bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hominid evolution: genetics versus memetics
Authors: Carter Brandon 
Published: September 2011

AbstractThe last few million years on planet Earth have witnessed two remarkable phases of hominid development, starting with a phase of biological evolution characterized by rather rapid increase of the size of the brain. This has been followed by a phase of even more rapid technological evolution and concomitant expansion of the size of the population that began when our own particular ‘sapiens’ species emerged, just a few hundred thousand years ago. The present investigation exploits the analogy between the neo-Darwinian genetic evolution mechanism governing the first phase, and the memetic evolution mechanism governing the second phase. From the outset of the latter until very recently – about the year 2000 – the growth of the global populationNwas roughly governed by an equation of the form dN/Ndt=N/T*, in whichT* is a coefficient introduced (in 1960) by von Foerster, who evaluated it empirically as about 200 000 million years. It is shown here how the value of this hitherto mysterious timescale governing the memetic phase is explicable in terms of what happened in the preceding genetic phase. The outcome is that the order of magnitude of the Foerster timescale can be accounted for as the product of the relevant (human) generation timescale, about 20 years, with the number of bits of information in the genome, of the order of 10 000 million. Whereas the origin of our ‘homo’ genus may well have involved an evolutionary hard step, it transpires that the emergence of our particular ‘sapiens’ species was rather an automatic process.
OneStop:JWS Online's access point to SBML,SBGN and MIRIAM compliant annotation
Authors: Snoep Jacky , Du Preez Franco , Owen Stuart , Wolstencroft Katherine , Krebs Olga , Müller Wolfgang , Goble Carole 
Published: September 2011

AbstractWe have developed an online model constructor and validator called OneStop, which is compliant with SBGN, SBML and MIRIAM standards. Key features of OneStop are: 1) a human readable input form (in addition to SBML upload and saving); 2) live visualization (SBGN graphics) of the reaction network during the construction phase; and 3) online access from any machine with a compatible browser. Sophisticated error feedback simplifies the debugging process during model construction significantly and guides the efforts of new users in a step by step fashion. OneStop is seamlessly integrated with the JWS Online model repository and simulator and also facilitates the importation of models from the BioModels database. In addition, OneStop is part of the SysMO-SEEK platform, which is used for data and model management in the Pan-European SysMO consortium.
Respiration characteristics of mitochondria in parental and giant transformed cells of the murine Nemeth—Kellner lymphoma
Authors: Horbay Rostyslav O. , Manko Bohdan O. , Manko Volodymyr V. , Lootsik Maxim D. , Stoika Rostyslav S. 
Published: September 2011

AbstractRespiration characteristics of mitochondria of the parental and giant cells of murine NK/Ly (Nemeth—Kellner lymphoma) were studied. The giant cell‐enriched ascites were obtained by serial intraperitoneal injections of vinblastine in tumour‐bearing mice. Ascites containing >70% giant cells were used. Their diameter of was over 17 μm (∼2800 μm3), while the diameter of the parental cells was 12.7 μm (1100 μm3). The respiration rate of mitochondria in situ was measured by oxygen consumption in intact and digitonin‐permeabilized NK/Ly cells. Endogenous respiration of intact giant NK/Ly cells was three times higher compared to the parental ones, roughly in agreement with the volume change. The giant NK/Ly cells were far more resistant to permeabilization with digitonin than the parental cells, as shown by Trypan Blue and LDH (lactate dehydrogenase) release tests. After digitonin permeabilization, oxygen consumption was reduced to a minimal level (0.06 ng atom O/(s × 106 cells) in both types of cells. Addition of α‐ketoglutarate or succinate to the incubation medium increased oxygen consumption in the parental cells by 46 and 164% respectively. In the giant NK/Ly cells, the corresponding increases were 164 and 276%. Addition of ADP to α‐ketoglutarate‐ or succinate‐supplemented medium further stimulated oxygen consumption of the permeabilized NK/Ly cells; however, the effect of ADP was more pronounced in the giant cells. In addition, indices of respiratory control were significantly higher in the giant cells. Oligomycin suppressed considerably the respiration of the intact giant cells but had a much weaker effect on parental cells. Thus, giant NK/Ly cells possess much higher respiration rates and show tighter coupling between the respiration and oxidative phosphorylation compared with parental cells.
Crystal structure of the hybrid state of ribosome in complex with the guanosine triphosphatase release factor 3
Authors: Jin Hong , Kelley Ann C. , Ramakrishnan V. 
Published: September 2011

