bluuebunny/crossref_metadata_2025 huggingface dataset:
Some illustrative vignettes on the uses of the seven principles and the faculty and institutional inventories
Authors: Barsi Louis M.
Published: October 2006

The Seven Principles and the Inventories for Good Practice have proven to be useful resources to colleges, universities, and national associations in fostering a spirit of collaboration and improving the quality of undergraduate education.
Using assessment data to improve teaching
Authors: Gray Peter J.
Published: October 2006

Merely conducting an assessment does not guarantee improvement. Improvement occurs when instructors, students, and others use data gathered through a comprehensive process to understand teaching and learning and to make well‐informed decisions about instructional development.
Report on a trip downtown
Authors: Doyle Kenneth O.
Published: October 2006

What on earth can we academics learn from business people about how to evaluate and improve college teaching? I learned a lot.
New directions for mentoring: An organizational development perspective
Authors: Wunsch Marie A.
Published: October 2006

This chapter posits the view that mentoring pmgrams should have
a conceptual framework and a structure that ensures benejts to
both individuals and the institution.
Mentoring: An adult developmental perspective
Authors: Otto Mary L.
Published: October 2006

A discussion of the impact of mentoring relationships in higher
education withfocus on the changing needs of adult mentors and
protkgks as they mature chronologically and professionally.
Forging the ties that bind: Peer mentoring part‐time faculty
Authors: Millis Barbara J.
Published: October 2006

A peer mentoring processfor part‐time faculty not only ensures
their teaching skill development, but breaks down colleague
isolation and contributes to their institutional commitment.
Mentoring faculty at the departmental level
Authors: Herr Kay U.
Published: October 2006

A discipline‐specific mentoring program in a department will
encourage the new colleague to grow and develop within that dis‐
ciplinary context. This, in turn, is essential for progress toward
and ultimate attainment of tenure and promotion. The successful
colleague retained by the institution is a manifestation of wise
stewardship of institutional resources and of service to ourselves as
persons.
Peer mentoring among graduate students of color: Expanding the mentoring relationship
Authors: Bonilla James , Pickron Carlton , Tatum Travis
Published: October 2006

This chapter examines the graduate school experiences of three
men of color who overcame signifcant obstacles in completing the
dissertation writing phase of their program by initiating a peer
mentoring group.
Mentoring minority graduate students: A west indian narrative
Authors: Stanley Christine A.
Published: October 2006

Foreign students in American universities can acquire cultural
understanding and increase self‐discovery through the support of
mentors and cultural guides.
Assessing interdisciplinary learning
Authors: Field Michael , Lee Russell , Field Mary Lee
Published: October 2006

Assessment procedures vary widely from local to national models.
This chapter surveys and evaluates recent developments in the
assessment of interdisciplinary studies.
Computer technology and collaborative learning
Authors: Sullivan Patricia
Published: October 2006

This chapterfocuses on the current andfuture use of technology in
collaborative learning Classrooms with practical reference to group
decision support systems, electronic classrooms, interactive video,
and hypermedia systems.
Case studies
Authors: Emerson Allen , Phillips Jerry , Hunt Cathy , Alexander Arlene Bowman
Published: October 2006

This chapter illustrates some applications of collaborative learning
in college classrooms.
Freedom transformed: Toward a developmental model for the construction of collaborative learning environments
Authors: Hamilton Sharon J.
Published: October 2006

This chapter proposes a developmental model for instructors who
wish to establish collaborative learning classrooms.
Supplemental instruction: From small beginnings to a national program
Authors: Widmar Gary E.
Published: October 2006

A historical review of development and implementation of Supplemented Instruction is presented by the cheif student affairs officer at the University of Missouri—Kansas City.
Steps in starting supplemental instruction
Authors: Ainsworth Len , Garnett Don , Phelps Danay , Shannon Scott , Ripperger‐Suhler Ken
Published: October 2006

An increasing number of students need developmental help.
Supplemental lnstruction can raise the level of success dramatically.
Faculty development through supplemental instruction
Authors: Marshall Sherrin
Published: October 2006

Supplemental Instruction can help all of us—including administrators
andfaculty—becorne active learners. Here is how Supplemental
Instruction contributed to one college'sfaculty development plan.
Supplemental instruction sessions in college algebra and calculus
Authors: Burmeister Sandra L. , Carter Jeanne M. , Hockenberger Lynn R. , Kenney Patricia Ann , McLaren Ann , Nice Doris L.
Published: October 2006

Look at the kinds of things that happen in specific Supplemental
Instruction sessions and see h collaborative learning in
mathematics takes place.
Research studies on the effectiveness of supplemental instruction in mathematics
Authors: Kenney Patricia Ann , Kallison James M.
Published: October 2006

Findings from research studies provide some evidence that
participation in Supplemental Instruction programs can have an effect
in thefollowing areasfor students: course grades, rates of D and F
grades and course withdrawals, and semester grade‐ point averages.
VSI: A pathway to mastery and persistence
Authors: Martin Deanna C. , Blanc Robert A.
Published: October 2006

