bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiperspectival news revisited: Journalism and representative democracy
Authors: Gans Herbert J 
Published: January 2011

Thirty years ago, I published an ethnographic study of four mainstream national news organizations entitled Deciding What’s News (Gans, 2004 [1979]). In a final chapter devoted to news policy, I urged that the news become more multiperspectival, that national news depend less on top down news from high level government and other official and authoritative sources. Instead, the news media should do more reporting from and about other levels and sectors of society and how these see and interpret the country and its problems. The mainstream news media as well as the economy and polity in which the news media are embedded have changed over the past decades and the arrival of the internet offers a chance to add different kinds of news. These changes justify a revisit to multiperspectival news which focuses particularly on the journalists’ role in representative democracy.
Randomized trials of alcohol-use interventions with college students and their parents: lessons from the Transitions Project
Authors: Fernandez AC , Wood MD , Laforge R , Black JT 
Published: January 2011

Background Matriculation from high school to college is typified by an increase in alcohol use and related harm for many students. Therefore, this transition period is an ideal time for preventive interventions to target alcohol use and related problems. Purpose The purpose of this report is to describe the design and methods used in the Transitions Project, a randomized controlled trial of two interventions designed to prevent and reduce heavy episodic drinking and alcohol-related negative consequences among incoming college students. Methods This study used a 2 × 2 factorial design to investigate the effects of a two-session brief motivational intervention delivered to students and a handbook-based parent intervention. Interventions were administered to students and parents. Follow-up assessment took place at 10- and 22-months post-baseline. Results The Transitions Project successfully recruited and retained participants across a major transition period (i.e., entering college), administered and compared two distinct but complementary interventions, and collected and analyzed highly skewed data. The application of a factorial design and two-part latent growth curve modeling allowed us to examine main and interactive intervention effects in terms of both initiation and growth in heavy drinking and alcohol-related problems. Limitations While we conducted successful tests of our primary and secondary study hypotheses over a lengthy follow-up period, our study design did not permit full interpretation of null findings. We suggest that researchers carefully consider assessment timing, tests of assessment reactivity, and ensure objective tests of intervention efficacy when conducting clinical trials of motivational interventions. Conclusions The lessons we learned while conducting this trial have the potential to assist other researchers designing and conducting future preventive interventions targeting parents and college students. The data analytic procedures presented can also help guide trials that plan to analyze zero-inflated non-normal outcome data.
E47 regulates hematopoietic stem cell proliferation and energetics but not myeloid lineage restriction
Authors: Yang Qi , Esplin Brandt , Borghesi Lisa 
Published: January 2011

Abstract
The immune system is replenished by self-renewing hematopoietic stem cells (HSCs) that produce multipotent progenitors (MPPs) with little renewal capacity. E-proteins, the widely expressed basic helix-loop-helix transcription factors, contribute to HSC and MPP activity, but their specific functions remain undefined. Using quantitative in vivo and in vitro approaches, we show that E47 is dispensable for the short-term myeloid differentiation of HSCs but regulates their long-term capabilities. E47-deficient progenitors show competent myeloid production in short-term assays in vitro and in vivo. However, long-term myeloid and lymphoid differentiation is compromised because of a progressive loss of HSC self-renewal that is associated with diminished p21 expression and hyperproliferation. The activity of E47 is shown to be cell-intrinsic. Moreover, E47-deficient HSCs and MPPs have altered expression of genes associated with cellular energy metabolism, and the size of the MPP pool but not downstream lymphoid precursors in bone marrow or thymus is rescued in vivo by antioxidant. Together, these observations suggest a role for E47 in the tight control of HSC proliferation and energy metabolism, and demonstrate that E47 is not required for short-term myeloid differentiation.
KNG1 Ile581Thr and susceptibility to venous thrombosis
Authors: Morange Pierre-Emmanuel , Oudot-Mellakh Tiphaine , Cohen William , Germain Marine , Saut Noémie , Antoni Guillemette , Alessi Marie-Christine , Bertrand Marion , Dupuy Anne-Marie , Letenneur Luc , Lathrop Mark , Lopez Lorna M. , Lambert Jean-Charles , Emmerich Joseph , Amouyel Philippe , Trégouët David-Alexandre 
Published: January 2011

