bluuebunny/crossref_metadata_2025 huggingface dataset:
The Use of Hymnic Elements in Preaching
Authors: Achtemeier Elizabeth
Published: October 2011

Understanding the form and content of the Bible's hymns allows the sermon to share their principal characteristic: praise to the honor and glory of God.
Psalm 23: Song of Passage
Authors: Lundbom Jack R.
Published: October 2011

Psalm 23 speaks to the Christian about life's final passage; but it also speaks about other passages, passages which can be negotiated through the whole of life because help comes from the Divine Shepherd.
Jesus and the Critics
Authors: Keller Joseph
Published: October 2011

A narrative pattern in which confrontational passages are followed by parables metaphorically clarifying the power of faith, and by miracles which show faith's power in act, enables Mark to show Jesus meeting opponents' objections by requiring a yet greater degree both of love and of faith than they.
Parabole and Parrhesia in Mark
Authors: Bishop Jonathan
Published: October 2011

Careful attention to the regular pattern of contrasting parable with explanation, mystery with interpretation, and crowd with disciples allows the careful reader to gain new insight into the scope and purpose of Mark's enterprise as a whole.
Wealthy Women at Ephesus
Authors: Padgett Alan
Published: October 2011

Careful attention to the social situations implied in the passages of First Timothy about women indicates there is nothing there that would limit the role of women in the church.
Polity of the Covenant People
Authors: McBride S. Dean
Published: October 2011

A work of extraordinary literary coherence and political sophistication, Deuteronomy's impact continues in our world through its influence on modern western constitutionalism.
Language for God and Feminist Language
Authors: Frye Roland Mushat
Published: October 2011

The assumption that we can exchange certain biblical figures for others that, for whatever reason, may seem preferable is not only linguistically and literarily wrong, but also leads to conclusions that are false both historically and theologically.
The Reformation and the Ten Commandments
Authors: Steinmetz David C.
Published: October 2011

Disagreement in the sixteenth century on the meaning of the First Commandment prompted dissension over such related issues as the nature of the Lord's Supper, the authority of the Old Testament for the church and the pace of ecclesiastical reform—issues that are still in dispute.
Images of Paul in the New Testament
Authors: Keck Leander E.
Published: October 2011

Standing literally at the center of the New Testament, the Paul who emerges from the letters and Acts is a richly diverse figure, about whom no easy conclusions can be reached concerning his historical shape or theological legacy.
Holding Your Own Against God!
Authors: Holmgren Fredrick C.
Published: October 2011

The community of faith finds blessing for itself when it gives due weight to the Old Testament insight that nearness to God is found by those who, like Job and Jacob, assertively engage the Covenant Partner.
Belonging to Christ
Authors: Furnish Victor Paul
Published: October 2011

Paul's ethical reflection in this letter to Corinthian Christians consists in an interesting combination of reminders and appeals reminders of the Christ to whom they belong and appeals that they allow their lives, individually and corporately, to be ruled by their new Lord
The Psalms as Instruction
Authors: McCann J. Clinton
Published: October 2011

Although the Psalms may have originated primarily within the liturgical life of ancient Israel and Judah, they were nonetheless appropriated, preserved, and transmitted as instruction for the faithful.
Theology and the Book of Psalms
Authors: Sheppard Gerald T.
Published: October 2011

While the Psalter imparts instruction to the faithful on the ways of God, it also teaches them to pray. Simply put, prayer is the effort to ask something of God and to anticipate a divine response in word, deed, or presence.
Toward a Narrative-Critical Understanding of Luke
Authors: Tannehill Robert C.
Published: October 2011

Tabitha and Cornelius, imaginary persons based on characters in Acts, occupy two different places in the first-century Mediterranean world. In hearing Luke's gospel-story, how would each construe the figure of Jesus? The social location of each would play a crucial role as each "builds" the character of Jesus in dialogue with Luke's story
The “Third Quest” and the Apostolic Faith
Authors: Boring M. Eugene
Published: October 2011

Whether or not one is justified in speaking of a “third quest of the historical Jesus” is open to debate. Any historical quest for Jesus, however, involves three stages of research: (a) establishing a data base of authentic materials; (b) reconstructing a plausible picture of Jesus; and (c) assessing the significance of one's reconstructed Jesus for later history.
The Salt of the Earth
Authors: Minear Paul S.
Published: October 2011

Despite much misunderstanding among modern readers and preachers, Jesus' saying in Matthew 5:13 (“You are the salt of the earth”) concerns sacrificing one's life to follow Christ. Moreover, this high cost of discipleship has cosmic significance.
To Ask A Better Question
Authors: Van Leeuwen Mary Stewart
Published: October 2011

Reclaiming the center of faith involves taking a critical look at both sides of the debate over same-sex unions and the ordination of homosexuals. The time has come to move beyond the nature-nurture debate and address the larger question of how Christians can rise above the sexual chaos of our age through sexual discipline and protection of the vulnerable.
Encroaching on the Sacred
Authors: Milgrom Jacob
Published: October 2011

As God's people prepare for their departure from Sinai, great care is given in matters of purity and blessing, revelation and ethics, to safeguard God's continued presence among them in the wilderness.
Life After Grace
Authors: Reynolds Carol Bechtel
Published: October 2011