A video‐based delivery system using Supplemental Instruction offers a
viable alternative to remedial course work, allowing underprepared
students to excel in historically dificult courses as they develop
needed basic skills.
Barriers to success in quantitative gatekeeper courses
Authors: Gainen Joanne
Published: October 2006

Faculty may be able to reduce student attrition from quantitative majors by addressing four barriers to success—precollege preparation, peer culture, classroom climate, and instructional style—in introductory courses in these fields.
Women's responses to an activity‐based introductory physics program
Authors: Laws Priscilla W. , Rosborough Pamela J. , Poodry Frances J.
Published: October 2006

This chapter considers some women's surprising responses to an introductory physics sequence in which lectures are abandoned in favor of activity‐based collaborative work enhanced by the use of integrated computer tools.
Professional development and training for faculty advisers
Authors: Ryan Carol C.
Published: October 2006

Faculty should regard advising as an extension of the teaching role. However, they need more general institutional information and training if they are to perform effectively as teacher‐advisers. Suggestions for formal and informal faculty advising development are made and three key elements in adviser preparation are identified.
Social science advising
Authors: Geis Gilbert , Huston Ted L.
Published: October 2006

This chapter provides a practical guide to advising social science students based on the experiences of two social scientists, a sociologist and psychologist, each of whom has taught in both discipline‐based and interdisciplinary departments.
The professional status of teachers and academic advisers: It matters
Authors: Wade Barbara K. , Yoder Edgar P.
Published: October 2006

This chapter considers various aspects of effective teaching and effective academic advising. Both occupations warrant professional status. In our analysis, it is concluded that effective academic advisers are teachers.
College faculty as educational researchers: Discipline‐focused studies of student motivation and self‐regulated learning
Authors: Karabenick Stuart A. , Collins‐Eaglin Jan
Published: October 2006

One part of a faculty development program that is based on the classroom research movement focuses on how faculty can use the research and methodological tools relating to student motivation and self‐regulation in research in their own classroom.
Approaches to studying and perceptions of the learning environment across disciplines
Authors: Entwistle Noel , Tait Hilary
Published: October 2006

Students in different disciplines develop characteristic ways of learning based on their perceptions of what is required in their academic work. Within a discipline, effective learning involves interplay between the characteristics of the student and those of the learning environment that is provided by the teacher and the department.
Disciplinary differences in students' perceptions of success: Modifying misperceptions with attributional retraining
Authors: Menec Verena H. , Perry Raymond P.
Published: October 2006

College students bring a variety of perceptions to the classroom about what it takes to succeed in a discipline. This chapter focuses on ways to modify potentially maladaptive perceptions into more adaptive ones, by focusing on a therapeutic technique referred to as attributional retraining.
Characteristics of exemplary teachers
Authors: Lowman Joseph
Published: October 2006

To honor exemplary teachers, we need to ask whether there are universal qualities of effective teachers that we can agree upon as a community.
Using portfolios to document teaching excellence
Authors: Richlin Laurie , Manning Brenda
Published: October 2006

To follow good measurement practice, programs for exemplary teaching should gather more than one type of data from more than one source. This practice is consistent with the idea behind the teaching portfolio, a compilation of best work and thought that is gaining favor as a faculty evaluation strategy.
Honoring exemplary teaching in the liberal arts institution
Authors: Zahorski Kenneth J.
Published: October 2006

Liberal arts institutions have long been known for seeing teaching as a primary mission. Their methods for recognizing exemplary teaching are discussed in this chapter.
Decentralized/departmental reward systems
Authors: Lunde Joyce Povlacs , Barrett Leverne A.
Published: October 2006

One institution's attempt to review teaching at the departmental level reflects upon the argument that honoring teaching is best done departmentally due to disciplinary differences in norms and standards.
Promoting Exemplary Teaching: The Case of the U.S. Military Academy
Authors: Forsythe George B. , Gandolfo Anita
Published: October 2006

Because military academies approach higher education from a special perspective and faculty are mostly military officers with special experiences of evaluation, they approach honoring teaching somewhat differently from other institutions.
Teaching the subject: Developmental identities in teaching
Authors: Burgan Mary
Published: October 2006

Students' developmental stages affect their capacities to comprehend and absorb difficult texts and the moral problems embedded in them, and we should teach accordingly. Such attention to subjects whose identities are in flux will inevitably turn into transformations for both student and teacher.
The ethics of student‐faculty friendships
Authors: Baker Richard L.
Published: October 2006

Although the primary setting for the student‐teacher relationship is the classroom, an important ethical task is to handle the relationship well outside of the classroom. May Sarton's novel The Small Room depicts both success and failure in this task.
Between apathy and advocacy: Teaching and modeling ethical reflection
Authors: Hanson Karen
Published: October 2006

Advocacy may be unavoidable, but this tendency does not license use of classrooms as platforms for partisan persuasion. Teaching governed by fundamental academic virtues will responsibly call students to genuine, fruitful engagement with political and ethical issues.
Enhancing the lecture: Revitalizing a traditional format
Authors: Bonwell Charles C.
Published: October 2006

