bluuebunny/crossref_metadata_2025 huggingface dataset:
Microbial NAD Metabolism: Lessons from Comparative Genomics
Authors: Gazzaniga Francesca , Stebbins Rebecca , Chang Sheila Z. , McPeek Mark A. , Brenner Charles
Published: August 2009

NAD is a coenzyme for redox reactions and a substrate of NAD-consuming enzymes, including ADP-ribose transferases, Sir2-related protein lysine deacetylases, and bacterial DNA ligases. Microorganisms that synthesize NAD from as few as one to as many as five of the six identified biosynthetic precursors have been identified. De novo NAD synthesis from aspartate or tryptophan is neither universal nor strictly aerobic. Salvage NAD synthesis from nicotinamide, nicotinic acid, nicotinamide riboside, and nicotinic acid riboside occurs via modules of different genes. Nicotinamide salvage genes
nadV
and
pncA
, found in distinct bacteria, appear to have spread throughout the tree of life via horizontal gene transfer. Biochemical, genetic, and genomic analyses have advanced to the point at which the precursors and pathways utilized by a microorganism can be predicted. Challenges remain in dissecting regulation of pathways.
ON THE STRATIFIED VECTOR BUNDLES
Authors: BISWAS INDRANIL
Published: August 2009

The stratified vector bundles on a smooth variety defined over an algebraically closed field k form a neutral Tannakian category over k. We investigate the affine group-scheme corresponding to this neutral Tannakian category.
TWISTED MELLIN TRANSFORMS OF A REAL ANALYTIC RESIDUE OF SIEGEL–EISENSTEIN SERIES OF DEGREE 2
Authors: HASEGAWA YASUKO , MIYAZAKI TAKUYA
Published: August 2009

We study a residual form of a real analytic Siegel–Eisenstein series, which generates a certain derived functor module occurring in a degenerate principal series representation. We compute its Mellin transforms twisted by various Maass wave forms to get explicit formulas as our results. We apply them to prove meromorphic continuations together with functional equations which are satisfied by those twisted Mellin transforms.
EQUATIONS OF THE MODULI OF HIGGS PAIRS AND INFINITE GRASSMANNIAN
Authors: HERNÁNDEZ-SERRANO D. , MUÑOZ PORRAS J. M. , PLAZA MARTÍN F. J.
Published: August 2009

In this paper the moduli space of Higgs pairs over a fixed smooth projective curve with extra formal data is defined and is endowed with a scheme structure. We introduce a relative version of the Krichever map using a fibration of Sato Grassmannians and show that this map is injective. This, together with the characterization of the points of the image of the Krichever map, allows us to prove that this moduli space is a closed subscheme of the product of the moduli of vector bundles (with formal extra data) and a formal anologue of the Hitchin base. This characterization also provides us with a method for explicitly computing KP-type equations that describe the moduli space of Higgs pairs. Finally, for the case where the spectral cover is totally ramified at a fixed point of the curve, these equations are given in terms of the characteristic coefficients of the Higgs field.
A FINITENESS THEOREM FOR DUAL GRAPHS OF SURFACE SINGULARITIES
Authors: POPESCU-PAMPU PATRICK , SEADE JOSÉ
Published: August 2009

Consider a fixed connected, finite graph Γ and equip its vertices with weights pi which are non-negative integers. We show that there is a finite number of possibilities for the coefficients of the canonical cycle of a numerically Gorenstein surface singularity having Γ as the dual graph of the minimal resolution, the weights pi of the vertices being the arithmetic genera of the corresponding irreducible components. As a consequence we get that if Γ is not a cycle, then there is a finite number of possibilities of self-intersection numbers which one can attach to the vertices which are of valency ≥ 2, such that one gets the dual graph of the minimal resolution of a numerically Gorenstein surface singularity. Moreover, we describe precisely the situations when there exists an infinite number of possibilities for the self-intersections of the component corresponding to some fixed vertex of Γ.
CENTER PROBLEM AND MULTIPLE HOPF BIFURCATION FOR THE Z5-EQUIVARIANT PLANAR POLYNOMIAL VECTOR FIELDS OF DEGREE 5
Authors: LIU YIRONG , LI JIBIN
Published: September 2009

This paper proves that a Z5-equivariant planar polynomial vector field of degree 5 has at least five symmetric centers, if and only if it is a Hamltonian vector field. The characterization of a center problem is completely solved. The shortened expressions of the first four Lyapunov constants are given. Under small Z5-equivariant perturbations, the conclusion that the perturbed system has at least 25 limit cycles with the scheme 〈5 ∐ 5 ∐ 5 ∐ 5 ∐ 5〉 is rigorously proved.
A NEW CHAOTIC SYSTEM BASED ON MULTIPLE-ANGLE SINUSOIDAL FUNCTION: DESIGN AND IMPLEMENTATION
Authors: ZHANG CHAOXIA , TANG WALLACE K. S. , YU SIMIN
Published: September 2009