Abstract
Three single nucleotide polymorphisms (SNPs) were recently found to be associated with activated partial thromboplastin time (aPTT). Because shortened aPTT levels have been observed in patients experiencing venous thrombosis (VT), we investigated the effects of these 3 aPTT-associated SNPs, rs2731672, rs9898, and rs710446, on the risk of VT in a sample of 1110 healthy patients and 1542 patients with VT. Among the 3 tested SNPs, only rs710446 was associated with VT risk; the rs710446-C allele was associated with an increased risk of VT (odds ratio 1.196, 95% confidence interval 1.071-1.336, P = .0012). This association also was observed in an independent sample of 590 controls and 596 patients (odds ratio 1.171, 95% confidence interval 0.889-1.541, P = .059). We also confirmed that the rs710446-C allele was associated with decreased aPTT levels, making this nonsynonymous Ile581Thr variant a new genetic risk factor for VT.
ASPDock: protein-protein docking algorithm using atomic solvation parameters model
Authors: Li Lin , Guo Dachuan , Huang Yangyu , Liu Shiyong , Xiao Yi 
Published: January 2011

Abstract

Background
Atomic Solvation Parameters (ASP) model has been proven to be a very successful method of calculating the binding free energy of protein complexes. This suggests that incorporating it into docking algorithms should improve the accuracy of prediction. In this paper we propose an FFT-based algorithm to calculate ASP scores of protein complexes and develop an ASP-based protein-protein docking method (ASPDock).

Results
The ASPDock is first tested on the 21 complexes whose binding free energies have been determined experimentally. The results show that the calculated ASP scores have stronger correlation (r ≈ 0.69) with the binding free energies than the pure shape complementarity scores (r ≈ 0.48). The ASPDock is further tested on a large dataset, the benchmark 3.0, which contain 124 complexes and also shows better performance than pure shape complementarity method in docking prediction. Comparisons with other state-of-the-art docking algorithms showed that ASP score indeed gives higher success rate than the pure shape complementarity score of FTDock but lower success rate than Zdock3.0. We also developed a softly restricting method to add the information of predicted binding sites into our docking algorithm. The ASP-based docking method performed well in CAPRI rounds 18 and 19.

Conclusions
ASP may be more accurate and physical than the pure shape complementarity in describing the feature of protein docking.
Conservation genetics and phylogeography of endangered and endemic shrub Tetraena mongolica (Zygophyllaceae) in Inner Mongolia, China
Authors: Ge Xue-Jun , Hwang Chi-Chuan , Liu Zin-Huang , Huang Chi-Chun , Huang Wei-Hsiang , Hung Kuo-Hsiang , Wang Wei-Kuang , Chiang Tzen-Yuh 
Published: January 2011

Abstract

Background

Tetraena mongolica (Zygophyllaceae), an endangered endemic species in western Inner Mongolia, China. For endemic species with a limited geographical range and declining populations, historical patterns of demography and hierarchical genetic structure are important for determining population structure, and also provide information for developing effective and sustainable management plans. In this study, we assess genetic variation, population structure, and phylogeography of T. mongolica from eight populations. Furthermore, we evaluate the conservation and management units to provide the information for conservation.

Results
Sequence variation and spatial apportionment of the atp B-rbc L noncoding spacer region of the chloroplast DNA were used to reconstruct the phylogeography of T. mongolica. A total of 880 bp was sequenced from eight extant populations throughout the whole range of its distribution. At the cpDNA locus, high levels of genetic differentiation among populations and low levels of genetic variation within populations were detected, indicating that most seed dispersal was restricted within populations.