The traditional lecture can be enhanced by including active learning designed to further course goals of learning knowledge, developing skills, or fostering attitudes.
Using electronic tools to promote active learning
Authors: Gillette David H.
Published: October 2006

Electronic media provide faculty with new opportunities for designing strategies to engage students both in and out of the classroom.
Emerging issues in the discussion of active learning
Authors: Sutherland Tracey E.
Published: October 2006

Earlier chapters address a broad range of strategies for effectively engaging students in the learning process. While each chapter answers a number of questions about active learning approaches, each also highlights emerging issues in the discussion of involving students in learning.
Tutors and small groups in problem‐based learning: Lessons from the literature
Authors: Wilkerson Luann
Published: October 2006

Group size, teacher skills, problem types, and student behaviors are central concerns to PBL planners and teachers. In implementing problem‐based curricula, decisions about each of these dimensions have implications for the others.
The power of problem‐based learning in teaching introductory science courses
Authors: Allen Deborah E. , Duch Barbara J. , Groh Susan E.
Published: October 2006

In its use of complex, real‐world problems to introduce concepts and motivate learning in an active and cooperative learning environment, problem‐based learning provides a powerful alternative to the passive lecture tradition in introductory science courses in biology, physics, and chemistry.
Problem‐based learning in leadership education
Authors: Bridges Edwin M. , Hallinger Philip
Published: October 2006

Problem‐based learning has been used to address acknowledged shortcomings in leadership education. This innovative approach required changes in the nature of the learning materials, classroom process, instructor's role, and student assessment procedures.
Twenty‐up: Problem‐based learning with a large group
Authors: Rangachari P. K.
Published: October 2006

An inquiry course in an interdisciplinary program is described. The essence of problem‐based learning is preserved though the class is three times the size of a normal tutorial group.
Time expenditure, workload, and student satisfaction in problem‐based learning
Authors: Kingsland Arthur J.
Published: October 2006

In this approach to architecture education, the design project serves as the predominant learning tool. Working individually and in small groups, students use design problems to stimulate and organize their self‐directed learning of essential architectural concepts.
Merge and binding in child relative clauses: the case of Irish
Authors: GOODLUCK HELEN , GUILFOYLE EITHNE , HARRINGTON SÍLE
Published: October 2006

This study investigates whether children learning Irish as a first language show a preference for one or other of the two mechanisms for relative clause formation used in the adult language (movement and binding), and what details of the grammar of Irish relative clauses children are sensitive to. Our results suggest that Irish-speaking children have acquired both a movement and a binding mechanism for relativization by age five, and that they additionally have a non-movement mechanism for forming subject relatives, one that is not licensed in adult Irish. The data is discussed in the context of other studies of relativization in child language, cross-linguistic evidence and the computation of binding structures in language production and processing.
AMENABILITY, FREE SUBGROUPS, AND HAAR NULL SETS IN NON-LOCALLY COMPACT GROUPS
Authors: SOLECKI SŁAWOMIR
Published: October 2006

The paper has two objectives. On the one hand, we study left Haar null sets, a measure-theoretic notion of smallness on Polish, not necessarily locally compact, groups. On the other hand, we introduce and investigate two classes of Polish groups which are closely related to this notion and to amenability. We show that left Haar null sets form a $\sigma$-ideal and have the Steinhaus property on Polish groups which are ‘amenable at the identity’, and that they lose these two properties in the presence of appropriately embedded free subgroups. As an application we prove an automatic continuity result for universally measurable homomorphisms from inverse limits of sequences of amenable, locally compact, second countable groups to second countable groups.
INTRANSITIVE GEOMETRIES
Authors: GRAMLICH RALF , VAN MALDEGHEM HENDRIK
Published: October 2006

A lemma of Tits establishes a connection between the simple connectivity of an incidence geometry and the universal completion of an amalgam induced by a sufficiently transitive group of automorphisms of that geometry. In the present paper, we generalize this lemma to intransitive geometries, thus opening the door for numerous applications. We treat ourselves some amalgams related to intransitive actions of finite orthogonal groups, as a first class of examples.
ON A GENERALIZATION OF SZEMERÉDI'S THEOREM
Authors: SHKREDOV I. D.
Published: October 2006

Let $N$ be a natural number and $A \subseteq [1, \dots, N]^2$ be a set of cardinality at least $N^2 / (\log \log N)^c$, where $c > 0$ is an absolute constant. We prove that $A$ contains a triple $\{(k, m), (k+d, m), (k, m+d) \}$, where $d > 0$. This theorem is a two-dimensional generalization of Szemerédi's theorem on arithmetic progressions.
Endogenous regionalism
Authors: HERRMANN-PILLATH CARSTEN
Published: October 2006

For more than a decade regionalism has been on the rise in the global economy. Based on the concept of allocative efficiency, standard trade theory regards regionalism as a form of protectionism. The paper confronts this view with an institutionalist explanation and draws on recent research on the role of specific investments into international market access, uncertainty and asymmetric information in policy coordination. A distinction between regionalism and regionalist policies is proposed. Endogenous regionalism reflects the economic forces of path-dependent comparative advantage and manifests the embeddedness of trade relations in social networks. Regionalism translates into regionalist policies via political entrepreneurship in policy networks that aims at stabilizing expectations about future market access and balancing negotiation power in a multilateral setting. Regionalism is thus presented as the standard case in global economic integration between the two extremes of unilateral liberalization and complete multilateralism.
Aquatic geochemistry of the rare earth elements and yttrium in the Pioneer River catchment, Australia
Authors: Lawrence Michael G. , Jupiter Stacy D. , Kamber Balz S.
Published: October 2006