This paper proposes a new three-dimensional chaotic generator, for which the nonlinearity is based on sinusoidal function. Based on a practical circuit design for realizing a wide angular range of sinusoidal functions, chaotic attractors with large number of scrolls have been obtained. Different types of attractors are available, governed by the choices of variables used in the sinusoidal function. The design is illustrated with both simulations and experiments.
ALMOST UNKNOTTED EMBEDDINGS OF GRAPHS IN Z3 AND HIGHER DIMENSIONAL ANALOGUES
Authors: MADRAS N. , SUMNERS D. W. , WHITTINGTON S. G.
Published: August 2009

We consider the number of almost unknotted embeddings of graphs in Z3. We show that the number of such embeddings is the same, to exponential order, as the number of unknotted embeddings. We also consider some higher dimensional analogues, ie almost unknotted embeddings of surfaces which are p-dimensional analogues of Θ-graphs in Zp+2. We describe a lattice version of the spinning construction which establishes the embeddability of such surfaces in Zp+2 and show that the number of embeddings is the same, to exponential order, as the number of unknotted embeddings. The proofs of our upper bounds feature a novel application of the classical Loomis–Whitney inequality.
OKA'S CONJECTURE ON IRREDUCIBLE PLANE SEXTICS II
Authors: DEGTYAREV ALEX
Published: August 2009

We complete the proof of Oka's conjecture on the Alexander polynomial of an irreducible plane sextic. We also calculate the fundamental groups of irreducible sextics with a singular point adjacent to J10.
UNKNOTTING NUMBERS OF DIAGRAMS OF A GIVEN NONTRIVIAL KNOT ARE UNBOUNDED
Authors: TANIYAMA KOUKI
Published: August 2009

We show that for any nontrivial knot K and any natural number n, there is a diagram D of K such that the unknotting number of D is greater than or equal to n. It is well-known that twice the unknotting number of K is less than or equal to the crossing number of K minus one. We show that the equality holds only when K is a (2, p)-torus knot.
MINIMAL KNOTTING NUMBERS
Authors: MANN CASEY , MCLOUD-MANN JENNIFER , RANALLI RAMONA , SMITH NATHAN , MCCARTY BENJAMIN
Published: August 2009

This article concerns the minimal knotting number for several types of lattices, including the face-centered cubic lattice (fcc), two variations of the body-centered cubic lattice (bcc-14 and bcc-8), and simple-hexagonal lattices (sh). We find, through the use of a computer algorithm, that the minimal knotting number in sh is 20, in fcc is 15, in bcc-14 is 13, and bcc-8 is 18.
(ℓ, k)-ROUTING ON PLANE GRIDS
Authors: HUC FLORIAN , SAU IGNASI , ŽEROVNIK JANEZ
Published: September 2009

The packet routing problem plays an essential role in communication networks. It involves how to transfer data from some origins to some destinations within a reasonable amount of time. In the (ℓ, k)-routing problem, each node can send at most ℓ packets and receive at most k packets. Permutation routing is the particular case ℓ = k = 1. In the r-central routing problem, all nodes at distance at most r from a fixed node v want to send a packet to v.

In this article we study the permutation routing, the r-central routing and the general (ℓ, k)-routing problems on plane grids, that is square grids, triangular grids and hexagonal grids. We use the store-and-forward Δ-port model, and we consider both full and half-duplex networks. We first survey the existing results in the literature about packet routing, with special emphasis on (ℓ, k)-routing on plane grids. Our main contributions are the following:

1. Tight permutation routing algorithms on full-duplex hexagonal grids, and half duplex triangular and hexagonal grids.

2. Tight r-central routing algorithms on triangular and hexagonal grids.

3. Tight (k, k)-routing algorithms on square, triangular and hexagonal grids.

4. Good approximation algorithms (in terms of running time) for (ℓ, k)-routing on square, triangular and hexagonal grids, together with new lower bounds on the running time of any algorithm using shortest path routing.

These algorithms are all completely distributed, i.e., can be implemented independently at each node. Finally, we also formulate the (ℓ, k)-routing problem as a WEIGHTED EDGE COLORING problem on bipartite graphs.
BALANCING TRAFFIC LOAD USING ONE-TURN RECTILINEAR ROUTING
Authors: DUROCHER STEPHANE , KRANAKIS EVANGELOS , KRIZANC DANNY , NARAYANAN LATA
Published: September 2009

We consider the problem of load-balanced routing, where a dense network is modelled by a continuous square region, and origin-destination node pairs correspond to pairs of points in that region. The objective is to define a routing policy that assigns a continuous path to each origin-destination pair while minimizing the traffic, or load, passing through any single point. While the average load is minimized by straight-line routing, such a routing policy distributes the load non-uniformly, resulting in higher load near the center of the region. We consider one-turn rectilinear routing policies that divert traffic away from regions of heavier load, resulting in up to a 33% reduction in the maximum load while simultaneously increasing the path lengths by an average of less than 28%. Our policies are simple to implement, being both local and oblivious. We provide a lower bound that shows that no one-turn rectilinear routing policy can reduce the maximum load by more than 39% and we give a polynomial-time procedure for approximating the optimal randomized policy.
NONLINEAR MECHANICS OF SINGLE-ATOMIC-LAYER GRAPHENE SHEETS
Authors: LU QIANG , HUANG RUI
Published: September 2009

