bluuebunny/crossref_metadata_2025 huggingface dataset:
GNRH Induces the Unfolded Protein Response in the LβT2 Pituitary Gonadotrope Cell Line
Authors: Do Minh-Ha T. , Santos Sharon J. , Lawson Mark A.
Published: October 2008

The neuropeptide GNRH 1 stimulates the secretion of the reproductive hormone LH in pituitary gonadotropes. Other secretory cell types depend on the unfolded protein response (UPR) pathway to regulate protein synthesis and protect against endoplasmic reticulum (ER) stress in response to differentiation or secretory stimuli. This study investigated the role of the UPR in GNRH action within the LβT2 gonadotrope model. Cells were treated with GNRH, and the activation of UPR signaling components and general translational status was examined. The ER-resident stress sensors, Atf6, Eif2ak3, and Ern1, are all present, and GNRH stimulation results in the phosphorylation of eukaryotic translation initiation factor 2A kinase 3 and its downstream effector, eukaryotic translation initiation factor 2A. Additionally, activation of the UPR was confirmed both in LβT2 as well as mouse primary pituitary cells through identifying GNRH-induced splicing of Xbp1 mRNA, a transcription factor activated by splicing by the ER stress sensor, ER to nucleus signaling 1. Ribosome profiling revealed that GNRH stimulation caused a transient attenuation in translation, a hallmark of the UPR, remodeling ribosomes from actively translating polysomes to translationally inefficient ribonucleoprotein complexes and monosomes. The transient attenuation of specific mRNAs was also observed. Overall, the results show that GNRH activates components of the UPR pathway, and this pathway may play an important physiological role in adapting the ER of gonadotropes to the burden of their secretory demand.
Reports on Stage Censorship and Suppression
Authors: Olyaie Donesh , Rokem Freddie , Mannex Colin , Chon Walter Byongsok , Sellar Tom , Rodríguez Jorge J. , Grennan Alex , Gallagher-Ross Jacob , Valencia Brian , Daisey Mike , Billy Reverend , Barker Howard , Mroué Rabih , Toufiq Fadi , Cantu Maya , Bishop-Stone Sarah , Felton-Dansky Miriam
Published: October 2008

This section presents a series of reports and commentary on recent incidents of theater censorship and suppression from around the world, arranged roughly according to chronology. Contributors include Theater magazine staff as well as artists and scholars from around the world, including Howard Barker, Freddie Rokem, Mike Daisey, Rabih Mroué, Reverend Billy, and Dean Damjanovski.
Messages in a Bottle: An Interview with Filmmaker Masao Adachi
Authors: Harootunian Harry , Kohso Sabu
Published: October 2008

In the summer of 2006, Sabu Kohso, an independent writer, translator, and activist, and Harry Harootunian, a historian at New York University, interviewed the prominent filmmaker and political activist Masao Adachi. The occasion for the interview was the completion of his first film in Japan after years of imprisonment in Lebanon and Japan. Adachi's career and activities spanned the crucial decades of the 1950s and 1960s, perhaps the most intense period of radical protest in Japan's postwar period. His experimental work constituted a significant intervention in these years of revolutionary promise and failure. After the failed revolution in Japan, he spent almost a quarter of a century in exile in Lebanon and Palestine, often working for Palestinian organizations.
The Infinite Rehearsals of the Critique of Religion: Theological Thinking After Humanism
Authors: Walker Corey D. B.
Published: October 2008

What are the conditions of possibility for a critique of religion in a moment when the languages of religion and politics saturate and (over)determine critical discourse? How does one critically interrogate the contemporary manifestation of the phenomenon of religion when the imbrications of religion, power, and authority are such that religion is always already reduced to a function of either power or authority? How are we to formulate the question of a critique of religion when the very languages, concepts, and theories of critique are in question? In wrestling with these questions, this essay develops the notion of theological thinking as a form of critique and a critical theoretical practice for a moment bisected by the (re)turn to theology and the seeming permanence of the theologico-political. Following the examples of James Baldwin and W. E. B. Du Bois, theological thinking outlines a practice of criticism that responds to our moment not by rejecting or reducing the presence of the theological but rather by thinking through the very heart of it in order to expose the totalizing logics within the theologico-political, all the while locating and mobilizing those discarded critical practices that illuminate new directions for constructing alternative futures.
Ang Lee's Lust, Caution and Its Reception
Authors: Lee Leo Ou-fan
Published: October 2008