An unfairly neglected book, Numbers is a rich resource for preachers. It provides compelling models of sanctified living. For a church beset with new questions and challenges, it offers much-needed guidance through the wilderness.
Principalities, Powers, and Preaching
Authors: Campbell Charles L.
Published: October 2011

The current revival of William Stringfellow's theological ethics is a challenge for preachers. Stringfellow's theology of the powers provides a compelling contemporary interpretation of the demonic forces that shape human life and confront Christian preachers. His work has extraordinary implications for those who seek to proclaim the Word amidst the chaos and death of the contemporary world.
Atonement in the Book of Leviticus
Authors: Hayes John H.
Published: October 2011

Within the world of Israel's sacrificial system, atonement brought about the restoration of right relations between God and Israel through the cleansing of the sanctuary and between human beings through restitution. Despite its many complexities, the work of atonement had a distinctly pastoral function.
“Standing in the Breach”
Authors: Schroeder Christoph
Published: October 2011

Wrath is often understood as the dark and irrational side of God that can be appeased only through the offering of a scapegoat. The metaphor of a human “standing in the breach” defies this common understanding and points to the moral dimension of God's wrath.
A New Heaven and New Earth
Authors: Smylie James H.
Published: October 2011

As far as American religion is concerned, the countdown to the year 2000 began centuries ago. From the “Great Awakening” through Scofield's Reference Bible and on to Hal Lindsey's Late Great Planet Earth, Americans have been fascinated with the millennium.
Job After Auschwitz
Authors: Haar Murray J.
Published: October 2011

More than any other book of the Bible, Job lends itself to addressing the theological implications of the Holocaust. As the biblical Job called God to account for his own suffering, so God—and we—must be called to account for the victims of the Holocaust.
Functional Top Management Team Members
Authors: Menz Markus
Published: October 2011

Functional top management team (TMT) members, defined as senior executives in the TMT responsible for one or more functional areas in their organizations, have received increased attention from scholars from different fields over the past few years. The purpose of this article is to review the disconnected research on various functional TMT members; to identify the variables of interest, the dominant relationships, and the contributions; and to organize the existing knowledge into a framework. On the basis of a synthesis of the literature, the author discusses the shortcomings and gaps and presents an agenda for future research that contributes to our understanding of functional TMT members and, thus, of TMT structure and composition.
Spontaneous Occurrence of Dissecting Aneurysms in the Region of the Ductus Arteriosus in Four-Day-Old Wistar Rat Pups
Authors: Treumann Silke , Schneider Steffen , Gröters Sibylle , Moore Nigel P. , Boor Paul J.
Published: October 2011

Dissecting aortic aneurysms, generally involving the thoracic aorta, have been shown to be caused by specific aliphatic amines in developing rats. Whether such lesions might occur spontaneously in control rats is not known. Therefore, in this study, 1,016 four-day-old, untreated rats culled from ongoing scheduled breeding studies were subjected to gross and histopathological examination in order to create a background control data base on the incidence of spontaneous aortic dissecting aneurysms. Two animals (0.2%) were found to have small dissecting aortic aneurysms, and an additional 2 (0.2%) had only hemorrhagic lesions. All of these lesions were limited to the region of the ductus arteriosus. An additional 18 findings were judged to be artifacts. These findings suggest that small vascular dissections may rarely occur in the aortic arch adjacent to the ductus arteriosus. Special attention should be paid in experimental studies to avoid confusing these small spontaneous lesions with treatment-induced lesions or artifacts.
A randomized controlled trial of electrostimulation effects on effussion, swelling and pain recovery after anterior cruciate ligament reconstruction: a pilot study
Authors: Ediz Levent , Ceylan Mehmet Fethi , Turktas Ugur , Yanmis Ibrahim , Hiz Ozcan
Published: October 2011

Objective: To evaluate rehabilitation results of electrostimulation especially on joint effusion, swelling and pain recovery after anterior cruciate ligament reconstruction.

Design: A randomized controlled trial; the assessor was not blinded to the group allocation.

Setting: Orthopaedics-traumatology and physical medicine-rehabilitation departments.

Subjects: Twenty-nine consecutive patients underwent anterior cruciate ligament reconstruction.

Interventions: Both groups began the voluntary exercise protocol one day post-surgery. The intervention group ( n = 15) also received 30 sessions electrostimulation treatment protocol started four days after the operation.

Main measures: Numerical bulge-dancing patella signs for effusion assessment; differences in circumferences of the mid-centre of the patella between operated and non-operated knees for swelling assessment. Aself-report of average daily resting pain assessed by visual analogue scale; Intenational Knee Documentation Committee scoring system and Tegner Activity Scale for subjective response assessment.

Results: Twenty-six subjects including 13 patients from the intervention group completed the study. Significantly less effusion and swelling were determined in the intervention group after seven days (1.8 ± 1.3 versus 2.4 ± 1.7 for effusion and 1.7 ± 1.2 versus 3.4 ± 1.5 for swelling) to 12 weeks (0.2 ± 0.7 versus 0.6 ± 0.8 for effusion and 0.2 ± 0.8 versus 0.8 ± 0.9 for swelling) postoperative ( P < 0.05). Patients treated with electrostimulation had significantly lower pain scores from seven days up to 12 weeks after the operation ( P < 0.05).