The unique lattice structure and properties of graphene have drawn tremendous interests recently. By combining continuum and atomistic approaches, this paper investigates the mechanical properties of single-atomic-layer graphene sheets. A theoretical framework of nonlinear continuum mechanics is developed for graphene under both in-plane and bending deformation. Atomistic simulations are carried out to deduce the effective mechanical properties. It is found that graphene becomes highly nonlinear and anisotropic under finite-strain uniaxial stretch, and coupling between stretch and shear occurs except for stretching in the zigzag and armchair directions. The theoretical strength (fracture strain and fracture stress) of perfect graphene lattice also varies with the chiral direction of uniaxial stretch. By rolling graphene sheets into cylindrical tubes of various radii, the bending modulus of graphene is obtained. Buckling of graphene ribbons under uniaxial compression is simulated and the critical strain for the onset of buckling is compared to a linear buckling analysis.
Input-sensitive scalable continuous join query processing
Authors: Agarwal Pankaj K. , Xie Junyi , Yang Jun , Yu Hai
Published: September 2009

This article considers the problem of scalably processing a large number of continuous queries. Our approach, consisting of novel data structures and algorithms and a flexible processing framework, advances the state-of-the-art in several ways. First, our approach is query sensitive in the sense that it exploits potential overlaps in query predicates for efficient group processing. We partition the collection of continuous queries into groups based on the clustering patterns of the query predicates, and apply specialized processing strategies to heavily clustered groups (or
hotspots
). We show how to maintain the hotspots efficiently, and use them to scalably process continuous select-join, band-join, and window-join queries. Second, our approach is also data sensitive, in the sense that it makes cost-based decisions on how to process each incoming tuple based on its characteristics. Experiments demonstrate that our approach can improve the processing throughput by orders of magnitude.
HMD calibration and its effects on distance judgments
Authors: Kuhl Scott A. , Thompson William B. , Creem-Regehr Sarah H.
Published: September 2009

Most head-mounted displays (HMDs) suffer from substantial optical distortion, and vendor-supplied specifications for field-of-view often are at variance with reality. Unless corrected, such displays do not present perspective-related visual cues in a geometrically correct manner. Distorted geometry has the potential to affect applications of HMDs, which depend on precise spatial perception. This article provides empirical evidence for the degree to which common geometric distortions affect one type of spatial judgment in virtual environments. We show that minification or magnification in the HMD that would occur from misstated HMD field of view causes significant changes in distance judgments. Incorrectly calibrated pitch and pincushion distortion, however, do not cause statistically significant changes in distance judgments for the degree of distortions examined. While the means for determining the optical distortion of display systems are well known, they are often not used in non-see-through HMDs due to problems in measuring and correcting for distortion. As a result, we also provide practical guidelines for creating geometrically calibrated systems.
Reductive thinking in a quantitative perspective
Authors: Armoni Michal
Published: September 2009

The research described in this paper continues a previous, qualitative (mostly interview-based) study that examined the ways undergraduate computer science students perceive, experience, and use reduction as a problem-solving strategy. The current study examines the same issue, but in the context of a larger population, using quantitative analysis methods, and focusing on algorithmic problems.
A data type to exploit online data sources
Authors: Thornton Matthew , Edwards Stephen H.
Published: September 2009

Recent work in developing student assignments has involved making use of online data resources to make them more interesting and to give students real world information to interact with in some manner. While definitely a practical approach, the work that has been done so far is either for "CS0" courses targeted at non-majors, often using tools like Microsoft Excel, or courses that require a level of skill at programming from the students. Additionally, existing tools are specific to a particular structure of the data (CSV, XML, and others). As a result, these constraints make on-line real-world data sets difficult to use in typical introductory programming courses for majors.

Objects-first approaches to teaching introductory programming advocate the use of objects early on. Consequently, students are able to take advantage of using data types early on. We have created an interface that allows students to access real-world data sets from online (or local) sources in a uniform fashion. This abstraction allows students with minimal programming experience to load, process, and manipulate external data sets in a variety of formats. We also developed a lab assignment where students accessed an online CSV data source to demonstrate feasibility and to gain experience with classroom use of this approach.
Teaching students to develop thread-safe java classes
Authors: Fekete Alan D.
Published: September 2009

Concurrent programming was once the preserve of experts writing systems internals; but recently the growing importance of application servers, and the excellent support in Java and C# for thread handling, has brought threads and locking as topics that every software developer might experience, and therefore every computer science graduate ought to know. In this paper we report on several years of experience teaching this material in the early years of the curriculum. We focus on one aspect of multi-threaded code, namely how to write sensible thread-safe classes. We identify the learning outcomes we aim to deliver, and we discuss the main pedagogic difficulties students find. We present some examples that can help students avoid common erroneous views.
Test-driven development in education
Authors: Kollanus Sami , Isomöttönen Ville
Published: September 2009