Conclusions
Demographic fluctuations, which led to random losses of genetic polymorphisms from populations, due to frequent flooding of the Yellow River and human disturbance were indicated by the analysis of BEAST skyline plot. Nested clade analysis revealed that restricted gene flow with isolation by distance plus occasional long distance dispersal is the main evolutionary factor affecting the phylogeography and population structure of T. mongolica. For setting a conservation management plan, each population of T. mongolica should be recognized as a conservation unit.
Genome-wide patterns of promoter sharing and co-expression in bovine skeletal muscle
Authors: Gu Quan , Nagaraj Shivashankar H , Hudson Nicholas J , Dalrymple Brian P , Reverter Antonio 
Published: January 2011

Abstract

Background
Gene regulation by transcription factors (TF) is species, tissue and time specific. To better understand how the genetic code controls gene expression in bovine muscle we associated gene expression data from developing Longissimus thoracis et lumborum skeletal muscle with bovine promoter sequence information.

Results
We created a highly conserved genome-wide promoter landscape comprising 87,408 interactions relating 333 TFs with their 9,242 predicted target genes (TGs). We discovered that the complete set of predicted TGs share an average of 2.75 predicted TF binding sites (TFBSs) and that the average co-expression between a TF and its predicted TGs is higher than the average co-expression between the same TF and all genes. Conversely, pairs of TFs sharing predicted TGs showed a co-expression correlation higher that pairs of TFs not sharing TGs. Finally, we exploited the co-occurrence of predicted TFBS in the context of muscle-derived functionally-coherent modules including cell cycle, mitochondria, immune system, fat metabolism, muscle/glycolysis, and ribosome. Our findings enabled us to reverse engineer a regulatory network of core processes, and correctly identified the involvement of E2F1, GATA2 and NFKB1 in the regulation of cell cycle, fat, and muscle/glycolysis, respectively.

Conclusion
The pivotal implication of our research is two-fold: (1) there exists a robust genome-wide expression signal between TFs and their predicted TGs in cattle muscle consistent with the extent of promoter sharing; and (2) this signal can be exploited to recover the cellular mechanisms underpinning transcription regulation of muscle structure and development in bovine. Our study represents the first genome-wide report linking tissue specific co-expression to co-regulation in a non-model vertebrate.
TNFA deletion alters apoptosis as well as caspase 3 and 4 expression during otitis media
Authors: Ebmeyer Joerg , Leichtle Anke , Hernandez Michelle , Ebmeyer Umay , Husseman Jacob , Pak Kwang , Sudhoff Holger , Broide David , Wasserman Stephen I , Ryan Allen F 
Published: January 2011

Abstract

Background
Tumor necrosis factor (TNFA) is the canonical member of the TNF superfamily, which plays a major role in both inflammation and apoptosis. To evaluate the role of TNFs in otitis media (OM), the most common disease of childhood, we evaluated middle ear (ME) expression of genes encoding the TNF and TNF receptor superfamilies during bacterial OM in the mouse, characterized OM in TNFA-deficient mice, and assessed apoptosis during OM in normal versus TNF-deficient MEs.

Results
TNFs and TNF receptors were broadly regulated during OM, with TNFA showing the highest level of up-regulation. TNF deficient mice exhibited mucosal hyperplasia even in the absence of infection and exuberant growth of the mucosa during OM, including the formation of mucosal polyps. Mucosal recovery during OM was also delayed, in parallel with a delay in mucosal apoptosis and reduced caspase gene expression.

