bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary analysis of probabilities at the termination of a group sequential phase II trial
Authors: Liu Aiyi , Wu Chengqing , Yu Kai F. , Gehan Edmund
Published: November 2004

We consider estimation of various probabilities after termination of a group sequential phase II trial. A motivating example is that the stopping rule of a phase II oncologic trial is determined solely based on response to a drug treatment, and at the end of the trial estimating the rate of toxicity and response is desirable. The conventional maximum likelihood estimator (sample proportion) of a probability is shown to be biased, and two alternative estimators are proposed to correct for bias, a bias‐reduced estimator obtained by using Whitehead's bias‐adjusted approach, and an unbiased estimator from the Rao–Blackwell method of conditioning. All three estimation procedures are shown to have certain invariance property in bias. Moreover, estimators of a probability and their bias and precision can be evaluated through the observed response rate and the stage at which the trial stops, thus avoiding extensive computation. Copyright © 2004 John Wiley & Sons, Ltd.
Statistical discrimination in the presence of selection effects
Authors: Hilliam R. M.
Published: November 2004

Discrimination between diseases is a complex task. Cases may present contradictory information and diseases can present with unusual or atypical symptoms. In many diagnostic problems the recorded diagnosis is either a true diagnosis, based on hard evidence, or a working diagnosis, not necessarily equivalent to the true underlying disease with an associated level of uncertainty. This problem is often confounded since the type of diagnosis given may be subjected to selection effects. Much medical data is categorical in nature, hence existing techniques for identifying selection effects are inappropriate. This paper provides a method of obtaining a single parameter modelling, the probability of giving a true diagnosis dependent on the nature of the true disease, thereby offering a simple measure for the presence of selection effects. When the size of the data is limited identifiability problems exist with calculating this parameter, however this paper shows how a sensitivity analysis based on the profile likelihood can be used to identify the presence of selection effects even in this difficult situation. Copyright © 2004 John Wiley & Sons, Ltd.
Where do capabilities come from and how do they matter? A study in the software services industry
Authors: Ethiraj Sendil K. , Kale Prashant , Krishnan M. S. , Singh Jitendra V.
Published: November 2004

Recent years have witnessed a surge of interest in the notion of capabilities as an important source of competitive advantage. This recognition has, in turn, placed emphasis on the question of where and how these capabilities emerge and how they influence firm performance. The present paper is an attempt to address this question. Using a large sample of detailed project‐level data from a leading firm in the global software services industry, we attempt to empirically study the importance of capabilities. We find that two broad classes of capabilities are significant. The first class, which we label client‐specific capabilities, is a function of repeated interactions with clients over time and across different projects. This learning from repeated interactions with a given client reduces project execution costs and helps improve project contribution. The second class, termed project management capabilities, is acquired through deliberate and persistent investments in infrastructure and systems to improve the firm's software development process. Our empirical results suggest that the marginal returns to acquiring different capabilities may be different and an understanding of such trade‐offs can improve firm decisions to improve and/or acquire such capabilities. We discuss the key contributions of our paper and the implications for future research on capabilities. Copyright © 2004 John Wiley & Sons, Ltd.
Security issues in IEEE 802.11 wireless local area networks: a survey
Authors: Mishra Arunesh , Petroni Nick L. , Arbaugh William A. , Fraser Timothy
Published: November 2004

In the past few years, wireless networks, specifically those based on the IEEE 802.11 standard, have experienced tremendous growth. However, numerous security problems have dampened this growth. The IEEE and vendors sensitive to these issues began a wholesale redesign of the security architecture, while simultaneously producing measures for mitigating existing problems. In this paper, we describe the past and future security architectures as well as the problems and concerns with both. Copyright © 2004 John Wiley & Sons, Ltd.
Adapting physical carrier sensing to maximize spatial reuse in 802.11 mesh networks
Authors: Zhu Jing , Guo Xingang , Lily Yang L. , Steven Conner W. , Roy Sumit , Hazra Mousumi M.
Published: November 2004

Spatial reuse in a mesh network can allow multiple communications to proceed simultaneously, hence proportionally improve the overall network throughput. To maximize spatial reuse, the MAC protocol must enable simultaneous transmitters to maintain the minimal separation distance that is sufficient to avoid interference. This paper demonstrates that physical carrier sensing enhanced with a tunable sensing threshold is effective at avoiding interference in 802.11 mesh networks without requiring the use of virtual carrier sensing. We present an analytical model for deriving the optimal sensing threshold given network topology, reception power and data rate. A distributed adaptive scheme is also presented to dynamically adjust the physical carrier sensing threshold based on periodic estimation of channel conditions in the network. Simulation results are shown for large‐scale 802.11b and 802.11a networks to validate both the analytical model and the adaptation scheme. It is demonstrated that the enhanced physical carrier sensing mechanism effectively improves network throughput by maximizing the potential of spatial reuse. With dynamically tuned physical carrier sensing, the end to end throughput approaches 90% of the predicted theoretical upper‐bound assuming a perfect MAC protocol, for a regular chain topology of 90 nodes. Copyright © 2004 John Wiley & Sons, Ltd.
Energy decay of damped systems
Authors: Veselić K.
Published: November 2004