Test-Driven Development (TDD) was applied in educational setting right after it became well-known as a key practice of Extreme Programming (XP). Basically, there are many studies reporting positive experiences on TDD applied in different levels of a curriculum. In this paper, we discuss the role of TDD in education through the students' experiences. In our experiment, a challenging programming task was applied in order to see what kind of difficulties the students would encounter and discuss. The students' answers revealed several topics that require a careful treatment in teaching to avoid conceptual confusion. For example, the topics include the scalability of TDD, extent of single test, and discipline.
Group work support for the BlueJ IDE
Authors: Fisker Kasper , McCall Davin , Kölling Michael , Quig Bruce
Published: September 2009

Learning to work in teams is essential for every software professional. Developing software as a team project is the standard practice in industry, and should be practiced in university courses. Starting effective group work practices early can lead to better acceptance of group work as a standard development mode.

Nonetheless, group work is often not included in introductory programming courses. The reason is often the necessary overhead associated with developing software in groups. We present a design and implementation of group work support tools integrated into the educational BlueJ IDE, which remove much of the tool overhead and make it easier to include group work in introductory courses.
Perceived behavior control and its influence on the adoption of software tools
Authors: Levy Ronit Ben-Bassat , Ben-Ari Mordechai
Published: September 2009

Animation systems-software tools that show a dynamic view of the execution of a program-can help novices improve their learning of programming and facilitate teaching. However, the use of such visualization tools is not as widespread as one would expect. This paper presents the results of a study of the attitudes that teachers possess on the use of the Jeliot animation system as a pedagogical tool. The results show that in spite of the fact that computer science teachers have positive behavioral beliefs about the use of animation systems in their classrooms, most of them feel a low level of
perceived behavior control
, and this can explain the low rate of using such tools in practice. We conclude that developers and educators should give attention to control issues relevant to the tools they develop and use.
Sorting out sorting
Authors: Furcy David , Naps Thomas , Wentworth Jason
Published: September 2009

Ronald Baecker's
Sorting Out Sorting (SOS)
set the stage for much of what has followed in the evolution of algorithm visualization (AV). That period of evolution has now spanned over a quarter century, and we have learned much about how to effectively use AV. This paper addresses how we can incorporate that knowledge into a new rendition of SOS, which we call
SOS - The Sequel
. In this sequel we attempt to transform Baecker's original video into a highly interactive multimedia learning resource delivered over the Web using Macromedia Flash. The paper describes the design and use of this new resource and reports on a small empirical study designed to measure its effectiveness.
Cognitive dimensions questionnaire applied to exploratory algorithm design
Authors: Martin Chris J. , Hughes Janet M.
Published: September 2009

In software engineering, the stage between problem realization and implementation of a solution is not well supported by technology. It is common to see work being carried out on paper or whiteboards. This paper documents a pilot study to identify some reasons as to why paper and whiteboards are useful tools in early exploratory design and exposes some questions about where technology may fit in augmenting this stage of software engineering. The cognitive dimensions questionnaire was used to investigate notations and devices used in exploratory algorithm design.
Distributed application launching for high quality graphics in synchronous distance education
Authors: Pullen J. Mark , Chen Jim X.
Published: September 2009

Previous ITiCSE papers have reported on Network EducationWare (NEW), an open source software system that supports synchronous and asynchronous distance education easily and inexpensively via the Internet. This paper reports on an innovative capability recently added to NEW that enables simultaneous execution of applications on all participating computers in both Windows and Linux systems, and explains how we have used this capability to teach a course in Computer Graphics online. Teaching graphics in this way previously was impossible because transmitting the visual output of graphics programs in real time with good quality is too demanding for normal Internet connections. This problem was solved by using the NEW application launcher to invoke Java classes, provided by the instructor, on all student computers simultaneously. The capability works with modest Internet capacity and also is captured in recorded sessions for asynchronous use. We explain how the NEW capability works and describe its use in online teaching of Computer Graphics.
Teaching software quality assurance by encouraging student contributions to an open source web-based system for the assessment of programming assignments
Authors: Gotel Olly , Scharff Christelle , Wildenberg Andrew
Published: September 2009

This paper presents a novel and innovative pedagogical approach for teaching software quality assurance in the undergraduate computer science curriculum. The approach is based on students contributing programming problems to an open source web-based system that is used for student practice and instructor assessment of assignments. WeBWorK, and some of the latest web-based systems, use a mechanism based on unit testing to account for variation in the way in which the same problem can be answered in an accurate manner, making such systems highly appealing for education. Tackling open-ended programming problems within WeBWorK therefore requires students to write a code fragment that is then checked for semantic correctness. Given that WeBWorK is open source, the teaching approach that we have evolved revolves around students creating their own problems for other students to practice with. This requires students to construct comprehensive unit tests that can assure both the usability and accuracy of their work prior to deployment. The paper describes this approach, gives examples of student work, presents findings from the experience of using the approach in the classroom, and discusses broader lessons and reasons for integrating software quality assurance practices into the computer science curriculum.
Wu's castle
Authors: Eagle Michael , Barnes Tiffany
Published: September 2009