The rare earth elements are strong provenance indicators in geological materials, yet the potential for tracing provinciality in surface freshwater samples has not been adequately tested. Rare earth element and yttrium concentrations were measured at 33 locations in the Pioneer River catchment, Mackay, central Queensland, Australia. The rare earth element patterns were compared on the basis of geological, topographical and land-use features in order to investigate the provenancing potential of these elements in a small freshwater system. The rare earth element patterns of streams draining single lithological units with minor land modification show strongly coherent normalised behaviour, with a loss of coherence in agricultural locations. Evidence is reported for an anthropogenic Gd anomaly that may provide a useful hydrological tracer in this region since the introduction of magnetic resonance imaging in 2003. Several samples display a superchondritic Y/Ho mass ratio (up to 44), which is not explainable within the constraints imposed by local geology. Instead, it is suggested that the additional Y is derived from a marine source, specifically marine phosphorites, which are a typical source of fertiliser phosphorus. The data indicate that, under some circumstances, scaled and normalised freshwater rare earth patterns behave conservatively.
Limited grazing pressure by native herbivores on the invasive seaweed Caulerpa taxifolia in a temperate Australian estuary
Authors: Gollan John R. , Wright Jeffrey T.
Published: October 2006

Caulerpa taxifolia is an invasive alga threatening biodiversity in invaded regions. Its proliferation in recipient communities will be due to several factors including limited grazing effects by native herbivores. However, little is known about grazing pressure exerted by native herbivores on C. taxifolia relative to native macrophytes or its attractiveness to them as habitat. The present study determined which herbivores co-occurred with invasive C. taxifolia in a temperate Australian estuary and documented their abundance, relative grazing effects, habitat preference and survivorship on C. taxifolia compared with native macrophytes. Four herbivores co-occurred with C. taxifolia and their densities were often low or zero at the sites studied. Feeding experiments showed that compared with C. taxifolia: the fish, Girella tricuspidata, preferred Ulva sp.; the sea-hare, Aplysia dactylomela, preferred Laurencia sp.; whereas the mesograzers, Cymadusa setosa and Platynereis dumerilii antipoda, both consumed Cystoseira trinodus and Sargassum sp. at higher rates. The two mesograzers also showed strong habitat preference for C. trinodus and Sargassum sp. Cymadusa setosa had poor survivorship on Caulerpa taxifolia whereas P. dumerilii antipoda had 100% survivorship on C. taxifolia after 41 days. We consider that the low diversity and abundance of native herbivores, their weak grazing pressure on C. taxifolia and its low attractiveness as habitat may facilitate further local spread in this estuary, and potentially in other invaded locations.
Age, growth and preliminary estimates of maturity of bigeye tuna, Thunnus obesus, in the Australian region
Authors: Farley Jessica H. , Clear Naomi P. , Leroy Bruno , Davis Tim L. O. , McPherson Geoff
Published: October 2006

Biological parameters such as age, growth and age (or size) at maturity are vital for accurate stock assessments and management plans to ensure that fisheries develop sustainably. Despite this, very few validated age studies have been conducted for large tropical pelagic species within the Australian region. Age and growth parameters were estimated for bigeye tuna, Thunnus obesus (Lowe, 1839), sampled from longline fisheries in the Australian region using validated techniques based on counts of annual increments. Poor increment clarity reduced the number of otoliths included in the final analysis to only 50% of the 3200 selected for reading (39–178-cm fork length). Microincrement analysis confirmed the position of the first two annual increments in these otoliths. A maximum age of 16 years was obtained, but over 80% of fish in the Australian catch were <5 years old. Growth is most rapid in the first few years of life and asymptotic length is reached at about age 9 to 10 years. The von Bertalanffy growth parameters were estimated at L∞ = 169.09, k = 0.238, and to = –1.706 for the south-west Pacific Ocean and L∞ = 178.41, k = 0.176, and to = –2.500 for the eastern Indian Ocean. These parameters were significantly different, suggesting that there is little mixing between populations in the Pacific and Indian Oceans. Length at 50% maturity for females sampled in northern Queensland was estimated to be 102.4-cm fork length.
Tdrd1/Mtr-1
, a
tudor
-related gene, is essential for male germ-cell differentiation and nuage/germinal granule formation in mice
Authors: Chuma Shinichiro , Hosokawa Mihoko , Kitamura Kouichi , Kasai Shinya , Fujioka Makio , Hiyoshi Masateru , Takamune Kazufumi , Noce Toshiaki , Nakatsuji Norio
Published: October 2006

Embryonic patterning and germ-cell specification in mice are regulative and depend on zygotic gene activities. However, there are mouse homologues of
Drosophila
maternal effect genes, including
vasa
and
tudor
, that function in posterior and germ-cell determination. We report here that a targeted mutation in