We present a new and simple bound for the exponential decay of second order systems using the spectral shift. This result is applied to finite matrices as well as to partial differential equations of Mathematical Physics. The type of the generated semigroup is shown to be bounded by the upper real part of the numerical range of the underlying quadratic operator pencil.
WITCHCRAFT, ANTI-WITCHCRAFT AND TRANS-REGIONAL RITUAL INNOVATION IN EARLY COLONIAL GHANA: SAKRABUNDI AND ABEREWA, 1889–1910
Authors: PARKER JOHN
Published: November 2004

This article examines the origins and dynamics of Aberewa, an anti-witchcraft movement that rose to prominence in the Akan forest region of Asante and the Gold Coast (Ghana) in 1906–10. It suggests that while the political, social and economic changes of the early colonial period acted as a catalyst for its widespread expansion, Aberewa emerged from an earlier cult called Sakrabundi that was already moving from the savanna into the northern reaches of the Asante empire by the 1880s. The ritual trajectory and popular appeal of Sakrabundi and Aberewa are explored within the context of the ambivalent relationship between the Akan peoples and their northern savanna neighbours. An argument is made for the need to consider witchcraft and anti-witchcraft in Africa as historical processes rather than as a set of structural beliefs and practices.
SLAVE EMANCIPATION, TRANS-LOCAL SOCIAL PROCESSES AND THE SPREAD OF ISLAM IN FRENCH COLONIAL BUGUNI (SOUTHERN MALI), 1893–1914
Authors: PETERSON BRIAN J.
Published: November 2004

This article explores the relationship between slave emancipation and the spread of Islam in early colonial French Buguni (southern Mali). It examines the reconstitution of village communities in the wake of violence and enslavement during the late nineteenth and early twentieth centuries, and documents the ways in which widespread mobility and trans-local social processes fostered the emergence of new forms of religious identification and practice. It demonstrates that many of the region's first Muslims were returning slaves whose conversion was a cultural consequence of slavery. Oral accounts of village histories of Islam are used in reconstructing a history that has left few traces in the archival record.
‘RUBBER FEVER’, COMMERCE AND FRENCH COLONIAL RULE IN UPPER GUINÉE, 1890–1913
Authors: LYNN OSBORN EMILY
Published: November 2004

This article examines the trade in wild rubber that emerged in Upper Guinée, in the colony of Guinée Française, at the end of the nineteenth century. Guinée's rubber boom went through two phases. The first, from the 1880s to 1901, was dominated by local collectors and Muslim traders who directed the trade to the British port of Freetown, Sierra Leone. In the second phase, 1901–13, expatriate merchant houses entered the long-distance trade and, with the help of the colonial state, reoriented the commerce to Conakry, port city and capital of Guinée. The Guinée case offers an alternative perspective to that provided by the better studied rubber markets of Central Africa and South America, and contributes to scholarly debates about export economies, colonial rule and social change. In Guinée, local production and commercial networks maintained significant influence in the market throughout the rubber boom, thwarting colonial efforts to control the trade. The colonial state proved particularly challenged by the practice of rubber adulteration, whereby local collectors and traders corrupted rubber with foreign objects to increase its weight. While the trade exposes the limits of colonial power, rubber also played a largely overlooked role in the social and economic transformations of the period. Evidence suggests that profits from the rubber trade enabled peasants, escaped slaves and former masters to alter their circumstances, accumulate wealth and rebuild homes and communities destroyed during the preceding era of warfare and upheaval.
Priority Contribution West Nile virus in the New World: potential impacts on bird species
Authors: PETERSON A. TOWNSEND , KOMAR NICHOLAS , KOMAR OLIVER , NAVARRO-SIGÜENZA ADOLFO , ROBBINS MARK B. , MARTÍNEZ-MEYER ENRIQUE
Published: November 2004

The past five years have seen the arrival and extremely rapid expansion of West Nile virus (WNV) in the Western Hemisphere. The rapid sweep across North America has permitted little time for developing knowledge of the virus's potential impacts on wildlife in the New World. Given this information gap, we here summarize for the ornithological community what is known or can be anticipated for WNV's effect on bird communities in coming years. Our particular focus is on impacts of WNV on the conservation status of birds, the principal vertebrate reservoir for the virus.
Black Harrier Circus maurus of the Fynbos biome, South Africa: a threatened specialist or an adaptable survivor?
Authors: CURTIS ODETTE , SIMMONS ROBERT E. , JENKINS ANDREW R.
Published: November 2004