This essay aims to gauge the different receptions of Ang Lee's recent film Lust, Caution between American and Chinese publics and across a cultural landscape of the pan-Chinese regions of Mainland China, Hong Kong, and Taiwan. It also brings a contextual and historical dimension to bear on Ang Lee's intentions in making this film as well as on the differences of style and approach between Ang Lee and Eileen Chang, on whose original story the film is based. The essay pays particular attention to Ang Lee's diasporic background as a Chinese filmmaker from Taiwan with a cultural sensibility that makes his films not imitations of Hollywood products but manifestations of a particular sense of “repression” that stems from this background. Such symptoms of repression must be understood in terms of the historical context in which the story and film are based—Japanese Shanghai under the repressive collaborationist regime of Wang Jingwei (1939–1945). The film's plot takes off directly from this context, which in turn informs Ang Lee's adaptation. The competing “structures of domination” come from two rivaling regimes of the Guomindang (Nationalist Party) as well as the Japanese military, which imprisons both the young heroine, a novice spy, and the villain, a security police chief of the “puppet” regime. Their sentimental and romantic entanglement, not pronounced in the original Eileen Chang story, bears a distinct trait of Ang Lee's directorial style as an artistic articulation of this sense of repression.
Hindutva and Informatic Modernization
Authors: Basu Anustup
Published: October 2008

This essay is a critical evaluation of contemporary urban Hindutva in the light of Carl Schmitt's famous assertion that all liberal political concepts are transposed theological ones. Without agreeing with Schmitt's hard-right nationalism, one can see that from the discursive beginnings of Hindu nationalism in the latter half of the nineteenth century there has been an effort to “monothematize” a pan-Indian Hindu identity. That is, in the absence of an axiomatic church of “Hinduism,” there was a literary-modern effort to telescope myriad devotional traditions, eclectic beliefs, practices, and customs into a single edifice of Hinduness. This effort, however, failed to overcome the historical differences of caste, gender, class, and region and invent a singular, constitutive discourse of Hindu being. The essay speculates that perhaps, in recent times, this project toward a Hindu normative literary modernity has been displaced by an “informatic modernization.” A new urban Hinduness asserts itself more by its affects and spectacles than through the act of narration. This “informatic” public culture can orchestrate signs, emblems, mantras, and doctrines of disparate affiliations without completing a “story” as such. That is, it can do so without trying to resolve historical disputes that have dogged the career of Indian modernity (e.g., how exactly can caste be squared with scientific and democratic tempers?). The image of a “shining” Hindu normative metropolitanism is consolidated by groundless and nonobligatory mergers between neoliberal postulates and the pieties of a so-called tradition. The essay illustrates this phenomenon through some examples from popular Hindi cinema.
Stereotypy, flexibility and coordination: key concepts in behavioral functional morphology
Authors: Wainwright Peter C. , Mehta Rita S. , Higham Timothy E.
Published: October 2008

Animal movement and its muscular control are central topics in functional morphology. As experimentalists we often manipulate stimuli in a controlled setting or compare species to observe the degree of variation in movement and motor control of particular behaviors. Understanding and communicating the biological significance of these sources of variability requires a universal terminology that is presently lacking in the functional morphology literature. We suggest that `stereotypy' be used to refer to the degree of variability observed in a behavior across trials under a given set of conditions. The ability of an organism to alter its behavior across experimental treatments is referred to as `flexibility'. We discuss how there has been a tendency to confound the phenomenon of a behavior exhibiting low variability, which we refer to as stereotyped, with inflexibility, or the inability to alter the behavior in response to a change in stimulus. The degree of stereotypy and flexibility in a behavior need not be correlated, nor need they have a common underlying basis. Coordination, a term used to describe the relationship between different body parts during movement, can be stereotyped and can show flexibility. Stereotypy of coordination can be assessed by the strength of correlations between movements of two body parts. The influence of coordination coherence on behavioral performance has rarely been considered,and could shed light on how taxa differ in their ability to perform behaviors. We suggest definitions of the terms stereotypy, flexibility and coordination,and provide examples of how and when these terms could be used when discussing behavioral changes in functional morphology.
Mother–young vocal communication and acoustic recognition promote preferential nursing in sheep
Authors: Sèbe Frédéric , Aubin Thierry , Boué Amélie , Poindron Pascal
Published: October 2008

In mammals with precocial neonates, exclusive maternal care and investment depend on mutual mother–young recognition. In sheep, this is ensured by rapid olfactory recognition of the neonate by its mother. However, recent studies suggest that other processes may participate in preferential maternal care. We investigated the possibility that acoustic communication promotes preferential nursing of the lamb. In the first of two studies, we examined the association between nursing and vocal activity in ewes and their lambs during the first 2 weeks of lactation. As early as 3 and 6 h postpartum, vocal activity was preferentially concentrated before nursing and by day 15 all vocal activity occurred within 2.5 min before nursing. In the second study, we tested the responses of ewes and lambs at 15 days postpartum to the playback of recorded bleats of their partner or from unrelated ewes and lambs. When playback was performed 30 min after a nursing episode, both ewes and lambs responded to bleats of their partner but not to bleats from alien subjects. When playback was performed 5 min after nursing, ewes did not respond to any lamb's bleats, while lambs continued responding to the bleats of their mothers, but significantly less than 30 min after nursing. Nursing therefore appears to play an important role in structuring very early vocal communication between the mother and her neonate. In turn, if the motivational state of the members of the mother–young dyad is adequate, this ensures the display of mutual acoustic recognition and prepares them for preferential nursing before maternal olfactory recognition of the lamb comes into play.
Hearing and spatial behavior in Gryllotalpa major Saussure(Orthoptera: Gryllotalpidae)
Authors: Howard Daniel R. , Mason Andrew C. , Hill Peggy S. M.
Published: October 2008