Tudor domain containing 1
/
mouse tudor repeat 1

(

Tdrd1
/
Mtr-1

), a
tudor
-related gene in mice, leads to male sterility because of postnatal spermatogenic defects. TDRD1/MTR-1 predominantly localizes to nuage/germinal granules, an evolutionarily conserved structure in the germ line, and its intracellular localization is downstream of

mouse vasa homologue
/
DEAD box polypeptide 4

(

Mvh
/
Ddx4

), similar to

Drosophila vasa
-
tudor

.
Tdrd1/Mtr-1
mutants lack, and

Mvh
/
Ddx4

mutants show, strong reduction of intermitochondrial cement, a form of nuage in both male and female germ cells, whereas chromatoid bodies, another specialized form of nuage in spermatogenic cells, are observed in
Tdrd1/Mtr-1
mutants. Hence, intermitochondrial cement is not a direct prerequisite for oocyte development and fertility in mice, indicating differing requirements for nuage and/or its components between male and female germ cells. The result also proposes that chromatoid bodies likely have an origin independent of or additional to intermitochondrial cement. The analogy between

Mvh
-
Tdrd1

in mouse spermatogenic cells and

vasa
-
tudor

in
Drosophila
oocytes suggests that this molecular pathway retains an essential role(s) that functions in divergent species and in different stages/sexes of the germ line.
A tunable algorithm for collective decision-making
Authors: Pratt Stephen C. , Sumpter David J. T.
Published: October 2006

Complex biological systems are increasingly understood in terms of the algorithms that guide the behavior of system components and the information pathways that link them. Much attention has been given to robust algorithms, or those that allow a system to maintain its functions in the face of internal or external perturbations. At the same time, environmental variation imposes a complementary need for algorithm versatility, or the ability to alter system function adaptively as external circumstances change. An important goal of systems biology is thus the identification of biological algorithms that can meet multiple challenges rather than being narrowly specified to particular problems. Here we show that emigrating colonies of the ant
Temnothorax curvispinosus
tune the parameters of a single decision algorithm to respond adaptively to two distinct problems: rapid abandonment of their old nest in a crisis and deliberative selection of the best available new home when their old nest is still intact. The algorithm uses a stepwise commitment scheme and a quorum rule to integrate information gathered by numerous individual ants visiting several candidate homes. By varying the rates at which they search for and accept these candidates, the ants yield a colony-level response that adaptively emphasizes either speed or accuracy. We propose such general but tunable algorithms as a design feature of complex systems, each algorithm providing elegant solutions to a wide range of problems.
Ultrashort antibacterial and antifungal lipopeptides
Authors: Makovitzki Arik , Avrahami Dorit , Shai Yechiel
Published: October 2006

Host-defense cationic antimicrobial peptides (≈12–50 aa long) play an essential protective role in the innate immune system of all organisms. Lipopeptides, however, are produced only in bacteria and fungi during cultivation, and they are composed of specific lipophilic moieties attached to anionic peptides (six to seven amino acids). Here we report the following. (
i
) The attachment of an aliphatic chain to otherwise inert, cationic D,L tetrapeptides endows them with potent activity against various microorganisms including antibiotic resistance strains. (
ii
) Cell specificity is determined by the sequence of the short peptidic chain and the length of the aliphatic moiety. (
iii
) Despite the fact that the peptidic chains are very short, their mode of action involves permeation and disintegration of membranes, similar to that of many long antimicrobial peptides. Besides adding important information on the parameters necessary for host-defense lipopeptides to kill microorganisms, the simple composition of these lipopeptides and their diverse specificities should make them economically available, innate immunity-mimicking antimicrobial and antifungal compounds for various applications.
Structural basis for mRNA and tRNA positioning on the ribosome
Authors: Berk Veysel , Zhang Wen , Pai Raj D. , Cate Jamie H. D.
Published: October 2006

Protein synthesis requires the accurate positioning of mRNA and tRNA in the peptidyl-tRNA site of the ribosome. Here we describe x-ray crystal structures of the intact bacterial ribosome from
Escherichia coli
in a complex with mRNA and the anticodon stem-loop of P-site tRNA. At 3.5-Å resolution, these structures reveal rearrangements in the intact ribosome that clamp P-site tRNA and mRNA on the small ribosomal subunit. Binding of the anticodon stem-loop of P-site tRNA to the ribosome is sufficient to lock the head of the small ribosomal subunit in a single conformation, thereby preventing movement of mRNA and tRNA before mRNA decoding.
Measuring covariation in RNA alignments: physical realism improves information measures
Authors: Lindgreen S. , Gardner P. P. , Krogh A.
Published: October 2006

Motivation: The importance of non-coding RNAs is becoming increasingly evident, and often the function of these molecules depends on the structure. It is common to use alignments of related RNA sequences to deduce the consensus secondary structure by detecting patterns of co-evolution. A central part of such an analysis is to measure covariation between two positions in an alignment. Here, we rank various measures ranging from simple mutual information to more advanced covariation measures.