Conclusion: Electrostimulation along with exercise therapy appears superior to exercise alone regarding knee effusion, swelling and pain recovery after anterior cruciate ligament reconstruction. Still, there is need for further clinical studies using a radiologic method to demonstrate this effect of electrostimulation.
Coup-Proofing and Military Effectiveness in Interstate Wars, 1967–99
Authors: Pilster Ulrich , Böhmelt Tobias
Published: October 2011

This study examines the influence of civil–military relations on military effectiveness. More specifically, we investigate how coup-proofing, that is, the strategies and tactics employed to prevent the military from seizing power, affects battlefield performance. The main argument claims that coup-proofing has a negative impact on soldiers’ leadership qualities, initiative, and the ability to coordinate different military units. Ultimately, the higher a country’s coup-proofing efforts relative to its opponent, the worse its effectiveness on the battlefield. We test this hypothesis using data on battlefield outcomes and coup-proofing between 1967 and 1999.
Preparing Students for Careers in the Global Apparel Industry
Authors: Karpova Elena , Jacobs Bertha , Lee Ju Young , Andrew Arnold
Published: October 2011

The study investigated the learning experiences and outcomes of students participating in a virtual team-based multinational collaboration project. The participants in the project were 172 undergraduate students enrolled in three apparel programs located in three different countries: Australia, South Africa, and the United States. To explore student learning experiences and outcomes, 66 anonymous reflective essays were analyzed. As a result of the interpretive analysis, the three topical areas emerged: Discovering New Knowledge, Acquiring New Skills, and Personal Development. Results indicate that participation in the unique learning experience helped students acquire new knowledge and skills, become more mature, and, ultimately, feel better prepared to enter the global apparel industry. Based on our findings, we propose three components that are necessary for a successful preparation of students for the careers in the global apparel industry: (a) obtaining both general and industry-specific knowledge, (b) acquiring professional skills, and (c) personality growth and development.
Conceptual Development of an Instrument to Measure the Internalized Stigma of AIDS Based on the Roy Adaptation Model
Authors: Phillips Kenneth D.
Published: October 2011

In this column the author describes the development of an instrument to measure internalized stigma of HIV/AIDS based on the self-concept adaptive mode of the Roy adaptation model. The Internalized Stigma of AIDS Tool is a 10-item instrument that is derived from the physical self (body sensation and image) and personal self (self-consistency, self-ideal and moral-ethical-spiritual self) as set forth by Roy. An overview of the Roy adaptation model and the theory of the person as an adaptive system illustrates how this instrument was derived.
Reading Between the Lines
Authors: Milton Constance L.
Published: October 2011

The climate of contemporary healthcare is chaotic and in constant change. University faculty members receive incessant societal calls to better educate and graduate greater numbers of nurse leaders. Healthcare literature is replete with discussions of the desired qualities of successful leaders. In this column, readers are invited to reflect upon potential meanings for holding up the mirror and for the metaphor of reading between the lines from a humanbecoming theoretical perspective in leading-following situations.
Limits on the Predictive Power of Domain-Specific Experience and Knowledge in Skilled Performance
Authors: Hambrick David Z. , Meinz Elizabeth J.
Published: October 2011

It is clear from decades of research that, to a very large degree, success in music, games, sports, science, and other complex domains reflects knowledge and skills acquired through experience. However, it is equally clear that basic abilities, which are known to be substantially heritable, also contribute to performance differences in many domains, even among highly skilled performers. As we discuss here, our research shows that working memory capacity predicts performance in complex tasks even in individuals with high levels of domain-specific experience and knowledge. We discuss implications of our findings for the understanding of individual differences in skill and identify challenges for future research.
Dropping damage evaluation for a hyperbolic tangent cushioning system with a critical component
Authors: Wang Jun , Duan Fang , Jiang Jiu-hong , Lu Li-xin , Wang Zhi-wei
Published: October 2011

A new concept of dropping damage boundary surface is proposed to evaluate the dropping damage of a critical component for a hyperbolic tangent nonlinear packaging system. A novel dynamic model is established to analyze the effect of three key coordinate parameters, i.e., the non-dimensional dropping shock velocity, the frequency parameter ratio and the defined system parameter, on dropping damage potential. An experiment, which showed good agreement, was conducted to verify the theory proposed.
A simplified probabilistic macroscopic model for estimating microscopic fracture development in idealized planar fiber network materials
Authors: Isaksson Per
Published: October 2011