Protein release factor 3 (RF3), a guanosine triphosphatase, binds to ribosome after release of the nascent peptide and promotes dissociation of the class I release factors during the termination of protein synthesis. Here we present the crystal structure of the 70S ribosome with RF3 in the presence of a nonhydrolyzable GTP analogue, guanosine 5′-β,γ-methylenetriphosphate (GDPCP), refined to 3.8 Å resolution. The structure shows that the subunits of the ribosome are rotated relative to each other compared to the canonical state, resulting in a P/E hybrid state for the transfer RNA. The substantial conformational rearrangements in the complex are described and suggest how RF3, by stabilizing the hybrid state of the ribosome, facilitates the dissociation of class I release factors.
The Development of Social Identity through Dramatherapy
Authors: Jennings Sue 
Published: September 2011

This paper is concerned with the process of structured application of dramatherapy as a means of discovering, developing and re-learning of social identity which as such can be integrated into a clinical programme of therapy, re-habilitation or re-education. In order for this to be effective we need to understand the nature of rôle and its relationship to the psyche, especially the ego. Only through the realisation that man both thinks and feels in dramatic form can we appreciate the implications of dramatherapy application within the clinical framework.
A New Beginning – A Dramatherapy Group for Participants with Co-Occurring Mental Illness and Substance Abuse in a Mental Health Setting
Authors: Jaaniste Joanna 
Published: September 2011

Rehabilitation for people with dual diagnosis (co-existing mental illness and substance dependence) has existed in many forms over the past thirty years and has become more urgently needed over time. Treatment for this population inevitably requires a team effort (Schwartz & Lehman, 1998). These people are difficult to engage in treatment and it takes time to unravel the interacting effects of substance abuse and their mental illness. Social relationships may also be problematic, particularly once the person has decided to discontinue drug or alcohol abuse. Often such clients find it easier to communicate socially with people who have similar problems (Hatfield, 1993). Improvements in self-esteem and reduced intake of drugs and alcohol are rarely monitored in the one community psychiatric facility, as in this study. The method of treatment in this case was to run a small group for participants over an extended period with support from multidisciplinary teams, using a Dutch model for drug and alcohol rehabilitation. By targeting psychiatric relapse prevention and people's life stories, using a biographical developmental framework and dramatherapy interventions, the intention was to achieve outcomes of higher self esteem and reduced intake of recreational drugs. In fact the pre and post measures chosen did not show significant variance. For all participants, including those who were already abstinent, changes in lifestyle and achievement of life goals were sought. As a result, there was reported enjoyment of mutual support, sharing and understanding of individual life stories, together with strategies to increase resilience. Further research is needed to identify how best to measure outcomes. Hatfield, A. (1993) ‘Dual Diagnosis and Mental Illness’, Journal of National Alliance for the Mentally Ill, (Online), retrieved 11.1.08 Schwartz, R. & Lehman, A. (1995) in ‘Overview of Treatment Principles’ in Lehman, A. & Dixon, L. (eds.) Double Jeopardy, Harwood Academic Publishers, Chur, Switzerland, p.77
Reconstructing the 3D etch rate distribution of silicon in anisotropic etchants using data from vicinal {1 0 0}, {1 1 0} and {1 1 1} surfaces
Authors: Gosálvez M A , Pal Prem , Sato K 
Published: September 2011