The prairie mole cricket (Gryllotalpa major Saussure) is a rare orthopteran insect of the tallgrass prairie ecosystem of the south central USA. Populations are known to currently occupy fragmented prairie sites in Oklahoma, Arkansas, Kansas and Missouri, including The Nature Conservancy's Tallgrass Prairie Preserve in north central Oklahoma. Prairie mole cricket populations were surveyed at this site and at another site in Craig County, OK during the spring of 2005 and 2006, using the male cricket's acoustic call to locate advertising aggregations of males. Five males from one large aggregation were removed in a study to describe (1) the hearing thresholds across the call's range of frequencies, (2) the distances over which the higher harmonic components of the male's calls are potentially detectable, (3)the species' sensitivity to ultrasound and (4) the spatio-auditory dynamics of the prairie mole cricket lek. Results indicate that G. major has a bimodal pattern of frequency tuning, with hearing sensitivities greatest at the 2 kHz carrier frequency (41 dB SPL) and declining through the call's frequency range (84 dB at 10 kHz). A second sensitivity peak is evident in the ultrasound range at 25 kHz (62 dB SPL). Spatial analysis of G. majorlek sites indicates that approximately 73% of males within the lek are spaced in such a way as to allow acoustic interaction at the species' carrier frequency, while any information in higher harmonic overtones in the call appears to be available only to nearest neighbors.
Metabolic costs of foraging and the management of O2 and CO2 stores in Steller sea lions
Authors: Fahlman Andreas , Svärd Caroline , Rosen David A. S. , Jones David R. , Trites Andrew W.
Published: October 2008

The metabolic costs of foraging and the management of O2 and CO2 stores during breath-hold diving was investigated in three female Steller sea lions (Eumetopias jubatus) trained to dive between 10 and 50 m (N=1142 dives). Each trial consisted of two to eight dives separated by surface intervals that were determined by the sea lion(spontaneous trials) or by the researcher (conditioned trials). During conditioned trials, surface intervals were long enough for O2 to return to pre-dive levels between each dive. The metabolic cost of each dive event (dive+surface interval; DMR) was measured using flow-through respirometry. The respiratory exchange ratio(V̇O2/V̇CO2)was significantly lower during spontaneous trials compared with conditioned trials. DMR was significantly higher during spontaneous trials and decreased exponentially with dive duration. A similar decrease in DMR was not as evident during conditioned trials. DMR could not be accurately estimated from the surface interval (SI) following individual dives that had short SIs (<50 s), but could be estimated on a dive by dive basis for longer SIs (>50 s). DMR decreased by 15%, but did not differ significantly from surface metabolic rates (MRS) when dive duration increased from 1 to 7 min. Overall,these data suggest that DMR is almost the same as MRS, and that Steller sea lions incur an O2 debt during spontaneous diving that is not repaid until the end of the dive bout. This has important consequences in differentiating between the actual and `apparent' metabolic rate during diving, and may explain some of the differences in metabolic rates reported in pinniped species.
Fuel economy and NOx emission potential investigation and trade-off of a hybrid electric vehicle based on dynamic programming
Authors: Ao G-Q , Qiang J-X , Zhong H , Mao X-J , Yang L , Zhuo B
Published: October 2008

Hybrid electric vehicles (HEVs) combined with more than one power source offer additional flexibility to improve the fuel economy and to reduce pollutant emissions. The dynamic-programming-based supervisory controller (DPSC) presented here investigates the fuel economy improvement and emissions reduction potential and demonstrates the trade-off between fuel economy and the emission of nitrogen oxides (NO x) for a state-of-charge-sustaining parallel HEV. A weighted cost function consisting of fuel economy and emissions is proposed in this paper. Any possible engine-motor power pairs meeting with the power requirement is considered to minimize the weighted cost function over the given driving cycles through this dynamic program algorithm. The fuel-economy-only case, the NO x-only case, and the fuel-NO x case have been achieved by adjusting specific weighting factors, which demonstrates the flexibility and advantages of the DPSC. Compared with operating the engine in the NO x-only case, there is 17.4 per cent potential improvement in the fuel-economy-only case. The fuel-NO x case yields a 15.2 per cent reduction in NO x emission only at the cost of 5.5 per cent increase in fuel consumption compared with the fuel-economy-only case.
Investigation of transition between spark ignition and controlled auto-ignition combustion in a V6 direct-injection engine with cam profile switching
Authors: Kalian N , Zhao H , Qiao J
Published: October 2008