We are developing games to teach introductory computer science concepts to increase student motivation and engagement in learning to program.
Wu's Castle
is a two-dimensional role playing game that teaches loops and arrays in an interactive, visual way. In this game, the player interactively programs magical creatures to create armies of snowmen. The game provides immediate feedback and helps students visualize the execution of their code in a safe environment. We tested the game in a CS1 course, where students could earn extra credit to play
Wu's Castle
. Our results show learning gains for game players, compared both through pre- and post-tests differences and improved performance on relevant final exam questions when compared to students who did not play the game. The results of this study suggest that
Wu's Castle
implements good practices for teaching programming within a game.
Improving student performance using automated testing of simulated digital logic circuits
Authors: Kurmas Zachary
Published: September 2009

JLSCircuitTester
helps automate the testing and grading of circuits built using digital logic simulators. With many simulators, the testing and grading of circuits is tedious and time consuming enough that students do not test their circuits thoroughly.
JLSCircuitTester
addresses this problem by simplifying the means by which users specify sets of input and expected output values. In addition, it automatically verifies that the circuit under test produces the correct output. The projects submitted during the pilot semester contained approximately half as many errors as the previous semester's projects. The automatic evaluation has also simplified the grading of those projects.
Practical tips for creating podcasts in higher education
Authors: Sheridan-Ross Jakki , Gorra Andrea , Finlay Janet
Published: September 2009

Podcasts are of particular interest in order to promote flexibility in teaching and learning. In this note, we provide tips for creating podcasts with a particular relevance for computing students, based on our experience at Leeds Metropolitan University.

A number of trials have taken place within Innovation North Faculty of Information and Technology including the development of learning materials and support mechanisms for academic staff wishing to develop new (or adapt existing) resources to this new format. To date, podcasts have been created to support the teaching of motion capture, advanced video technologies, and project-based work for computing students. CETL ALiC (Active Learning in Computing) is supporting the trials through the development of a Podcast Solutions Pilot which has allowed us to observe, support, develop and explore some of the issues around using this type of technology in a teaching and learning environment.
Teaching push-down automata and turing machines
Authors: García-Osorio César , Mediavilla-Sáiz Iñigo , Jimeno-Visitación Javier , García-Pedrajas Nicolás
Published: September 2009

In this paper we present the new version of a tool to assist in teaching formal languages and automata theory. In the previous version the tool provided algorithms for regular expressions, finite automata and context free grammars. The new version can simulate as well push-down automata and Turing machines.
A tool for teaching LL and LR parsing algorithms
Authors: García-Osorio César , Gómez-Palacios Carlos , García-Pedrajas Nicolás
Published: September 2009

In this paper we present a tool to assist in teaching top-down and bottom-up analysis algorithms. The tool provides simulation for the following analysis algorithms: LL, SLR, LALR and LR. During the simulation the student can simultaneously see the pending input, the analysis stack and tables, the generated output and the parse tree.
The use of role play to simulate a tethered swarm of robots for urban search and rescue (USAR)
Authors: Albin-Clark Adrian , Vishnu Arun Kumar T. R.
Published: September 2009

A role play activity, in which people become tethered search robots, was trialled. The main constraint was space on the science centre floor, which reduced the effectiveness of the message.
A method for analyzing reading comprehension in computer science courses
Authors: Gunawardena Ananda , Barr John , Owens Andrew
Published: September 2009

Reading has traditionally been seen as an essential component in learning, especially at the university level. However, many instructors in higher education, especially in technical courses, do not emphasize reading or try to evaluate it. In this abstract we present an automated system designed to measure and improve reading comprehension and describe preliminary results using the system.
Reevaluating and refining the engagement taxonomy
Authors: Lauer Tobias
Published: September 2009

We propose extensions to the
engagement taxonomy
, based on a comparative review of several experiments carried out within that framework to assess the effectiveness of algorithm visualization.
Potential benefits of corrected-errors in AVBL
Authors: Saravanos Antonios
Published: September 2009

This paper proposes the examination of the potential role that corrected-errors can play in asynchronous online video-based learning of troubleshooting education within the context of computer programming language pedagogy.
Flower Evolution: The Origin and Subsequent Diversification of the Angiosperm Flower
Authors: Specht Chelsea D. , Bartlett Madelaine E.
Published: August 2009

Developmental genetic pathways involved in flower formation in model plants such as Arabidopsis and maize enable us to identify genes, gene families, and gene networks that are involved in the regulation of flower initiation, growth and differentiation. These genes can then function as “candidate genes” and their expression, function, and biochemical interactions can be explored in other lineages to determine if they provide a necessary and sufficient toolkit for the development of the flower. Likewise, a view to the fossil record can provide documentation of reproductive innovations occurring within gymnosperms or along the stem lineage leading to angiosperms, elucidating the transitions required for the evolution of the angiosperm flower from an ancestral reproductive strobilus. Here we discuss the origin and subsequent evolution in form of the flower, highlighting recent studies in paleobotany, morphology, evolution, and developmental genetics with the goal of outlining advances in our understanding of flower evolution.
Evolution of Placentas in the Fish Family Poeciliidae: An Empirical Study of Macroevolution
Authors: Pollux B.J.A. , Pires M.N. , Banet A.I. , Reznick D.N.
Published: August 2009