We consider the reconstruction of the complete three-dimensional distribution of etch rates for crystalline silicon in a total of six markedly different etching conditions. The procedure is based on data points that, on the unit sphere, are located along the high-symmetry lines connecting the three main surface orientations Si{1 1 1}, Si{1 1 0} and Si{1 0 0}. Novel, compact formulas are presented in order to perform trilinear, triquadratic and higher order interpolations in h
k
l space. A wide variety of surface triangulations and tessellations are proposed in order to apply the trilinear and higher order formulas. A statistical analysis concludes that trilinear interpolation over three particular triangulations, and triquartic interpolation over a specific tessellation provide the best reconstructions for the six considered etching conditions. By combining the three triangulations and tessellation using a weighted average, the mean error is found to be less than 13% for reconstructions involving noisy experimental etch rates, while it decreases to 2–5% for less unruly distributions. The results strongly indicate that the complete orientation dependence of the etch rate can be derived from an alternative, more feasible experiment than the traditional hemispherical specimen.
Reconstructing transcription factor activities in hierarchical transcription network motifs
Authors: Ocone Andrea , Sanguinetti Guido 
Published: September 2011

Abstract
Motivation: A knowledge of the dynamics of transcription factors is fundamental to understand the transcriptional regulation mechanism. Nowadays, an experimental measure of transcription factor activities in vivo represents a challenge. Several methods have been developed to infer these activities from easily measurable quantities such as mRNA expression of target genes. A limitation of these methods is represented by the fact that they rely on very simple single-layer structures, typically consisting of one or more transcription factors regulating a number of target genes.
Results: We present a novel statistical inference methodology to reverse engineer the dynamics of transcription factors in hierarchical network motifs such as feed-forward loops. The approach we present is based on a continuous time representation of the system where the high-level master transcription factor is represented as a two state Markov jump process driving a system of differential equations. We solve the inference problem using an efficient variational approach and demonstrate our method on simulated data and two real datasets. The results on real data show that the predictions of our approach can capture biological behaviours in a more effective way than single-layer models of transcription, and can lead to novel biological insights.
Availability: http://homepages.inf.ed.ac.uk/gsanguin/software.html
Contact: g.sanguinetti@ed.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Comparing bioassay response and similarity ensemble approaches to probing protein pharmacology
Authors: Chen Bin , McConnell Kevin J. , Wale Nikil , Wild David J. , Gifford Eric M. 
Published: September 2011

Abstract
Motivation: Networks to predict protein pharmacology can be created using ligand similarity or using known bioassay response profiles of ligands. Recent publications indicate that similarity methods can be highly accurate, but it has been unclear how similarity methods compare to methods that use bioassay response data directly.
Results: We created protein networks based on ligand similarity (Similarity Ensemble Approach or SEA) and ligand bioassay response-data (BARD) using 155 Pfizer internal BioPrint assays. Both SEA and BARD successfully cluster together proteins with known relationships, and predict some non-obvious relationships. Although the approaches assess target relations from different perspectives, their networks overlap considerably (40% overlap of the top 2% of correlated edges). They can thus be considered as comparable methods, with a distinct advantage of the similarity methods that they only require simple computations (similarity of compound) as opposed to extensive experimental data.
Contacts: djwild@indiana.edu; eric.gifford@pfizer.com
Supplementary Information: Supplementary data are available at Bioinformatics online.
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
Authors: Li Heng 
Published: September 2011

Abstract
Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample low-coverage sequencing or somatic mutation discovery). These applications press for the development of new methods for analyzing sequence data with uncertainty.
Results: We present a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation. On real data, we demonstrate that our method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping. We also highlight the necessity of using symmetric datasets for finding somatic mutations and confirm that for discovering rare events, mismapping is frequently the leading source of errors.
Availability: http://samtools.sourceforge.net
Contact: hengli@broadinstitute.org
Finding stable local optimal RNA secondary structures
Authors: Li Yuan , Zhang Shaojie 
Published: September 2011