Results: Mutual information is still used for secondary structure prediction, but the results of this study indicate which measures are useful. Incorporating more structural information by considering e.g. indels and stacking improves accuracy, suggesting that physically realistic measures yield improved predictions. This can be used to improve both current and future programs for secondary structure prediction. The best measure tested is the RNAalifold covariation measure modified to include stacking.

Availability: Scripts, data and supplementary material can be found at

Contact:  stinus@binf.ku.dk

Supplementary information: Supplementary data are available at Bioinformatics online.
Repseek, a tool to retrieve approximate repeats from large DNA sequences
Authors: Achaz Guillaume , Boyer Frédéric , Rocha Eduardo P. C. , Viari Alain , Coissac Eric
Published: October 2006

Summary: Chromosomes or other long DNA sequences contain many highly similar repeated sub-sequences. While there are efficient methods for detecting strict repeats or detecting already characterized repeats, there is no software available for detecting approximate repeats in large DNA sequences allowing for weighted substitutions and indels in a coherent statistical framework. Here, we present an implementation of a two-steps method (seed detection followed by their extension) that detects those approximate repeats. Our method is computationally efficient enough to handle large sequences and is flexible enough to account for influencing factors, such as sequence-composition biases both at the seed detection and alignment levels.

Availability:  

Contact:  achaz@abi.snv.jussieu.fr
Maximum likelihood inference of imprinting and allele-specific expression from EST data
Authors: Seoighe Cathal , Nembaware Victoria , Scheffler Konrad
Published: October 2006

Motivation: In a diploid organism the proportion of transcripts that are produced from the two parental alleles can differ substantially due, for example to epigenetic modification that causes complete or partial silencing of one parental allele or to cis acting polymorphisms that affect transcriptional regulation. Counts of SNP alleles derived from EST sequences have been used to identify both novel candidates for genomic imprinting as well as examples of genes with allelic differences in expression.

Results: We have developed a set of statistical models in a maximum likelihood framework that can make highly efficient use of public transcript data to identify genes with unequal representation of alternative alleles in cDNA libraries. We modelled both imprinting and allele-specific expression and applied the models to a large dataset of SNPs mapped to EST sequences. Using simulations, matched closely to real data, we demonstrate significantly improved performance over existing methods that have been applied to the same data. We further validated the power of this approach to detect imprinting using a set of known imprinted genes and inferred a set of candidate imprinted genes, several of which are in close proximity to known imprinted genes. We report evidence that there are undiscovered imprinted genes in known imprinted regions. Overall, more than half of the genes for which the most data are available show some evidence of allele-specific expression.

Availability: Software is available from the authors on request.

Contact:  cathal@science.uct.ac.za

Supplementary information:
Experimental validation of predicted mammalian erythroid cis-regulatory modules
Authors: Wang Hao , Zhang Ying , Cheng Yong , Zhou Yuepin , King David C. , Taylor James , Chiaromonte Francesca , Kasturi Jyotsna , Petrykowska Hanna , Gibb Brian , Dorman Christine , Miller Webb , Dore Louis C. , Welch John , Weiss Mitchell J. , Hardison Ross C.
Published: October 2006

Multiple alignments of genome sequences are helpful guides to functional analysis, but predicting cis-regulatory modules (CRMs) accurately from such alignments remains an elusive goal. We predict CRMs for mammalian genes expressed in red blood cells by combining two properties gleaned from aligned, noncoding genome sequences: a positive regulatory potential (RP) score, which detects similarity to patterns in alignments distinctive for regulatory regions, and conservation of a binding site motif for the essential erythroid transcription factor GATA-1. Within eight target loci, we tested 75 noncoding segments by reporter gene assays in transiently transfected human K562 cells and/or after site-directed integration into murine erythroleukemia cells. Segments with a high RP score and a conserved exact match to the binding site consensus are validated at a good rate (50%–100%, with rates increasing at higher RP), whereas segments with lower RP scores or nonconsensus binding motifs tend to be inactive. Active DNA segments were shown to be occupied by GATA-1 protein by chromatin immunoprecipitation, whereas sites predicted to be inactive were not occupied. We verify four previously known erythroid CRMs and identify 28 novel ones. Thus, high RP in combination with another feature of a CRM, such as a conserved transcription factor binding site, is a good predictor of functional CRMs. Genome-wide predictions based on RP and a large set of well-defined transcription factor binding sites are available through servers at http://www.bx.psu.edu/.
Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin
Authors: Johnson Steven M. , Tan Frederick J. , McCullough Heather L. , Riordan Daniel P. , Fire Andrew Z.
Published: October 2006