Controlled auto-ignition (CAI) combustion, also known as homogeneous charge compression ignition (HCCI), can be achieved by trapping residuals with early exhaust valve closure in a direct-fuel-injection in-cylinder four-stroke gasoline engine (through the employment of low-lift cam profiles). Because the operating region is limited to low-load and midload operation for CAI combustion with a low-lift cam profile, it is important to be able to operate spark ignition (SI) combustion at high loads with a normal cam profile. A 3.0l prototype engine was modified to achieve CAI combustion, using a cam profile switching mechanism that has the capability to switch between high- and low-lift cam profiles. A strategy was used where a high-lift profile could be used for SI combustion and a low-lift profile was used for CAI combustion. Initial analysis showed that for a transition from SI to CAI combustion, misfire occurred in the first CAI transitional cycle. Subsequent experiments showed that the throttle opening position and switching time could be controlled to avoid misfire. Further work investigated transitions at different loads and from CAI to SI combustion.
A soot prediction for a taxi cycle of a diesel engine
Authors: Stotsky A A
Published: October 2008

The time and cost associated with running long-term tests to acquire data on the soot percentage in the oil of a diesel engine necessitate the development of a new method for a model-based prediction of the soot accumulation performance. A new method for a model-based prediction of the soot percentage for a vehicle that sequentially executes a number of taxi cycles is proposed. The method is based on the steady-state soot accumulation rate measurements that are made in the engine test cell, and is used for a relative soot percentage judgement and selection of the most suitable data set among several candidates. The method provides significant savings with respect to the direct long-term soot percentage measurements on a vehicle.
Rate of Increasing Concentrations of Atmospheric Carbon Dioxide Controlled by Natural Temperature Variations
Authors: Goldberg Fred
Published: October 2008

Studies of the temperature anomalies during the last 27 years show a close relationship with the varying increase of CO2 in the atmosphere. Volcanic eruptions and La Niñas reduce CO2 values and El Niños increase them. This close relationship strongly indicates that ocean temperatures and the solubility of CO2 in seawater control the amount of CO2 being absorbed or released by the oceans. It is therefore likely that the increased CO2 concentration in the atmosphere is due to a natural global warming and that CO2 produced through fossil fuel combustion by humans can not disrupt this balance. An advanced statistical multiregression analysis confirms this conclusion. Therefore it is likely that there is no anthropogenic climate change on a global scale. The natural exchange of CO2 between ocean, biomass on land and the atmosphere is very large. In only four to five years all the CO2 in the atmosphere has been recycled through the oceans and the biomass system. The annual anthropogenic human production of CO2 is neutralized by nature in as little as 12 days. Recent studies of the solar forcing, changes in cosmic radiation and its role in cloud formations explain the global warming that has taken place since 1910.
A Method for Estimating the Noise Level of Unstable Combustion Based on the Flame Describing Function
Authors: Noiray N. , Durox D. , Schuller T. , Candel S.
Published: October 2008

Practical combustion is often coupled by the system acoustics and under some conditions the process may become unstable giving rise to oscillations of finite amplitude and to discrete tone noise radiation. The objective of this investigation is to model the nonlinear features of unstable combustion to predict limit cycle amplitudes and thus get an estimation of the radiated noise level under such regimes of operation. The present study is based on an analysis derived in a companion paper (Noiray et al. (2008)) which contains a complete nonlinear description of the thermo-acoustic coupling encountered in an unconfined reaction zone layout. Theoretical predictions are successfully compared with a set of measurements. It is shown that nonlinear phenomena such as frequency shifts, triggering or hysteresis may be suitably predicted by an analytical model based on the flame describing function (FDF). The objective of the present paper is to make use of this method to investigate nonlinear acoustic-combustion dynamics in a confined geometry comprising an upstream manifold, an injector and a flame tube. The flame is identified as the main nonlinear element in the system and its response to perturbations is characterized in terms of a describing function which assumes that the gain and phase depend on the amplitude level of the input. A frequency domain analysis is then carried out by solving the dispersion relation for a range of amplitudes. This yields growth rates and eigenfrequencies, which depend on the amplitude level of perturbations impinging on the flame. The growth rates and eigenfrequencies are determined for a wide range of upstream manifold lengths while keeping equivalence ratio and mass flow rate constant. For certain values of this parameter one finds a positive growth rate for vanishingly small amplitude levels indicating that the system is linearly unstable. The growth rate then changes as the amplitude is increased and eventually vanishes for a finite amplitude indicating the existence of a limit cycle. For other values of the length, the growth rate is initially negative, becomes positive for a finite amplitude and drops to zero for a higher level. This indicates that the system is linearly stable but nonlinearly unstable. Using calculated growth rates it is effectively possible to predict amplitudes of acoustic pressure oscillations in the system when it operates on a limit cycle and thus determine the noise level generated under such conditions.
Analysis of Different Sound Source Formulations to Simulate Combustion Generated Noise Using a Hybrid LES/APE-RF Method
Authors: Bui T. Ph. , Ihme M. , Schröder W. , Pitsch H.
Published: October 2008