Abstract
Motivation: Many RNAs, such as riboswitches, can fold into multiple alternate structures and perform different biological functions. These biologically functional structures usually have low free energies in their local energy landscapes and are very stable such that they cannot easily jump out of the current states and fold into other stable conformations. The conformational space of feasible RNA secondary structures is prohibitively large, and accurate prediction of functional structure conformations is challenging. Because the stability of an RNA secondary structure is determined predominantly by energetically favorable helical regions (stacks), we propose to use configurations of putative stacks to represent RNA secondary structures. By considering a reduced conformational space of local optimal stack configurations instead of all feasible RNA structures, we first present an algorithm for enumerating all possible local optimal stack configurations. In addition, we present a fast heuristic algorithm for approximating energy barriers encountered during folding pathways between each pair of local optimal stack configurations and finding all the stable local optimal structures.
Results: Benchmark tests have been conducted on several RNA riboswitches, whose alternate secondary structures have been experimentally verified. The benchmark results show that our method can successfully predict the native ‘on’ and ‘off’ secondary structures, and better rank them compared with other state-of-art approaches.
Availability: The software is freely available and can be downloaded at http://genome.ucf.edu/RNASLOpt.
Contact: shzhang@eecs.ucf.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
An empirical comparison of several recent epistatic interaction detection methods
Authors: Wang Yue , Liu Guimei , Feng Mengling , Wong Limsoon 
Published: September 2011

AbstractMotivation: Many new methods have recently been proposed for detecting epistatic interactions in GWAS data. There is, however, no in-depth independent comparison of these methods yet.Results: Five recent methods—TEAM, BOOST, SNPHarvester, SNPRuler and Screen and Clean (SC)—are evaluated here in terms of power, type-1 error rate, scalability and completeness. In terms of power, TEAM performs best on data with main effect and BOOST performs best on data without main effect. In terms of type-1 error rate, TEAM and BOOST have higher type-1 error rates than SNPRuler and SNPHarvester. SC does not control type-1 error rate well. In terms of scalability, we tested the five methods using a dataset with 100 000 SNPs on a 64 bit Ubuntu system, with Intel (R) Xeon(R) CPU 2.66 GHz, 16 GB memory. TEAM takes ~36 days to finish and SNPRuler reports heap allocation problems. BOOST scales up to 100 000 SNPs and the cost is much lower than that of TEAM. SC and SNPHarvester are the most scalable. In terms of completeness, we study how frequently the pruning techniques employed by these methods incorrectly prune away the most significant epistatic interactions. We find that, on average, 20% of datasets without main effect and 60% of datasets with main effect are pruned incorrectly by BOOST, SNPRuler and SNPHarvester.Availability: The software for the five methods tested are available from the URLs below. TEAM: http://csbio.unc.edu/epistasis/download.php BOOST: http://ihome.ust.hk/~eeyang/papers.html. SNPHarvester: http://bioinformatics.ust.hk/SNPHarvester.html. SNPRuler: http://bioinformatics.ust.hk/SNPRuler.zip. Screen and Clean: http://wpicr.wpic.pitt.edu/WPICCompGen/.Contact: wangyue@nus.edu.sg
Impact of high‐risk classification by FISH: an Eastern Cooperative Oncology Group (ECOG) study E4A03
Authors: Jacobus Susanna J. , Kumar Shaji , Uno Hajime , Van Wier Scott A. , Ahmann Greg J. , Henderson Kimberly J. , Callander Natalie S. , Williams Michael E. , Siegel David S. , Greipp Philip R. , Rajkumar S. Vincent , Fonseca Rafael 
Published: September 2011