The placenta is a complex organ that mediates all physiological and endocrine interactions between mother and developing embryos. Placentas have evolved throughout the animal kingdom, but little is known about how or why the placenta evolved. We review hypotheses about the evolution of placentation and examine empirical evidence in support for these hypotheses by drawing on insights from the fish family Poeciliidae. The placenta evolved multiple times within this family, and there is a remarkable diversity in its form and function among closely related species, thus providing us with ideal material for studying its evolution. Current hypotheses fall into two categories: adaptive hypotheses, which propose that the placenta evolved as an adaptation to environmental pressures, and conflict hypotheses, which posit that the placenta evolved as a result of antagonistic coevolution. These hypotheses are not mutually exclusive. Each may have played a role at different stages of the evolutionary process.
Belowground Herbivory and Plant Defenses
Authors: van Dam Nicole M.
Published: August 2009

Belowground-feeding herbivores may be very destructive to plants. Roots are known to produce various defense compounds to protect themselves against these herbivores, both with direct and indirect—inducible—defense compounds. Recent literature reviews reveal no overall pattern for root-shoot defense allocation. Optimal defense allocation patterns within roots may be predicted with an ecophysiological model taking into account the value and vulnerability of root classes. Induced responses elicited by root herbivores are likely to result in systemic responses in the shoots. These systemic responses may affect aboveground herbivores and higher trophic levels. This calls into question whether root-to-shoot systemic induction is an adaptive response. Physiological responses conferring tolerance may co-occur with resistance responses, depending on the biotic and abiotic environment of the roots. More detailed analyses of root defenses and the feeding sites of herbivores are needed to gain a better understanding of optimal defense allocation in roots.
Molecular Estimation of Dispersal for Ecology and Population Genetics
Authors: Broquet Thomas , Petit Eric J.
Published: August 2009

The dispersal process, by which individuals or other dispersing agents such as gametes or seeds move from birthplace to a new settlement locality, has important consequences for the dynamics of genes, individuals, and species. Many of the questions addressed by ecology and evolutionary biology require a good understanding of species’ dispersal patterns. Much effort has thus been devoted to overcoming the difficulties associated with dispersal measurement. In this context, genetic tools have long been the focus of intensive research, providing a great variety of potential solutions to measuring dispersal. This methodological diversity is reviewed here to help (molecular) ecologists find their way toward dispersal inference and interpretation and to stimulate further developments.
Is There a Latitudinal Gradient in the Importance of Biotic Interactions?
Authors: Schemske Douglas W. , Mittelbach Gary G. , Cornell Howard V. , Sobel James M. , Roy Kaustuv
Published: August 2009

Biotic interactions are believed to play a role in the origin and maintenance of species diversity, and multiple hypotheses link the latitudinal diversity gradient to a presumed gradient in the importance of biotic interactions. Here we address whether biotic interactions are more important at low latitudes, finding support for this hypothesis from a wide range of interactions. Some of the best-supported examples are higher herbivory and insect predation in the tropics, and predominantly tropical mutualisms such as cleaning symbioses and ant-plant interactions. For studies that included tropical regions, biotic interactions were never more important at high latitudes. Although our results support the hypothesis that biotic interactions are more important in the tropics, additional research is needed, including latitudinal comparisons of rates of molecular evolution for genes involved in biotic interactions, estimates of gradients in interaction strength, and phylogenetic comparisons of the traits that mediate biotic interactions.
Spontaneous Mutation Accumulation Studies in Evolutionary Genetics
Authors: Halligan Daniel L. , Keightley Peter D.
Published: August 2009

Mutation accumulation (MA) experiments, in which mutations are allowed to drift to fixation in inbred lines, have been a principal way of studying the rates and properties of new spontaneous mutations. Phenotypic assays of MA lines inform us about the nature of new mutational variation for quantitative traits and provide estimates of the genomic rate and the distribution of effects of new mutations. Parameter estimates compared for a range of species suggest that the genomic mutation rate varies by several orders of magnitude and that the distribution of effects tends to be dominated by large-effect mutations. Some experiments suggest synergistic interactions between the effects of spontaneous deleterious mutations, whereas others do not. There is little reliable information on the distribution of dominance effects of new mutations. Most evidence does not suggest strong dependency of the effects of new mutations on the environment. Information from phenotypic assays has recently been augmented by direct molecular estimates of the mutation rate.
What Salamanders Have Taught Us About Evolution
Authors: Wake David B.
Published: August 2009