The overall aim of this study is to derive a simplified probabilistic theory to reveal the ‘hidden’ mechanisms controlling random fracture evaluation in idealized network structures observed as diffuse material failure on the macro scale. The model is based on the classical theory of combinatorics and the practical implications for understanding material failure in network materials, such as non-woven felts made of nanofibers or glass fibers, is addressed. The simplified theory reveals a number of important results regarding the evolution of microscopic fractures in planar random fiber networks where the only active microscopic fracture mechanism is bond fracture and the network is loaded so that a homogeneous macroscopic mechanical field is present. A simple probabilistic expression is derived that estimates the fraction of fractured bonds achieved during the loading history. The equation includes a term for potential energy and assumes that there exists an inherent characteristic bond-strength parameter that is the same for all bonds. Subsequent finite element analyses confirm the simplified probabilistic theory and lend confidence in the rather rough assumptions made. The model is justified by observations in acoustic emission monitored tensile experiments performed elsewhere.
Fathers’ Coping Resources and Children’s Socioemotional Adjustment Among Children With Learning Disabilities
Authors: Al-Yagon Michal
Published: October 2011

This study examined a cumulative model of vulnerability and protective factors at the individual level (children’s attachment relationships with father and children’s sense of coherence) and at the family level as manifested by fathers’ coping resources (fathers’ sense of coherence, fathers’ active and avoidant coping strategies) in helping to explain differences in socioemotional and behavioral adjustment among children at the age 8 to 12 years with learning disabilities (LD) and or with typical development. The sample included 205 father-child dyads: 107 fathers and their children having LD and 98 fathers and their children with typical development, from the same public elementary schools. Preliminary analyses indicated significant group differences on all the children’s measures as well as on fathers’ avoidant coping strategies. Path analysis examined the multidimensional risk model for the LD and non-LD groups. The study found a high fit between the theoretical model and the empirical findings as well as a different pattern of relationship between the model’s components for the two populations studied. Discussion focuses on understanding the unique value of vulnerability and protective factors at the individual and family levels on children’s well-adjusted functioning.
An anatomy of a YouTube meme
Authors: Shifman Limor
Published: October 2011

Launched in 2005 as a video-sharing website, YouTube has become an emblem of participatory culture. A central feature of this website is the dazzling number of derivative videos, uploaded daily by many thousands. Using the ‘meme’ concept as an analytic tool, this article aims at uncovering the attributes common to ‘memetic videos’ – popular clips that generate extensive user engagement by way of creative derivatives. Drawing on YouTube popularity-measurements and on user-generated playlists, a corpus of 30 prominent memetic videos was assembled. A combined qualitative and quantitative analysis of these videos yielded six common features: focus on ordinary people, flawed masculinity, humor, simplicity, repetitiveness and whimsical content. Each of these attributes marks the video as incomplete or flawed, thereby invoking further creative dialogue. In its concluding section, the article addresses the skyrocketing popularity of mimicking in contemporary digital culture, linking it to economic, social and cultural logics of participation.
Teen conceptualization of digital technologies
Authors: Brito Pedro Quelhas
Published: October 2011

This research explores teenagers’ knowledge representation of six digital technologies – email, IM, internet, digital photos, sms and games. Instead of pre-imposing a specific structure, teens freely express everything they consider relevant by identifying the meanings associated with each digital technology. Drawing on cognitive psychology theories and teenagers’ social development theories, the data from thirteen focus groups were analyzed. The nature of attributes comprising technical features, personal and socially relevant activities/experiences, feelings and attitudes towards these instruments only partially matched other IT conceptualizations. However, those studies applied different methodological approaches. Among the 133 attributes suggested, 30 were shared by at least two digital technologies. The Multiple Correspondence Analysis showed that games were psychologically and functionally (physical attributes) more integrated with IM and internet whereas digital photos were segregated. The communicational and product design implications of assessing attributes are discussed.
Adherence and Preexisting Major Protease Inhibitor Resistance Mutations are Associated with Virologic Failure of a Dual-Class Antiretroviral Regimen with Inhibitors of HIV-1 Viral Protease and Integrase
Authors: Gardner Edward M. , Melendez Andre G. , Astiz Maria , Bray Kimberly
Published: October 2011

Objectives: Novel treatment strategies are needed for treatment-experienced HIV-infected individuals. We retrospectively evaluated virologic outcomes on a dual-class, protease inhibitor (PI) plus raltegravir, antiretroviral (ARV) regimen. Methods: Virologic success was defined by a plasma HIV-RNA level ≤200 copies/mL. Adherence was measured using pharmacy refill data. The association between adherence and virologic failure was assessed using bivariate logistic regression. Results: In 39 individuals, median prior antiretroviral therapy (ART) exposure was 11 years. Of 39 individuals, 36 (92%) achieved an HIV-RNA ≤200 copies/mL. After a median follow-up of 328 days (interquartile range [IQR] 190-737 days), 74% maintained an HIV-RNA <200 copies/mL but only 44% had <50 copies/mL. Median adherence was 96.4% (IQR 83.3%-100%). For every 10% decrease in adherence, the odds of virologic failure increased by 90% (odds ratio [OR] = 1.9, 95% confidence interval [CI] 1.1-3.3). In all, 4 individuals had ≥2 preexisting major PI resistance mutations and all 4 had virologic failure. Conclusions: Most treatment-experienced individuals achieved virologic suppression on a dual-class regimen of a PI plus raltegravir. Success was limited by poor medication adherence and preexisting major PI resistance mutations.
Outcomes Analysis and Quality Improvement for the Treatment of Patients With Pediatric and Congenital Cardiac Disease
Authors: Jacobs Jeffrey Phillip , Pasquali Sara K. , Jeffries Howard , Jones Schonay Barnett- , Cooper David S. , Vincent Robert
Published: October 2011