Combustion noise and sound source mechanisms of the DLR-A flame are investigated. A hybrid large-eddy simulation/computational aeracoustics (LES/CAA) approach is employed. In the first step of the hybrid analysis the flamelet/progress variable (FPV) model is employed as combustion model followed by the acoustic simulation in the second step using the acoustic perturbation equations for reacting flows (APE-RF). The flamelet/progress variable database has been extended in terms of acoustic source terms. The analysis of the acoustic field of low MACH number reacting flows induced by the thermoacoustic sources such as the unsteady heat release leads to a very stiff problem formulation, since the related sources require highly resolved regions in the source area, which restricts the possible time step. To simulate combustion generated noise using such a hybrid approach, a suitable source description has to be used, which preferably satisfies two requirements, i.e, to efficiently and accurately predict the generated sound field, while the source term can be easily evaluated from the LES. Using the source term, which is expressed via the scaled partial time derivative of the density, the acoustic field can be reproduced best up to a maximum Strouhal number of StD = 2. However, this source formulation requires a rigorous constraint at the interface of the hybrid approach to avoid spurious noise due to artificial acceleration caused by interpolation. To be more precise, the convection speed of density inhomogeneities has to be preserved during interpolation. A compromise between efficiency and accuracy can be achieved using the source formulation expressed via the scaled material derivative of the density, since by definition this formulation does not describe the convection of density inhomogeneities.
A Tool to Study Azimuthal Standing and Spinning Modes in Annular Combustors
Authors: Sensiau C. , Nicoud F. , Poinsot T.
Published: October 2008

A methodology for the computation of azimuthal combustion instabilities which can occur in annular combustors is proposed in this work. A thermoacoustic numerical tool using the n – τ model for the coupling of acoustic and combustion is required to solve the Helmholtz equation in reactive media. The methodology is based on the Independence Sector Assumption in Annular Combustor (ISAAC) which states that the heat release fluctuations in a given sector are driven only by the fluctuating mass flow rates due to the velocity perturbations through its own swirler. This assumption is first discussed with respect to a Large Eddy Simulation of an annular combustor. The methodology is then applied to an academic annular test case which exhibits amplified or damped, standing or rotating azimuthal eigenmodes depending on parameters n and τ.
Participation in Coaching by Canadian Immigrants: Individual Accommodations and Sport System Receptivity
Authors: Livingston Lori A. , Tirone Susan C. , Smith Emma L. , Miller A. Jordan
Published: October 2008

Little is known about the lived experiences of immigrants as coaches within the amateur sport ranks or about how amateur sport organizations are accommodating the needs of newcomers. The purpose of this study was to qualitatively explore these issues with the assistance of members of the newcomer and minority ethnic communities, and those who work as sport coaches, and administrators in a city in Atlantic Canada. Seventeen individuals participated in one-on-one semi-structured interviews and/or a follow-up focus group interview. Three major themes emerged: Differences in perceived versus expected levels of involvement and the influence of privilege on newcomers' involvement in sport; how to include newcomers in sport and, more specifically, barriers to and responsibility for inclusion in sport and coaching; and how sport organizations can best communicate information to newcomers about coaching opportunities. Barriers to participation in coaching by newcomers appear to be both personal and systemic in nature.
Pose® Method Technique Improves Running Performance without Economy Changes
Authors: Fletcher Graham , Bartlett Roger , Romanov Nicholas , Fotouhi Ali
Published: October 2008

The aim was to investigate the affects of the Pose® method intervention on running technique, on economy and a time-trial runs. A 2 × 2 mixed factorial ANOVA assessed sixteen research variables where group (Heel-toe vs. Pose®) and trial (pre to post changes) was used. Significant interactions were explored using Tukey post hoc tests, which found significance (Pose® runners pre-post test) for stance time ( p = 0.001), horizontal displacement of the centre of mass to support foot at 25 ms after impact (p = 0.042), centre of mass displacement during stance ( p = 0.001), knee flexion angular velocity during stance ( p = 0.005) and during swing to maximum knee flexion ( p = 0.043) and stride frequency ( p = 0.002). The Pose® group's post-test time-trial (2400 m) was not significant yet they improved by a mean of 24.7 s compared with a 3 s decrease in the heel-toe group. No significant changes pre-post test, were found for an economy run (2400 m) at 3.35 m/s.
The Conditioning Services in Elite Spanish Clubs of Team Sports
Authors: Reverter-Masía Joaquín , Legaz-Arrese Alejandro , Munguía-Izquierdo Diego , Barbany Joan Ramó
Published: October 2008

This study compares the conditioning services of Spanish sports teams: From soccer and basketball professional leagues, and top-division amateur leagues for handball, volleyball, indoor soccer, and field hockey. A survey was administered to those responsible for the conditioning preparation. The response rate was 82% (77 of 94). The teams were divided into class A and class B, with class A having the best performance. Fifty eight percent of the professional teams have hired a full-time person, with university degree, exclusively for the conditioning. The percentage was significantly less in amateur leagues for handball, volleyball, and field hockey: class A teams (41%), class B teams (0%). A small percentage of the Physical Conditioning Coaches (PCCs) continued their academic education (22%), and the consultation of scientific journals (5%). Only 6% of the PCCs did not mention deficiencies in the context of work. The main complaints are associated with the strength-training equipment and facilities. In class B teams of the amateur leagues, significant deficiencies were found in almost all the variables within the training environment. These results show significant deficiencies in the conditioning services offered by teams to their players, especially in no-professional teams and in the teams with lower performance level. Spanish PCCs should take advantage of advances made through scientific research in the area of conditioning by acquiring Master's Degrees and consulting peer-reviewed journals. The club's managers and/or coaches must be aware of the importance of conditioning for improving the training environment. Both aspects would increase the likelihood that better training or rehabilitation procedures would be developed at the club.
“Hard Work Beats Talent until Talent Decides to Work Hard”: Coaches' Perspectives regarding Differentiating Elite and Non-Elite Swimmers
Authors: Johnson Michael B. , Castillo Yvonne , Sacks David N. , Cavazos Javier , Edmonds William A. , Tenenbaum Gershon
Published: October 2008