Conclusions
The TNF and TNF receptor superfamilies mediate both inflammation and apoptosis during OM. TNF appears to be critical for the maintenance of mucosal architecture in both the normal and infected ME, since excessive accumulation of mucosal tissue is seen in TNFA-/- MEs both before and after bacterial inoculation of the ME. TNFA is also required for appropriate regulation of caspase genes.
Bimanual training in stroke: How do coupling and symmetry-breaking matter?
Authors: Sleimen-Malkoun Rita , Temprado Jean-Jacques , Thefenne Laurent , Berton Eric 
Published: January 2011

Abstract

Background
The dramatic consequences of stroke on patient autonomy in daily living activities urged the need for new reliable therapeutic strategies. Recently, bimanual training has emerged as a promising tool to improve the functional recovery of upper-limbs in stroke patients. However, who could benefit from bimanual therapy and how it could be used as a part of a more complete rehabilitation protocol remain largely unknown. A possible reason explaining this situation is that coupling and symmetry-breaking mechanisms, two fundamental principles governing bimanual behaviour, have been largely under-explored in both research and rehabilitation in stroke.

Discussion
Bimanual coordination emerges as an active, task-specific assembling process where the limbs are constrained to act as a single unit by virtue of mutual coupling. Consequently, exploring, assessing, re-establishing and exploiting functional bimanual synergies following stroke, require moving beyond the classical characterization of performance of each limb in separate and isolated fashion, to study coupling signatures at both neural and behavioural levels. Grounded on the conceptual framework of the dynamic system approach to bimanual coordination, we debated on two main assumptions: 1) stroke-induced impairment of bimanual coordination might be anticipated/understood by comparing, in join protocols, changes in coupling strength and asymmetry of bimanual discrete movements observed in healthy people and those observed in stroke; 2) understanding/predicting behavioural manifestations of decrease in bimanual coupling strength and/or increase in interlimb asymmetry might constitute an operational prerequisite to adapt therapy and better target training at the specific needs of each patient. We believe that these statements draw new directions for experimental and clinical studies and contribute in promoting bimanual training as an efficient and adequate tool to facilitate the paretic upper-limb recovery and to restore spontaneous bimanual synergies.

Summary
Since bimanual control deficits have scarcely been systematically investigated, the eventual benefits of bimanual coordination practice in stroke rehabilitation remains poorly understood. In the present paper we argued that a better understanding of coupling and symmetry-breaking mechanisms in both the undamaged and stroke-lesioned neuro-behavioral system should provide a better understanding of stroke-related alterations of bimanual synergies, and help clinicians to adapt therapy in order to maximize rehabilitation benefits.
Identification and Regulation of c-Myb Target Genes in MCF-7 Cells
Authors: Quintana Anita M , Liu Fan , O'Rourke John P , Ness Scott A 
Published: January 2011

Abstract

Background
The c-Myb transcription factor regulates differentiation and proliferation in hematopoietic cells, stem cells and epithelial cells. Although oncogenic versions of c-Myb were first associated with leukemias, over expression or rearrangement of the c-myb gene is common in several types of solid tumors, including breast cancers. Expression of the c-myb gene in human breast cancer cells is dependent on estrogen stimulation, but little is known about the activities of the c-Myb protein or what genes it regulates in estrogen-stimulated cells.

Methods
We used chromatin immunoprecipitation coupled with whole genome promoter tiling microarrays to identify endogenous c-Myb target genes in human MCF-7 breast cancer cells and characterized the activity of c-Myb at a panel of target genes during different stages of estrogen deprivation and stimulation.

Results
By using different antibodies and different growth conditions, the c-Myb protein was found associated with over 10,000 promoters in MCF-7 cells, including many genes that encode cell cycle regulators or transcription factors and more than 60 genes that encode microRNAs. Several previously identified c-Myb target genes were identified, including CCNB1, MYC and CXCR4 and novel targets such as JUN, KLF4, NANOG and SND1. By studying a panel of these targets to validate the results, we found that estradiol stimulation triggered the association of c-Myb with promoters and that association correlated with increased target gene expression. We studied one target gene, CXCR4, in detail, showing that c-Myb associated with the CXCR4 gene promoter and activated a CXCR4 reporter gene in transfection assays.