Tremendous progress has been made in the science of assessing the outcomes of the treatments of patients with pediatric and congenital cardiac disease. Multi-institutional databases have been developed that span subspecialty, geographic, and temporal boundaries. Linking of different databases enables additional analyses not possible using the individual data sets alone and can facilitate quality improvement initiatives. Measures of quality can be developed, in the domains of structure, process, and outcome, which can facilitate quality improvement. Parents are an integral part of the health care team and are key partners with regard to quality improvement. The role of the parent in the process of health care delivery can be facilitated by enhancing the organizational culture and creating methods of transparency, empowering parents, and implementing effective strategies of communication. The professionals caring for patients with pediatric and congenital cardiac disease, in collaboration with the patients and their families, now have the opportunity to capitalize on the power of our databases and move beyond outcome assessment and benchmarking, to collaborative quality improvement.
Left Ventricular Pseudoaneurysm
Authors: Sachdeva Ritu , Imamura Michiaki
Published: October 2011

Left ventricular (LV) pseudoaneurysm is rare in children. This report describes the case of a 2-year-old previously healthy girl who was diagnosed with endocarditis and underwent resection of a large mitral valve vegetation from the posterior mitral leaflet. One month after this surgery, she was diagnosed with a large LV pseudoaneurysm based on echocardiography performed during routine outpatient follow-up. Cardiac surgery was performed urgently to address the pseudoaneurysm, given its potential to rupture spontaneously. This case emphasizes the need for a close follow-up of children with endocarditis for development of pseudoaneurysms, which is a rare but potentially fatal complication of endocarditis.
Databases and Outcomes in Congenital Cardiac Anesthesia
Authors: Caplan Lisa , Vener David F.
Published: October 2011

Anesthesia practitioners have long been at the forefront of patient safety initiatives in the operating room and beyond. The Congenital Cardiac Anesthesia Society has partnered with the Society of Thoracic Surgeons Congenital Heart Surgery Database to develop a patient registry for patients with congenital heart defects in order to determine patient outcomes related to anesthesia in this high-risk population. A review of existing database efforts is also undertaken to determine their strengths and weaknesses.
Contegra Versus Pulmonary Homografts for Right Ventricular Outflow Tract Reconstruction: A Ten-Year Single-Institution Comparison
Authors: Brown John W. , Ruzmetov Mark , Rodefeld Mark D. , Eltayeb Osama , Yurdakok Okan , Turrentine Mark W.
Published: October 2011

Objective: Repair of congenital heart defects involving the right ventricular outflow tract (RVOT) may require pulmonary valve replacement at the time of primary repair or reoperation. This study compares the outcomes of bovine jugular vein grafts (BJV, Contegra, Medtronic Inc.) with cryopreserved pulmonary homografts (PHs) in patients with RVOT obstruction at a single institution. Methods: We reviewed the outcomes of all BJVs and PHs implanted for RVOT reconstruction from 1999 to 2010. Echocardiographic data were reviewed to evaluate valve performance. Graft dysfunction is defined as RVOT obstruction with peak echo-Doppler gradient >40 mm Hg and/or grade III/IV conduit valve regurgitation. Graft failure is defined as need for conduit replacement or need for catheter or surgical reintervention. Results: A total of 216 patients who received BJVs (n = 153) and PHs (n = 63) were studied. There was no significant difference between the groups with respect to mean age, body surface area, conduit indication, or conduit diameter, though mean follow-up duration was longer in patients that received homografts. Conduit dysfunction and conduit failure and need for explantation were worse for homografts, albeit at longer follow-up interval. Distal stenosis and actuarial survival were similar. Conclusions: In the first ten years after pulmonary implantation of BJVs and PHs, survival and freedom from distal stenosis are statistically similar, but freedom from failure, dysfunction, and explantation are significantly better for BJV conduits. The BJV conduit is a good alternative in patients who require RVOT reconstruction.
Current Trends in the Management of Neonates With Ebstein's Anomaly
Authors: Goldberg Steven P. , Jones Ryan C. , Boston Umar S. , Haddad Lauren M. , Wetzel Glenn T. , Chin Thomas K. , Knott-Craig Christopher J.
Published: October 2011