Nucleosome positions within the chromatin landscape are known to serve as a major determinant of DNA accessibility to transcription factors and other interacting components. To delineate nucleosomal patterns in a model genetic organism, Caenorhabditis elegans, we have carried out a genome-wide analysis in which DNA fragments corresponding to nucleosome cores were liberated using an enzyme (micrococcal nuclease) with a strong preference for cleavage in non-nucleosomal regions. Sequence analysis of 284,091 putative nucleosome cores obtained in this manner from a mixed-stage population of C. elegans reveals a combined picture of flexibility and constraint in nucleosome positioning. As has previously been observed in studies of individual loci in diverse biological systems, we observe areas in the genome where nucleosomes can adopt a wide variety of positions in a given region, areas with little or no nucleosome coverage, and areas where nucleosomes reproducibly adopt a specific positional pattern. In addition to illuminating numerous aspects of chromatin structure for C. elegans, this analysis provides a reference from which to begin an investigation of relationships between the nucleosomal pattern, chromosomal architecture, and lineage-based gene activity on a genome-wide scale.
Silencing of natural interferon producing cell activation by porcine circovirus type 2 DNA
Authors: Vincent Isabelle E. , Balmelli Carole , Meehan Brian , Allan Gordon , Summerfield Artur , McCullough Kenneth C.
Published: October 2006

Porcine circovirus type 2 (PCV2) infection of natural interferon producing cells (NIPCs) impairs the induction of interferon (IFN)‐α and tumour necrosis factor (TNF)‐α by cytosine‐phosphorothioate‐guanine (CpG) oligodeoxynucleotides (ODNs), thereby preventing both their autocrine maturation and the paracrine maturation of myeloid dendritic cells (DCs). The present study shows that the PCV2‐mediated inhibition of NIPCs was mediated by viral DNA, although it was independent of virus replication. The inhibitory effect of PCV2 DNA was more diversified than if it had simply targeted CpG‐ODN‐induced cytokines (IFN‐α, TNF‐α, interleukin‐6, IL‐12). A broad spectrum inhibition was noted, affecting responses induced by toll‐like receptor (TLR)‐7 and TLR9 agonists, as well as viruses including pseudorabies virus, transmissible gastroenteritis virus and classical swine fever virus. From these results, it would appear that PCV2 DNA can induce a dominant negative signal influencing independent pattern recognition receptor‐induced activation cascades. Despite a concomitant internalization of PCV2 DNA and CpG‐ODNs, no colocalization was observed, indicating that PCV2 DNA and CPG‐ODNs may not target the same receptor. This study describes a novel modulation of the innate immune response, which would render the host more susceptible to secondary or concomitant microbial infections.
Signal‐Averaged P Wave Reflects Change in Atrial Electrophysiological Substrate Afforded by Verapamil Following Cardioversion from Atrial Fibrillation
Authors: REDFEARN DAMIAN P. , SKANES ALLAN C. , LANE JOANNE , STAFFORD PETER J.
Published: October 2006

Background: Detailed analysis of signal‐averaged P waves (SAPW) can provide insights into atrial electrophysiology. Abbreviated dosing of verapamil prior to cardioversion improves outcome at 1 week postcardioversion. The mechanism by which verapamil manifests benefit is uncertain. We hypothesized the SAPW would reflect any change in atrial electrophysiologic substrate afforded by verapamil when compared with controls.

Methods: We investigated 23 patients attending external cardioversion of persistent atrial fibrillation (AF) (6 female; mean age 68 years). Patients were randomized to verapamil 240 mg daily in three divided doses 3 days before cardioversion and 1 week after, or usual medication. SAPW recordings were performed during sinus rhythm (SR) immediately after cardioversion, at 24 hours and 1 week.

Results: The groups were comparable in terms of age, gender, left atrial size, and duration of AF. Eight of nine patients prescribed verapamil maintained SR at 1 week postcardioversion compared with 6 of 14 controls (P = 0.027). SAPW spectral analysis delivered higher energy for patients prescribed verapamil (median (IQ range)); 40.8 (33.4–95.1) versus 25.7 (19.0–38.0) for energy within 20–150 Hz, P20 (μV2· s; P = 0.03). There was no difference in P‐wave duration (PWD) or root mean square of the terminal 30 ms between the two groups. Early reinitiation occurred in patients with significantly lower P‐wave energy 19.6 (12.9–24.6) versus 39.9 (24.0–47.0) (P = 0.017).

Conclusions: Verapamil 240 mg daily for 3 days prior to cardioversion and 1 week after reduces early recurrence of AF. The SAPW observations indicate change in atrial electrophysiologic substrate might be responsible for benefit afforded by verapamil.
Effect of Percutaneous Interventions within the Coronary Sinus on the Success Rate of the Implantations of Resynchronization Pacemakers
Authors: KOWALSKI OSKAR , LENARCZYK RADOSŁAW , PROKOPCZUK JANUSZ , PRUSZKOWSKA‐SKRZEP PATRYCJA , ZIELIŃSKA TERESA , ŚREDNIAWA BEATA , MUSIALIK‐ŁYDKA AGATA , PLUTA SŁAWOMIR , KUKULSKI TOMASZ , SZULIK MARIOLA , POLOŃSKI LECH , KALARUS ZBIGNIEW
Published: October 2006

Background: Cardiac resynchronization therapy (CRT) becomes a “gold standard” in therapy of selected patients with advanced heart failure. We set out to evaluate the feasibility and safety of percutaneous interventions within coronary sinus (CS) and their effect on the success rate of left ventricular (LV) lead implantation during CRT.

