approach to improving cardiovascular health?
Authors: Thompson David R , Chair Sek Y , Chan Sally W , Astin Felicity , Davidson Patricia M , Ski Chantal F 
Published: April 2011

Aim.  To review and synthesise, systematically, the research findings regarding motivational interviewing and to inform education, research and practice in relation to cardiovascular health.Background.  Motivational interviewing is designed to engage ambivalent or resistant clients in the process of health behaviour change, and it has been widely used in different clinical conditions such as substance abuse, dietary adherence and smoking cessation. Motivational interviewing has also been proposed as a method for improving modifiable coronary heart disease risk factors of patients.Design.  Systematic review.Method.  Eligible studies published in 1999–2009 were identified from the following databases: CINAHL, Medline, PsycINFO, Cochrane Library, EBSCO, Web of Science, Embase and British Nursing Index. A manual search was conducted of bibliographies of the identified studies and relevant journals. Two researchers independently reviewed the studies.Results.  Four meta‐analyses, one systematic review and three literature reviews of motivational interviewing and five primary studies of motivational interviewing pertaining to cardiovascular health were identified. Despite a dearth of primary studies in cardiovascular health settings, there appears to be strong evidence that motivational interviewing is an effective approach focusing on eliciting the person’s intrinsic motivation for change of behaviour.Conclusion.  Motivational interviewing is an effective approach to changing behaviour. It offers promise in improving cardiovascular health status.Relevance to clinical practice.  This review indicates that motivational interviewing is a useful method to help nurses improve health behaviour in people with coronary risk factors.