Research addressing elite athletes tends to either identify differences between high-level and low-level performers or the developmental histories of elite athletes. The current study culls input from six individuals who simultaneously coach both elite (e.g., World Record holders) and non-elite (e.g., regional-level) swimmers, and have done so for an extended period of time, thereby filling a void in the literature by providing their opinions and perceptions regarding how athletic performance differences develop. Responses by participants to the open-ended question, “What do you feel contributes to a swimmer achieving top performances (e.g., World Records) vs. excellent performances (e.g., a Top-8 finish at NCAAs)?” were analyzed. Emergent categories (i.e., intrapersonal, interpersonal, lifestyle, training, environment, and a systemic interaction among these) are presented and an interpretation is offered. Additionally, a critique of the methods implemented herein is offered and future research directions are proposed.
Genome 3′-end repair in dengue virus type 2
Authors: Teramoto Tadahisa , Kohno Yukari , Mattoo Pravina , Markoff Lewis , Falgout Barry , Padmanabhan Radhakrishnan
Published: October 2008

Genomes of RNA viruses encounter a continual threat from host cellular ribonucleases. Therefore, viruses have evolved mechanisms to protect the integrity of their genomes. To study the mechanism of 3′-end repair in dengue virus-2 in mammalian cells, a series of 3′-end deletions in the genome were evaluated for virus replication by detection of viral antigen NS1 and by sequence analysis. Limited deletions did not cause any delay in the detection of NS1 within 5 d. However, deletions of 7–10 nucleotides caused a delay of 9 d in the detection of NS1. Sequence analysis of RNAs from recovered viruses showed that at early times, virus progenies evolved through RNA molecules of heterogeneous lengths and nucleotide sequences at the 3′ end, suggesting a possible role for terminal nucleotidyl transferase activity of the viral polymerase (NS5). However, this diversity gradually diminished and consensus sequences emerged. Template activities of 3′-end mutants in the synthesis of negative-strand RNA in vitro by purified NS5 correlate well with the abilities of mutant RNAs to repair and produce virus progenies. Using the Mfold program for RNA structure prediction, we show that if the 3′ stem–loop (3′ SL) structure was abrogated by mutations, viruses eventually restored the 3′ SL structure. Taken together, these results favor a two-step repair process: non-template-based nucleotide addition followed by evolutionary selection of 3′-end sequences based on the best-fit RNA structure that can support viral replication.
Evidence of a novel RNA secondary structurein the coding region of HIV-1 pol gene
Authors: Wang Qi , Barr Ian , Guo Feng , Lee Christopher
Published: October 2008

RNA secondary structures play several important roles in the human immunodeficiency virus (HIV) life cycle. To assess whether RNA secondary structure might affect the function of the HIV protease and reverse transcriptase genes, which are the main targets of anti-HIV drugs, we applied a series of different computational approaches to detect RNA secondary structures, including thermodynamic RNA folding predictions, synonymous variability analysis, and covariance analysis. Each method independently revealed strong evidence of a novel RNA secondary structure at the junction of the protease and reverse transcriptase genes, consisting of a 107-nucleotide region containing three stems, A, B, and C. First, RNA folding calculations by mfold and RNAfold both predicted the secondary structure with high confidence. Moreover, the same structure was predicted in a diverse set of reference sequences in HIV-1 group M, indicating that it is conserved across this group. Second, the predicted base-pairing regions displayed markedly reduced synonymous variation (approximately threefold lower than average) in a data set of 20,000 HIV-1 subtype B sequences from clinical samples. Third, independent analysis of covariation between synonymous mutations in this data set identified 10 covariant mutation pairs forming two diagonals that corresponded exactly to the sites predicted to base-pair in stems A and B. Finally, this structure was validated experimentally using selective 2′-hydroxyl acylation and primer extension (SHAPE). Discovery of this novel secondary structure suggests many directions for further functional investigation.
The secondary structure of the 5′ end of the FIV genome reveals a long-range interaction between R/U5 and gag sequences, and a large, stable stem–loop
Authors: Kenyon Julia C. , Ghazawi Akela , Cheung Winsome K.S. , Phillip Pretty S. , Rizvi Tahir A. , Lever Andrew M.L.
Published: October 2008