Background: The optimal management strategy for neonates with Ebstein's anomaly is unknown. This analysis was undertaken to assess current trends in the management and prognosis of neonates born with Ebstein's anomaly in the United States, as reflected in an administrative database. Methods: The Pediatric Health Information System database (40 children’s hospitals) was used to review the reported incidence and available data on neonates with Ebstein's anomaly treated in the United States between 2003 and 2007. Primary outcome was hospital survival. Of the 415 patients identified, 257 (62%) did not undergo initial surgical intervention as neonates. Aortopulmonary shunt only was done on 63 patients (15%), single-ventricle palliation on 36 (9%), two-ventricle repair on 16 (4%), heart transplantation in 3 (1%), and a catheter-based intervention or a hybrid palliative approach was applied in 40 (10%). Intergroup comparisons were done using chi-square analyses. Results: Mortality for the entire cohort was 24% (100 of 415). For medically treated patients, this was 22% (56 of 257). For surgically treated and hybrid patients, this was 30% and 23%, respectively ( P = NS). Conclusions: The majority of patients born with Ebstein's anomaly currently do not undergo surgical intervention as neonates. Significant early mortality in this group suggests that certain subsets of patients may benefit from earlier surgical intervention. Among the severely symptomatic neonates who do undergo early surgical intervention, the mortality remains high, irrespective of the surgical approach taken. A multicenter trial may be appropriate to identify strategies to optimize care for these critically ill neonates. Further analysis of risk factors for early mortality is warranted.
LFA-1 blockade induces effector and regulatory T-cell enrichment in lymph nodes and synergizes with CTLA-4Ig to inhibit effector function
Authors: Reisman Natalie M. , Floyd Tamara L. , Wagener Maylene E. , Kirk Allan D. , Larsen Christian P. , Ford Mandy L.
Published: October 2011

Despite encouraging results using lymphocyte function antigen-1 (LFA-1) blockade to inhibit BM and solid organ transplantation rejection in nonhuman primates and humans, the precise mechanisms underlying its therapeutic potential are still poorly understood. Using a fully allogeneic murine transplantation model, we assessed the relative distribution of total lymphocyte subsets in untreated versus anti–LFA-1–treated animals. Our results demonstrated a striking loss of naive T cells from peripheral lymph nodes, a concomitant gain in blood after LFA-1 blockade, and a shift in phenotype of the cells remaining in the node to a CD62LloCD44hi profile. We determined that this change was due to a specific enrichment of activated, graft-specific effectors in the peripheral lymph nodes of anti–LFA-1–treated mice compared with untreated controls, and not to a direct effect of anti–LFA-1 on CD62L expression. LFA-1 blockade also resulted in a dramatic increase in the frequency of CD4+ FoxP3+ regulatory T cells in graft-draining nodes. Our results suggest that the differential impact of LFA-1 blockade on the distribution of naive versus effector and regulatory T cells may underlie its ability to inhibit alloreactive T-cell responses after transplantation.
iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex
Authors: Razick Sabry , Mora Antonio , Michalickova Katerina , Boddie Paul , Donaldson Ian M
Published: October 2011

Background

The iRefIndex consolidates protein interaction data from ten databases in a rigorous manner using sequence-based hash keys. Working with consolidated interaction data comes with distinct challenges: data are redundant, overlapping, highly interconnected and may be collected and represented using different curation practices. These phenomena were quantified in our previous studies.

Results

The iRefScape plug-in for the Cytoscape graphical viewer addresses these challenges. We show how these factors impact on data-mining tasks and how our solutions resolve them in a simple and efficient manner. A uniform accession space is used to limit redundancy and support search expansion and searching on multiple accession types. Multiple node and edge features support data filtering and mining. Node colours and features supply information about search result provenance. Overlapping evidence is presented using a multi-graph and a bi-partite representation is used to distinguish binary and n-ary source data. Searching for interactions between sets of proteins is supported and specifically includes searches on disease-related genes found in OMIM. Finally, a synchronized adjacency-matrix view facilitates visualization of relationships between sets of user defined groups.

Conclusions

The iRefScape plug-in will be of interest to advanced users of interaction data. The plug-in provides access to a consolidated data set in a uniform accession space while remaining faithful to the underlying source data. Tools are provided to facilitate a range of tasks from a simple search to knowledge discovery. The plug-in uses a number of strategies that will be of interest to other plug-in developers.
Detection of interaction articles and experimental methods in biomedical literature
Authors: Schneider Gerold , Clematide Simon , Rinaldi Fabio
Published: October 2011

Background

This article describes the approaches taken by the OntoGene group at the University of Zurich in dealing with two tasks of the BioCreative III competition: classification of articles which contain curatable protein-protein interactions (PPI-ACT) and extraction of experimental methods (PPI-IMT).

Results

Two main achievements are described in this paper: (a) a system for document classification which crucially relies on the results of an advanced pipeline of natural language processing tools; (b) a system which is capable of detecting all experimental methods mentioned in scientific literature, and listing them with a competitive ranking (AUC iP/R > 0.5).

Conclusions

The results of the BioCreative III shared evaluation clearly demonstrate that significant progress has been achieved in the domain of biomedical text mining in the past few years. Our own contribution, together with the results of other participants, provides evidence that natural language processing techniques have become by now an integral part of advanced text mining approaches.
Soft tagging of overlapping high confidence gene mention variants for cross-species full-text gene normalization
Authors: Kuo Cheng-Ju , Ling Maurice HT , Hsu Chun-Nan
Published: October 2011

Background

Previously, gene normalization (GN) systems are mostly focused on disambiguation using contextual information. An effective gene mention tagger is deemed unnecessary because the subsequent steps will filter out false positives and high recall is sufficient. However, unlike similar tasks in the past BioCreative challenges, the BioCreative III GN task is particularly challenging because it is not species-specific. Required to process full-length articles, an ineffective gene mention tagger may produce a huge number of ambiguous false positives that overwhelm subsequent filtering steps while still missing many true positives.