SummaryLenalidomide with dexamethasone is a standard induction treatment regimen for newly diagnosed myeloma (although a Federal Drug Administration indication is still absent). In the context of the Phase 3 clinical trial E4A03 (lenalidomide plus dexamethasone in low or high doses), we queried whether a fluorescence in situ hybridization (FISH)‐based genetic classification into high risk (HR) and standard risk (SR) multiple myeloma (MM) would remain clinically significant. Of 445 E4A03 patients, 126 had FISH analysis; 21 were classified HR with t(4;14), t(14;16), or 17p13 deletions. Median survival follow‐up approached 3 years. Patients with FISH data tended to be younger and healthier compared to the rest of the study population and, consequently, had superior overall survival (OS) results. Within the FISH cohort, shorter OS in the HR versus SR group (P = 0·004) corresponded to a hazard ratio of 3·48 [95% confidence interval: (1·42–8·53)], an effect also observed in multivariate analysis. Two‐year OS rates were 91% for SR MM and 76% for HR MM. There was also evidence of interaction between risk status and treatment (P = 0·026). HR patients were less likely to attain good partial response (SR 46% and HR 30%, Odds Ratio = 2·0 [0·7–5·6]), but overall response rates were not different. FISH‐based risk classification retained prognostic significance in patients receiving lenalidomide‐based induction.
A glycoengineered anti‐CD19 antibody with potent antibody‐dependent cellular cytotoxicity activity in vitro and lymphoma growth inhibition in vivo
Authors: Ward Elizabeth , Mittereder Nanette , Kuta Ellen , Sims Gary P. , Bowen Michael A. , Dall’Acqua William , Tedder Thomas , Kiener Peter , Coyle Anthony J. , Wu Herren , Jallal Bahija , Herbst Ronald 
Published: September 2011

SummaryHuman cluster of differentiation (CD) antigen 19 is a B cell‐specific surface antigen and an attractive target for therapeutic monoclonal antibody (mAb) approaches to treat malignancies of B cell origin. MEDI‐551 is an affinity‐optimized and afucosylated CD19 mAb with enhanced antibody‐dependent cellular cytotoxicity (ADCC). The results from in vitro ADCC assays with Natural Killer cells as effector cells, demonstrate that MEDI‐551 is effective at lower mAb doses than rituximab with multiple cell lines as well as primary chronic lymphocytic leukaemia and acute lymphoblastic leukaemia samples. Targeting CD19 with MEDI‐551 was also effective in several severe combined immunodeficiency lymphoma models. Furthermore, the combination of MEDI‐551 with rituximab resulted in prolonged suppression of tumour growth, demonstrating that therapeutic mAbs with overlapping effector function can be combined for greater tumour growth inhibition. Together, the data demonstrate that MEDI‐551 has potent antitumour activity in preclinical models of B cell malignancies. The results also suggest that the combination of the ADCC‐enhanced CD19 mAb with an anti‐CD20 mAb could be a novel approach for the treatment of B cell lymphomas.
The role of culture in theories of the intergenerational transmission of violence
Authors: Kim Kihyun 
Published: September 2011

ABSTRACTThe intergenerational transmission of violence has been one of the most rigorously researched hypotheses in violence research in recent decades. A number of previous studies have provided evidence supporting this hypothesis, and there has been a growing body of literature investigating its mechanism. However, the role of culture in the intergenerational transmission of violence has not received much research attention, and thus, it remains largely unknown. To suggest a better theoretical basis for understanding the role of culture in the transmission mechanism, the present paper examines three critical theories that address the intergenerational phenomenon: Dodge's social information processing theory, Nisbett's cultural cognitive theory and Turiel's social‐cognitive domain theory. The paper provides a review of the basic assumptions and core concepts of each theory and identifies the potential contributions and gaps of each theory. The three theories present different accounts of the ontogenetic origins of ideas about violence and convey different portraits of the intergenerational mechanism. However, these theories also show that they are highly likely to be related to one another and that they can help close one another's gaps. This paper suggests that a unified framework that can merge the personal and cultural factors of causation is necessary to better capture the dynamic interplay among culture, experiences with violence and the actual enactment of violent behaviours.