Feline immunodeficiency virus (FIV) is a lentivirus that infects cats and is related to human immunodeficiency virus (HIV). Although it is a common worldwide infection, and has potential uses as a human gene therapy vector and as a nonprimate model for HIV infection, little detail is known of the viral life cycle. Previous experiments have shown that its packaging signal includes two or more regions within the first 511 nucleotides of the genomic RNA. We have undertaken a secondary structural analysis of this RNA by minimal free-energy structural prediction, biochemical mapping, and phylogenetic analysis, and show that it contains five conserved stem–loops and a conserved long-range interaction between heptanucleotide sequences 5′-CCCUGUC-3′ in R/U5 and 5′-GACAGGG-3′ in gag. This long-range interaction is similar to that seen in primate lentiviruses where it is thought to be functionally important. Along with strains that infect domestic cats, this heptanucleotide interaction can also occur in species-specific FIV strains that infect pumas, lions, and Pallas' cats where the heptanucleotide sequences involved vary. We have analyzed spliced and genomic FIV RNAs and see little structural change or sequence conservation within single-stranded regions of the 5′ UTR that are important for viral packaging, suggesting that FIV may employ a cotranslational packaging mechanism.
Editor's Introduction
Authors: Greenberg Harvey J.
Published: October 2008

Welcome to the inaugural issue of the ORSA Journal on Computing, dedicated to the memory of one of its founders, Robert G. Jeroslow. I wish first to thank the members of the committee established by the ORSA Computer Science Technical Section who prepared the proposal for this journal: Karla Hoffman, Robert G. Jeroslow, Donald H. Kraft, and William P. Pierskalla. Their efforts for nearly 2 years was supplemented by additional help from Thomas Magnanti. I am most grateful to them and to ORSA Council for approving this long-needed journal.

Getting started is never easy, but I was fortunate to have chosen an outstanding editorial board (see inside front and back covers). Everyone helped to shape JoC's policies and obtain excellent papers to establish our scope and quality.

INFORMS Journal on Computing, ISSN 1091-9856, was published as ORSA Journal on Computing from 1989 to 1995 under ISSN 0899-1499.
Parallel Numerical Optimization: Current Status and an Annotated Bibliography
Authors: Zenios Stavros A.
Published: October 2008

Parallel computing is becoming a basic tool for research in several areas of computational mathematical programming. Algorithms and models that were intractable by the performance standards of von Neumann computers are becoming increasingly attractive. New algorithms are designed specifically for parallel architectures; the insight obtained from the design and implementation of such algorithms leads occasionally to improved sequential algorithms. Researchers report computational experiments with linear programming problems approaching a million variables and nonlinear problems with thousands of variables are solved routinely on state-of-the-art supercomputers. We classify and comment on the literature in parallel optimization with particular emphasis on the numerical and computational aspects of the field. Discussion of the parallel optimization literature is preceded by a tutorial on parallel computing in general. Work on the related areas of performance evaluation models, parallel linear algebra and benchmarks of high performance computers is presented through few representative publications.

INFORMS Journal on Computing, ISSN 1091-9856, was published as ORSA Journal on Computing from 1989 to 1995 under ISSN 0899-1499.
Editor's Introduction
Authors: Greenberg Harvey J.
Published: October 2008

We are now past initialization, and the papers in this second issue represent the diversity of the OR/CS interface. We see problems (or problem areas), like concurrent flow of information. We see pragmatics (focused on implementation), like sparse matrix techniques in implementing large-scale linear programming. We see new resources (soft and hard) for modeling and analysis, like graphics-based interfaces. We see insights into Markov chains (or general queueing processes), like reliability criteria for analysis of performance of operating systems.

INFORMS Journal on Computing, ISSN 1091-9856, was published as ORSA Journal on Computing from 1989 to 1995 under ISSN 0899-1499.
Input Proofs and Rank One Cutting Planes
Authors: Hooker John N.
Published: October 2008

Input resolution and “unit support” resolution (a generalization of unit resolution) are complete inference methods for Horn clauses in propositional logic. We show that they have a close analog in cutting plane theory. Namely, a logical clause can be deduced using input or unit support resolution if and only if it belongs to the elementary closure of the premises and is therefore a rank one cut in Chvátal's sense. This connection leads to a cutting plane algorithm for solving non-Horn inference problems.

INFORMS Journal on Computing, ISSN 1091-9856, was published as ORSA Journal on Computing from 1989 to 1995 under ISSN 0899-1499.
Possibilistic Linear Programming with Measurable Multiattribute Value Functions
Authors: Inuiguchi Masahiro , Ichihashi Hidetomo , Tanaka Hideo
Published: October 2008

In this paper, a possibilistic linear program is formulated when a measurable multiattribute value function is given. The possibilistic linear program in this paper is an unconstrained linear program with several objective functions whose coefficients are represented by possibility distributions. A possibility measure and a necessity measure are derived from a possibility distribution. Using fuzzy integrals of the measurable multiattribute value function with respect to the possibility measure and the necessity measure, the possible value and the necessary value are defined respectively. In an analogy of the expected utility, the principles of maximizing the possible value and the necessary value are considered as decision procedures under a possibility distribution. The possibilistic linear program is formulated based on these decision procedures and reduced to a nonlinear program. A solution method using linear programming technique is proposed.