Conclusions
Our results show that c-Myb associates with a surprisingly large number of promoters in human cells. The results also suggest that estradiol stimulation leads to large-scale, genome-wide changes in c-Myb activity and subsequent changes in gene expression in human breast cancer cells.
Differential molecular information of maurotoxin peptide recognizing IKCa and Kv1.2 channels explored by computational simulation
Authors: Yi Hong , Qiu Su , Wu Yingliang , Li Wenxin , Wang Baoshan 
Published: January 2011

Abstract

Background
Scorpion toxins are invaluable tools for ion channel research and are potential drugs for human channelopathies. However, it is still an open task to determine the molecular basis underlying the diverse interactions between toxin peptides and ion channels. The inhibitory peptide Maurotoxin (MTX) recognized the distantly related IKCa and Kv1.2 channel with approximately the same potency and using the same functional residues, their differential binding mechanism remain elusive. In this study, we applied computational methods to explore the differential binding modes of MTX to Kv1.2 and IKCa channels, which would help to understand the diversity of channel-toxin interactions and accelerate the toxin-based drug design.

Results
A reasonably stable MTX-IKCa complex was obtained by combining various computational methods and by in-depth comparison with the previous model of the MTX-Kv1.2 complex. Similarly, MTX adopted the β-sheet structure as the interacting surface for binding both channels, with Lys23 occluding the pore. In contrast, the other critical residues Lys27, Lys30, and Tyr32 of MTX adopted distinct interactions when associating with the IKCa channel. In addition, the residues Gln229, Ala230, Ala233, and Thr234 on the IKCa channel turret formed polar and non-polar interactions with MTX, whereas the turret of Kv1.2 was almost not involved in recognizing MTX. In all, the pairs of interacting residues on MTX and the IKCa channel of the bound complex indicated that electrostatic and Van der Waal interactions contributed equally to the formation of a stable MTX-IKCa complex, in contrast to the MTX-Kv1.2 binding that is dominantly mediated by electrostatic forces.

Conclusions
Despite sharing similar pharmacological profiles toward both IKCa and Kv1.2 channels, MTX adopted totally diverging modes in the two association processes. All the molecular information unveiled here could not only offer a better understanding about the structural differences between the IKCa and Kv1.2 channels, but also provide novel structural clews that will help in the designing of more selective molecular probes to discriminate between these two channels.
Socio-demographic factors and processes associated with stages of change for smoking cessation in pregnant versus non-pregnant women
Authors: Buja Alessandra , Guarnieri Emanuela , Forza Giovanni , Tognazzo Federica , Sandonà Paolo , Zampieron Alessandra 
Published: January 2011

Abstract

Background
The tobacco control community assumes that the most effective interventions are personalized. Nevertheless, little attention is paid to understanding differences between pregnant and non-pregnant European women in terms of the social factors that influence tobacco use and the processes of change used to quit smoking.

Methods
The study consecutively enrolled 177 pregnant women who acknowledged smoking the year before pregnancy and 177 non-pregnant women who acknowledged smoking the year before their clinic visit for a Pap test.

Results
With respect to socio-demographic factors, the stages of change in pregnant women were associated with level of education, marital status, and the presence of roommates, partners and friends who smoke. In pregnant women, there was no statistically significant difference in the processes used to stop smoking among the stages of change. Furthermore, behavioral processes were higher in non-pregnant women than in pregnant women, and the difference was statistically significant in the advanced stages of behavioral change. Both pregnant and non-pregnant women showed higher levels of acceptance towards smoking in the earlier stages of change, but the acceptability of smoking in the pre-contemplative stage was higher in non-pregnant women. Greater craving was detected in non-pregnant vs. pregnant women at all stages and reached a statistically significant level at the pre-contemplative stage.

Conclusion
Pregnancy is a favorable time to stop smoking since pregnant women are more likely to be in an advanced stage of behavioral change. Pregnant and non-pregnant women are distinct populations in the types and processes of change involved in smoking cessation. The intervention programs to promote smoking cessation and prevent relapses will need to take these differences into account.