Results

We present our GN system participated in the BioCreative III GN task. Our system applies a typical 2-stage approach to GN but features a soft tagging gene mention tagger that generates a set of overlapping gene mention variants with a nearly perfect recall. The overlapping gene mention variants increase the chance of precise match in the dictionary and alleviate the need of disambiguation. Our GN system achieved a precision of 0.9 (F-score 0.63) on the BioCreative III GN test corpus with the silver annotation of 507 articles. Its TAP-k scores are competitive to the best results among all participants.

Conclusions

We show that despite the lack of clever disambiguation in our gene normalization system, effective soft tagging of gene mention variants can indeed contribute to performance in cross-species and full-text gene normalization.
Genome dedoubling by DCJ and reversal
Authors: Thomas Antoine , Varré Jean-Stéphane , Ouangraoua Aïda
Published: October 2011

Background

Segmental duplications in genomes have been studied for many years. Recently, several studies have highlighted a biological phenomenon called breakpoint-duplication that apparently associates a significant proportion of segmental duplications in Mammals, and the Drosophila species group, to breakpoints in rearrangement events.

Results

In this paper, we introduce and study a combinatorial problem, inspired from the breakpoint-duplication phenomenon, called the Genome Dedoubling Problem. It consists of finding a minimum length rearrangement scenario required to transform a genome with duplicated segments into a non-duplicated genome such that duplications are caused by rearrangement breakpoints. We show that the problem, in the Double-Cut-and-Join (DCJ) and the reversal rearrangement models, can be reduced to an APX-complete problem, and we provide algorithms for the Genome Dedoubling Problem with 2-approximable parts. We apply the methods for the reconstruction of a non-duplicated ancestor of Drosophila yakuba.

Conclusions

We present the Genome Dedoubling Problem, and describe two algorithms solving the problem in the DCJ model, and the reversal model. The usefulness of the problems and the methods are showed through an application to real Drosophila data.
Evolution of the apomixis transmitting chromosome in Pennisetum
Authors: Akiyama Yukio , Goel Shailendra , Conner Joann A , Hanna Wayne W , Yamada-Akiyama Hitomi , Ozias-Akins Peggy
Published: October 2011

Background

Apomixis is an intriguing trait in plants that results in maternal clones through seed reproduction. Apomixis is an elusive, but potentially revolutionary, trait for plant breeding and hybrid seed production. Recent studies arguing that apomicts are not evolutionary dead ends have generated further interest in the evolution of asexual flowering plants.

Results

In the present study, we investigate karyotypic variation in a single chromosome responsible for transmitting apomixis, the Apospory-Specific Genomic Region carrier chromosome, in relation to species phylogeny in the genera Pennisetum and Cenchrus. A 1 kb region from the 3' end of the ndhF gene and a 900 bp region from trnL-F were sequenced from 12 apomictic and eight sexual species in the genus Pennisetum and allied genus Cenchrus. An 800 bp region from the Apospory-Specific Genomic Region also was sequenced from the 12 apomicts. Molecular cytological analysis was conducted in sixteen Pennisetum and two Cenchrus species. Our results indicate that the Apospory-Specific Genomic Region is shared by all apomictic species while it is absent from all sexual species or cytotypes. Contrary to our previous observations in Pennisetum squamulatum and Cenchrus ciliaris, retrotransposon sequences of the Opie-2-like family were not closely associated with the Apospory-Specific Genomic Region in all apomictic species, suggesting that they may have been accumulated after the Apospory-Specific Genomic Region originated.

Conclusions

Given that phylogenetic analysis merged Cenchrus and newly investigated Pennisetum species into a single clade containing a terminal cluster of Cenchrus apomicts, the presumed monophyletic origin of Cenchrus is supported. The Apospory-Specific Genomic Region likely preceded speciation in Cenchrus and its lateral transfer through hybridization and subsequent chromosome repatterning may have contributed to further speciation in the two genera.
An integrated approach identifies IFN-regulated microRNAs and targeted mRNAs modulated by different HCV replicon clones
Authors: Bruni Roberto , Marcantonio Cinzia , Tritarelli Elena , Tataseo Paola , Stellacci Emilia , Costantino Angela , Villano Umbertina , Battistini Angela , Ciccaglione Anna Rita
Published: October 2011

Background

Infections with hepatitis C virus (HCV) progress to chronic phase in 80% of patients. To date, the effect produced by HCV on the expression of microRNAs (miRs) involved in the interferon-β (IFN-β) antiviral pathway has not been explored in details. Thus, we compared the expression profile of 24 selected miRs in IFN-β-treated Huh-7 cells and in three different clones of Huh-7 cells carrying a self-replicating HCV RNA which express all viral proteins (HCV replicon system).

Methods

The expression profile of 24 selected miRs in IFN-β-treated Huh-7 cells and in HCV replicon 21-5 clone with respect to Huh-7 parental cells was analysed by real-time PCR. To exclude clone specific variations, the level of 16 out of 24 miRs, found to be modulated in 21-5 clone, was evaluated in two other HCV replicon clones, 22-6 and 21-7. Prediction of target genes of 3 miRs, confirmed in all HCV clones, was performed by means of miRGator program. The gene dataset obtained from microarray analysis of HCV clones was farther used to validate target prediction.