INFORMS Journal on Computing, ISSN 1091-9856, was published as ORSA Journal on Computing from 1989 to 1995 under ISSN 0899-1499.
A New Estimator of Sensitivity Measures for Simulations Based on Light Traffic Theory
Authors: Simon Burton
Published: October 2008

Consider an open queueing system that is stable for arrival rates, 0 ≤ λ < c. Let f(λ) be some function such as the mean sojourn time of a customer. Normally, light traffic theory is concerned with limits as λ → 0, e.g., f(n)(0), n = 0, 1, …. Here we use light traffic theory to obtain derivatives of f(·) at any value of λ for which the system is stable. The derivatives, f(n)(λ), n = 0, 1, …, are obtained by perturbing a system with arrival rate, λ, with a small auxiliary arrival process. The nth derivative is obtained by looking at sample paths of the original system with k auxiliary customers thrown in, k = 0, 1, …, n. In practice, the only way to obtain f(n)(λ) for λ > 0 is by observing the effect of additional customers on the sample path of a simulation. We make this technique rigorous by showing that a certain function of the sample paths is “admissible.” The analysis suggests a method for analytically bounding the derivatives, and yields a proof that a large class of queueing functions are infinitely differentiable with respect to λ. The calculations are reminiscent of other sensitivity analyses of simulations such as (infinitesimal) perturbation analysis and the likelihood ratio method. The method described here (the “light traffic perturbation method”) shares the rigorous foundation of the likelihood ratio method and numerical evidence suggests that (at least for simple systems) it has convergence properties similar to perturbation analysis.

INFORMS Journal on Computing, ISSN 1091-9856, was published as ORSA Journal on Computing from 1989 to 1995 under ISSN 0899-1499.
On the Greedy Solution of Ordering Problems
Authors: Dechter Avi , Dechter Rina
Published: October 2008

The greedy method is a well-known approach for problem solving directed mainly at the solution of optimization problems. Leading theoretical frameworks dealing with the optimality of greedy solutions (e.g., the matroid and greedoid theories) tacitly assume that the greedy algorithm is always guided by the cost function to be optimized, namely, it builds a solution by adding, in each step, an element that contributes the most to the value of the cost function. This paper studies a class of problems for which this type of a greedy algorithm does not optimize the given cost function, but for which there exists a secondary objective function, called a greedy rule, such that applying the greedy algorithm to the secondary objective function yields a solution which is optimal with respect to the original cost function.

INFORMS Journal on Computing, ISSN 1091-9856, was published as ORSA Journal on Computing from 1989 to 1995 under ISSN 0899-1499.
Editor's Introduction
Authors: Greenberg Harvey J.
Published: October 2008

This last issue of Volume 1 reflects growing interests in the interfaces between operations research (OR) and computer science (CS). The following papers span optimization and stochastic processes; modeling and methodology; theory and application; established and uncharted topics. All this is without dichotomy, building on integration of concepts.

INFORMS Journal on Computing, ISSN 1091-9856, was published as ORSA Journal on Computing from 1989 to 1995 under ISSN 0899-1499.
Series-Parallel Bounds for the Two-Terminal Reliability Problem
Authors: Aboelfotoh Hosam M. , Colbourn Charles J.
Published: October 2008

The two-terminal reliability problem for communication networks with unreliable links is a computationally difficult problem. Upper and lower bounds can be efficiently computed using graph-theoretical techniques based on edge-packing. We present a new technique for improving these bounds via approximation by series-parallel graphs. We also present some computational results for comparison with the known edge-packing bounds.

INFORMS Journal on Computing, ISSN 1091-9856, was published as ORSA Journal on Computing from 1989 to 1995 under ISSN 0899-1499.
A Cutting Plane Algorithm for Multicommodity Survivable Network Design Problems
Authors: Dahl Geir , Stoer Mechthild
Published: October 2008

We present a cutting plane algorithm for solving the following telecommunications network design problem: given point-to-point traffic demands in a network, specified survivability requirements and a discrete cost/capacity function for each link, find minimum cost capacity expansions satisfying the given demands. This algorithm is based on the polyhedral study described in [19]. In this article we describe the underlying problem, the model and the main ingredients in our algorithm. This includes: initial formulation, feasibility test, separation for strong cutting planes, and primal heuristics. Computational results for a set of real-world problems are reported.
Sparse Matrix Ordering Methods for Interior Point Linear Programming
Authors: Rothberg Edward , Hendrickson Bruce
Published: October 2008

The main cost of solving a linear programming problem using an interior point method is usually the cost of solving a series of sparse, symmetric linear systems of equations, AΘATx = b. These systems are typically solved using a sparse direct method. The first step in such a method is a reordering of the rows and columns of the matrix to reduce fill in the factor and/or reduce the required work. This article evaluates several methods for performing fill-reducing ordering on a variety of large-scale linear programming problems. We find that a new method, based on the nested dissection heuristic, provides significantly better orderings than the most commonly used ordering method, minimum degree.