Taxon-based research in evolution permits the development of a multidimensional approach, illustrated here with lessons learned from research on salamanders. The clade is widespread and diverse, yet sufficiently small that one can keep all of the species in mind. This facilitates research from diverse perspectives: systematics and phylogenetics, morphology, development, ecology, neurobiology, behavior, and physiology. Different avenues of research offer unique perspectives on how a relatively old vertebrate clade has diversified. An integrated, hierarchically organized, multidimensional program of research on a taxon illuminates many general principles and processes. Among these are the nature of species and homology, adaptation and adaptive radiations, size and shape in relation to issues in organismal integration, ontogeny and development in relation to phylogeny, the ubiquity of homoplasy, ecological niche conservation, species formation, biodiversity, and conservation. Opportunities for future research and threats to the continued existence of salamanders are briefly outlined.
Anorexia Nervosa: Current Status and Future Directions
Authors: Attia Evelyn
Published: August 2009

Anorexia nervosa (AN) is a serious mental illness categorized by a failure to maintain a minimally normal weight, a fear of gaining weight or becoming fat, and preoccupations about body shape or weight. AN is associated with significant morbidity and a mortality rate as high as that seen in any psychiatric illness. Biological factors, including genetic predisposition, appear to play a role in the development of AN. Treatment is challenging both because interventions with clear empirical support have not been identified and because individuals affected by AN are typically reluctant to undergo weight restoration. Preliminary studies suggest that family-based treatment may be useful for younger patients with AN. Treatment development for adults with AN and pursuit of neurobiological correlates of AN remain high-priority research areas.
Progressive Multifocal Leukoencephalopathy in Patients on Immunomodulatory Therapies
Authors: Major Eugene O.
Published: August 2009

Progressive multifocal leukoencephalopathy (PML) is a demyelinating disease of the white matter of the human brain caused by lytic infection of oligodendrocytes with the human polyomavirus JCV. Although the majority of PML cases occur in severely immune-suppressed individuals, with HIV-1 infection as the predominant factor, PML has been increasingly diagnosed in patients treated with biological therapies such as monoclonal antibodies that modulate immune system functions. Monoclonal antibodies that target the cell adhesion molecules VLA-4 (natalizumab; Tysabri® for multiple sclerosis and Crohn's disease) or LFA-1 (efalizumab; Raptiva® for severe forms of plaque psoriasis) to prevent extravasation of inflammatory T cells into tissues, or target the cell surface marker CD20 (rituximab; Rituxan® for hematologic malignancies and rheumatoid arthritis) to deplete peripheral circulating B cells, have all been associated with PML. The link between the effects of these therapies on the immune system and the occurrence of PML has prompted investigations on JCV sites of latency in the bone marrow, the migration of bone marrow derived cells into the circulation, and intracellular virus entry into the brain.
Selecting the Best Forecasting-Implied Volatility Model Using Genetic Programming
Authors: Abdelmalek Wafa , Ben Hamida Sana , Abid Fathi
Published: August 2009

The volatility is a crucial variable in option pricing and hedging strategies. The aim of this paper is to provide some initial evidence of the empirical relevance of genetic programming to volatility's forecasting. By using real data from S&P500 index options, the genetic programming's ability to forecast Black and Scholes-implied volatility is compared between time series samples and moneyness-time to maturity classes. Total and out-of-sample mean squared errors are used as forecasting's performance measures. Comparisons reveal that the time series model seems to be more accurate in forecasting-implied volatility than moneyness time to maturity models. Overall, results are strongly encouraging and suggest that the genetic programming approach works well in solving financial problems.
The Spectrum of Autoimmune Thyroid Disease in the Short to Medium Term Following Interferon‐α Therapy for Chronic Hepatitis C
Authors: Tran Huy A. , Reeves Glenn E. M.
Published: August 2009

Autoimmune thyroid diseases are common manifestations of hepatitis C infection, exacerbated by interferon‐based treatment. However, the occurrence and pattern of thyroid disease in the short/medium term following the completion of IFN‐based therapy is relatively unknown and there are very few previous reports regarding the specific spectrum of autoimmune thyroid disease that may follow such therapy. We hereby report 3 cases which demonstrate the range of thyroid diseases that may occur following interferon therapy. The hypothesis advanced is that in the pathogenesis of these conditions there must be both triggering and sustaining mechanisms as thyroid diseases occur well outside the immediate effect window of pegylated interferon. This paper suggests the need to continue thyroid surveillance in IFN‐treated HCV patients following the completion of therapy, perhaps for the first 6 months.
Positive Correlation of PTH-Related Peptide with Glucose in Type 2 Diabetes
Authors: Legakis Ioannis , Mantzouridis Timos
Published: August 2009