Methods: The study analyzed eight consecutive patients with the indications for CRT, who needed additional procedures within CS to overcome technical problems during left ventricular (LV) electrode implantation. The analyzed group consisted of three subgroups: patients in whom percutaneous balloon angioplasty within CS was needed (n = 4); patients with acute instability of the lead, requiring stenting of the vein to fix the electrode (n = 2); and patients with the stenting of CS due to late dislocation of the lead (n = 2). Success rate, procedure duration, fluoroscopy, complications, and electrical parameters of leads were analyzed.

Results: Success rate of the procedures was 87.5%; additional interventions increased overall efficacy of CRT implantation at our center from 88% to 98% (P < 0.05). Procedure duration (155.0 minute) and fluoroscopy time (42.5 minute) remained acceptable for the patient and operator; however, both were higher than in the procedures performed routinely in our hospital. Electrical properties of the LV leads were stable and within normal ranges during the observation period. We noted two local dissections of CS during the procedure, which remained clinically silent.

Conclusion: Percutaneous interventions within CS seem to be feasible and safe treatment options, which can improve the short‐ and long‐term success rates of CRT.
Atrioventricular Junction Ablation Followed by Resynchronization Therapy in Patients with Congestive Heart Failure and Atrial Fibrillation (AVERT‐AF) Study Design
Authors: HAMDAN MOHAMED H. , FREEDMAN ROGER A. , GILBERT EDWARD M. , DIMARCO JOHN P. , ELLENBOGEN KENNETH A. , PAGE RICHARD L.
Published: October 2006

Atrial fibrillation (AF) and congestive heart failure (CHF) affect millions of patients in the United States. Several studies suggest that AF and in particular the irregular ventricular response might be contributing to the left ventricular dysfunction. Studies that compared pharmacologic rate control to atrioventricular junction (AVJ) ablation followed by right ventricular pacing which restores a regular ventricular response, failed to show an improvement when compared to pharmacological rare control. These results might be explained by the fact that while AVJ ablation restored a regular ventricular response, it subjected patients to the detrimental effects of RV apical pacing. The AVERT‐AF trial (Atrio‐VEntricular Junction Ablation Followed by Resynchronization Therapy in patients with CHF and AF) is a prospective, randomized, double‐blinded, multicenter trial that will be testing the hypothesis that AVJ ablation followed by biventricular pacing significantly improves exercise capacity and functional status compared to pharmacologic rate control in patients with chronic AF and depressed ejection fraction, regardless of rate or QRS duration. A total of 180 patients will be enrolled to test the primary endpoint, which is exercise duration. Patients_enrollment will begin in summer 2006 and is expected to be completed in 2008. The results of this trial should help define the best treatment option for this common arrhythmia in patients with left ventricular dysfunction.
Syncope in Adults: Terminology, Classification, and Diagnostic Strategy
Authors: JHANJEE RAJAT , Van DIJK J. GERT , SAKAGUCHI SCOTT , BENDITT DAVID G.
Published: October 2006

Syncope is a relatively common clinical syndrome that is a subset of a broader range of conditions that cause transient loss of consciousness (TLOC). Other TLOC conditions include seizures, concussions, and intoxications. However, despite frequent confusion in the medical literature, syncope is and should be clearly distinguished from those other causes of TLOC by virtue of its pathophysiology; specifically, syncope is the result of self‐terminating inadequacy of global cerebral nutrient perfusion, while the other forms of TLOC have different etiologies. Unfortunately, the diagnostic evaluation of syncope remains for the most part poorly managed and inefficient. Careful history‐taking, physical examination, and judicious use of tests can not only increase the diagnostic yield of the evaluation, but also increase patient safety and reduced overall healthcare costs.
Inadequate ICD Discharges Due to Diaphragmatic Electromyopotential Oversensing as the First Sign of Right Ventricular Lead Perforation
Authors: WIEGAND UWE K. H. , WILKE IRIS , BONNEMEIER HENDRIK , EBERHARDT FRANK , BODE FRANK
Published: October 2006

Right ventricular lead perforation, when acute, is a rare but potentially life‐threatening complication of implantable cardioverter defibrillator (ICD) therapy. We report about a patient with early lead perforation presenting with repetitive ICD discharges due to oversensing of diaphragmatic electromyopotentials and describe the management of this complication.
Atrio‐Ventricular Synchronization by Single VDD Lead Inserted Through Persistent Left Superior Vena Cava in Patient with Turner's Syndrome
Authors: GOLZIO PIER GIORGIO , FRANCO ERICA , CHIRIBIRI AMEDEO
Published: October 2006

A 71‐year‐old woman with Turner's syndrome underwent pacemaker implantation for complete atrio‐ventricular block. During the procedure, the persistence of left sided superior vena cava (LSVC) was observed such that the lead, through the coronary sinus, reached the right atrium. By use of stylets, we could drive the lead against the lateral atrial wall and curve it through the tricuspid valve into the right ventricle. The tip reached an apical stable position, obtaining proper stimulation values. Moreover, the VDD dipole was positioned against high lateral atrial wall, adequately sensing the atrial potential. So, we could obtain an atrial synchronous ventricular pacing with only one VDD lead.