Results

The expression profile revealed that 16 out of 24 miRs were modulated in HCV replicon clone 21-5. Analysis in HCV replicon clones 22-6 and 21-7 indicated that 3 out of 16 miRs, (miR-128a, miR-196a and miR-142-3p) were modulated in a concerted fashion in all three HCV clones. Microarray analysis revealed that 37 out of 1981 genes, predicted targets of the 3 miRs, showed an inverse expression relationship with the corresponding miR in HCV clones, as expected for true targets. Classification of the 37 genes by Panther System indicated that the dataset contains genes involved in biological processes that sustain HCV replication and/or in pathways potentially implicated in the control of antiviral response by HCV infection.

Conclusions

The present findings reveal that 3 IFN-β-regulated miRs and 37 genes, which are likely their functional targets, were commonly modulated by HCV in three replicon clones. The future use of miR inhibitors or mimics and/or siRNAs might be useful for the development of diagnostic and therapeutic strategies aimed at the recovering of protective innate responses in HCV infections.
Artifact quantification and tractography from 3T MRI after placement of aneurysm clips in subarachnoid hemorrhage patients
Authors: Khursheed Faraz , Rohlffs Fiona , Suzuki Shuichi , Kim Dong H , Ellmore Timothy M
Published: October 2011

Background

The application of advanced 3T MRI imaging techniques to study recovery after subarachnoid hemorrhage (SAH) is complicated by the presence of image artifacts produced by implanted aneurysm clips. To characterize the effect of these artifacts on image quality, we sought to: 1) quantify extent of image artifact in SAH patients with implanted aneurysm clips across a range of MR sequences typically used in studies of volumetry, blood oxygen level dependent signal change (BOLD-fMRI), and diffusion-weighted imaging (DW-MRI) and 2) to explore the ability to reconstruct white matter pathways in these patients.

Methods

T1- and T2-weighted structural, BOLD-fMRI, and DW-MRI scans were acquired at 3T in two patients with titanium alloy clips in ACOM and left ACA respectively. Intensity-based planimetric contouring was performed on aligned image volumes to define each artifact. Artifact volumes were quantified by artifact/clip length and artifact/brain volume ratios and analyzed by two-way (scan-by-rater) ANOVAs. Tractography pathways were reconstructed from DW-MRI at varying distances from the artifacts using deterministic methods.

Results

Artifact volume varied by MR sequence for length (p = 0.007) and volume (p < 0.001) ratios: it was smallest for structural images, larger for DW-MRI acquisitions, and largest on fMRI images. Inter-rater reliability was high (r = 0.9626, p < 0.0001), and reconstruction of white matter connectivity characteristics increased with distance from the artifact border. In both patients, reconstructed white matter pathways of the uncinate fasciculus and inferior fronto-occipital fasciculus were clearly visible within 2 mm of the artifact border.

Conclusions

Advanced 3T MR can successfully image brain tissue around implanted titanium aneurysm clips at different spatial ranges depending on sequence type. White matter pathways near clip artifacts can be reconstructed and visualized. These findings provide a reference for designing functional and structural neuroimaging studies of recovery in aSAH patients after clip placement.
Development and reproducibility of a computed tomography-based measurement of renal sinus fat
Authors: Foster Meredith C , Hwang Shih-Jen , Porter Stacy A , Massaro Joseph M , Hoffmann Udo , Fox Caroline S
Published: October 2011

Background

Renal sinus fat may mediate obesity-related vascular disease, although this fat depot has not been assessed in a community-based sample. We sought to develop a protocol to quantify renal sinus fat accumulation using multi-detector computed tomography (MDCT).

Methods

Protocol development was performed in participants in the Framingham Offspring cohort who underwent MDCT. Volumetric renal sinus fat was measured separately within the right and left kidneys, and renal sinus fat area within a single MDCT scan slice was measured in the right kidney. Due to the high correlation of volumetric and single-slice renal sinus fat in the right kidney (Pearson correlation [r] = 0.85, p < 0.0001), we optimized a single-slice protocol to capture renal sinus fat in the right kidney alone. Pearson correlation coefficients were used to compare to assess the correlation of volumetric and single-slice renal sinus fat in the right kidney with other measures of adiposity. Inter- and intra-reader reproducibility was assessed using intra-class correlation coefficients.

Results

Single-slice measurements were obtained in 92 participants (mean age 60 years, 49% women, median renal sinus fat 0.43 cm2). Intra- and inter-reader intra-class correlation coefficients were 0.93 and 0.86, respectively. Single-slice renal sinus fat was correlated with body mass index (r = 0.35, p = 0.0006), waist circumference (r = 0.31, p = 0.003), and abdominal visceral fat (r = 0.48, p < 0.0001). Similar correlations were observed for volumetric renal sinus fat in the right kidney.

Conclusions

Measuring renal sinus fat is feasible and reproducible using MDCT scans in a community-based sample.