Type 2 diabetes is characterized by hyperglycemia resulting from insulin resistance in the setting of inadequate beta-cell compensation. Recent studies indicate that for attaining a well-functioning -cell mass, parathyroid hormone-related protein (PTHrP) is a very promising candidate among several insulinotropic peptides. In order to elucidate its role, we determine the levels of PTHrP, insulin and c-peptide in type 2 diabetics and in normal subjects in the fasting state. We enrolled 28 patients (16 men and 12 postmenopausal women) with type 2 diabetes and twenty eight aged-matched healthy individuals as control subjects (15 men and 13 women). PTHrP was statistically significant correlated with glucose in type 2 diabetes and in normal subjects in the fasting state. Additionally, PTHrP serum levels exhibited a significant increase in type 2 diabetes compared to control subjects. Interestingly, PTHrP showed a positive correlation with insulin levels only among healthy individuals presumably due to defective glucose stimulated insulin secretion known to occur in type 2 diabetics. In conclusion ,the strong positive relation of PTHrP with glucose in the fasting state in patients with type 2 diabetes mellitus raises several questions for further experimentation concerning its exact role and physiological significance.
Brachytherapy for Prostate Cancer: A Systematic Review
Authors: Koukourakis Georgios , Kelekis Nikolaos , Armonis Vassilios , Kouloulias Vassilios
Published: August 2009

Low-dose rate brachytherapy has become a mainstream treatment option for men diagnosed with prostate cancer because of excellent long-term treatment outcomes in low-, intermediate-, and high-risk patients. To a great extend due to patient lead advocacy for minimally invasive treatment options, high-quality prostate implants have become widely available in the US, Europe, and Japan. High-dose-rate (HDR) afterloading brachytherapy in the management of localised prostate cancer has practical, physical, and biological advantages over low-dose-rate seed brachytherapy. There are no free live sources used, no risk of source loss, and since the implant is a temporary procedure following discharge no issues with regard to radioprotection use of existing facilities exist. Patients with localized prostate cancer may benefit from high-dose-rate brachytherapy, which may be used alone in certain circumstances or in combination with external-beam radiotherapy in other settings. The purpose of this paper is to present the essentials of brachytherapies techniques along with the most important studies that support their effectiveness in the treatment of prostate cancer.
A Facial Expression Parameterization by Elastic Surface Model
Authors: Yano Ken , Harada Koichi
Published: August 2009

We introduce a novel parameterization of facial expressions by using elastic surface model. The elastic surface model has been used as a deformation tool especially for nonrigid organic objects. The parameter of expressions is either retrieved from existing articulated face models or obtained indirectly by manipulating facial muscles. The obtained parameter can be applied on target face models dissimilar to the source model to create novel expressions. Due to the limited number of control points, the animation data created using the parameterization require less storage size without affecting the range of deformation it provides. The proposed method can be utilized in many ways: (1) creating a novel facial expression from scratch, (2) parameterizing existing articulation data, (3) parameterizing indirectly by muscle construction, and (4) providing a new animation data format which requires less storage.
The Response of Hemostatic Marker Levels to Activated Factor VII in a Neonate following Cardiopulmonary Bypass
Authors: Eisses Michael J. , Richards Michael , Joffe Denise , Geiduschek Jeremy M. , Chandler Wayne L.
Published: August 2009

The primary function of recombinant activated factor VII (rFVIIa) is to increase thrombin formation which leads to increased fibrin and less “bleeding.” As a result, most of literature utilizes “bleeding” as the outcome measure with respect to rFVIIa. However, we report the actual effect of rFVIIa on changes in hemostatic markers such as prothrombin activation peptide F1.2, thrombin antithrombin complex (TAT), D-dimer, tissue plasminogen activator (tPA), and plasminogen activator inhibitor (PAI) in a neonate after cardiopulmonary bypass. A single dose of rFVIIa caused a 5.5-fold increase in F1.2, 3.5-fold increase in TAT, and a small increase in d-dimer compared to only a 1.5-fold increase, no increase, and a decrease, respectively, in two neonates undergoing the same procedure having not received rFVIIa. The patterns of change for tPA and PAI were similar.
Fabry‐Pérot Fiber‐Optic Sensors for Physical Parameters Measurement in Challenging Conditions
Authors: Pinet Éric
Published: August 2009

Optical fiber sensors have unique advantages and distinctive features that make them very attractive for many applications especially those involving challenging conditions where other traditional electrical sensors usually fail. Among the commercially available optical fiber sensors, the Fabry‐Pérot sensing technology is probably the most versatile and the most interesting one since a relatively low‐cost universal signal conditioner could easily read compatible Fabry Pérot sensors measuring different physical parameters such as strain, temperature, pressure, displacement, or refractive index. This papers details the numerous advantages of this optical sensing technology and also summarizes the operating modes of commercially available signal conditioners and sensors.
Virtual Instrument for Determining Rate Constant of Second‐Order Reaction by pX Based on LabVIEW 8.0
Authors: Meng Hu , Li Jiang-Yuan , Tang Yong-Huai
Published: August 2009

The virtual instrument system based on LabVIEW 8.0 for ion analyzer which can measure and analyze ion concentrations in solution is developed and comprises homemade conditioning circuit, data acquiring board, and computer. It can calibrate slope, temperature, and positioning automatically. When applied to determine the reaction rate constant by pX, it achieved live acquiring, real‐time displaying, automatical processing of testing data, generating the report of results; and other functions. This method simplifies the experimental operation greatly, avoids complicated procedures of manual processing data and personal error, and improves veracity and repeatability of the experiment results.