Black Harrier Circus maurus is a rare southern African endemic that may have lost over 50% of its core breeding habitat in the last century as a result of extensive land transformation by agriculture, invasive alien vegetation and urbanization in the Fynbos biome. We partially surveyed both the western (Swartland) and southern (Overberg) coastal plains of south-western South Africa, over 3 years (2000–2002) for breeding Black Harriers, and found a distinctly polarized distribution. Nests were concentrated either along the coastal strip or inland in montane habitats, and generally absent from heavily cultivated and transformed inland plains areas. Limited evidence (direct observations, prey remains) suggests that harriers forage in cereal croplands but generally do not breed in these modified environments. We recorded breeding success at nests in coastal (Dune Thicket) and montane (Mountain Fynbos) habitats. Harriers bred successfully along the coast and nests were aggregated in loose colonies around wetlands. Harriers in montane environments bred poorly, took a wide range of prey, and were subject to high levels of nest predation. We propose that Black Harriers have been displaced from lowland Renosterveld and Fynbos habitats (characterized by better foraging and nesting opportunities), primarily by the advent and spread of cereal agriculture. The conservation and future research implications of this hypothesis are discussed.
Status and trends of Gull-billed Tern Gelochelidon nilotica in Europe and Africa
Authors: SÁNCHEZ J. M. , DEL VIEJO A. MUNOZ , CORBACHO C. , COSTILLO E. , FUENTES C.
Published: November 2004

Gull-billed Tern Gelochelidon nilotica is classed as Endangered in Europe (Tucker and Heath 1994, Hagemeijer and Blair, 1997), but there have been no detailed studies of the trends in the different populations occurring in Europe and Africa. Here we study the status and trends of the species in Europe and north and north-east Africa. We estimate the total population at 10,500–12,900 breeding pairs, and recognize two biogeographical populations in this region. The western population, comprising colonies in northern Europe (Denmark, Netherlands, Germany), France, Italy, Spain, and north and north-east Africa, consists of at most 6,200 pairs, 1,800 of which are in African colonies. The eastern population, comprising colonies in the Balkan Peninsula, Greece, shores of the Black Sea and Sea of Azov, and Turkey, consists of at most 6,800 pairs. Two trends were observed: a first phase from 1900 up to the mid-1970s in which the northern European populations practically disappeared; and a second phase of stabilization, or even increase, in some of the western colonies, while the eastern population continued to decline. There is a marked concentration of the species in just a few localities in the countries of the Mediterranean basin.
Unattended Distractor-Induced Priming in a Visual Selective Attention Task
Authors: Heil Martin , Rolke Bettina
Published: November 2004

Abstract: Event-related potentials (ERPs) were recorded from 24 subjects in a visual selective-attention task in which two words were each presented both in a prime display and in a probe display with the target word defined by color. Subjects' task for the prime display was a physical one (target word presented in upper or lower case letters), while the probe display task was a lexical decision. In addition to a neutral condition, four conditions were realized by varying the target probe: The target probe word was (1) a repetition of the target prime (attended repetition), (2) a semantically associated word to the target prime (attended semantic), (3) a repetition of the distractor prime (unattended repetition), or (4) a word semantically associated to the distractor prime (unattended semantic). An attended semantic and an attended repetition priming effect was observed by means of both RT and N400. The N400 differentiated between these two attended priming conditions while RT did not. No unattended priming effects were found with behavioral data. The N400 amplitude modulation, however, was also present for unattended priming but was attenuated compared to the attended condition. The data suggest (1) that automatic processes are sufficient to evoke an N400 effect, and (2) that the N400 effect is a more sensitive indicator for priming effects than response times.
Cardiovascular Correlates of Misconduct in Children and Adolescents
Authors: Kibler Jeffrey L. , Prosser Vicki L. , Ma Mindy
Published: November 2004

Abstract: Prior literature reviews addressing cardiovascular correlates of misconduct have focused on resting heart rate (HR) and skin conductance (SC). The present paper is a quantitative review of studies that tested the relationship between child/adolescent misconduct and cardiovascular regulation. An additional selection criterion for the present review was that the study examined physiological variables beyond resting HR and SC (e.g., cardiovascular reactivity). Misconduct was related to low HR reactivity, low resting parasympathetic nervous system (PNS) control, and less withdrawal of PNS control during mental challenge. These findings expand on prior reviews that indicated resting sympathetic nervous system underarousal is associated with antisocial behavior/misconduct. Cardiovascular reactivity to stress and PNS control may also be important correlates of misconduct.
Wheat and canola response to concentrations of phosphorus and cadmium in a sandy soil
Authors: Brennan R. F. , Bolland M. D. A.
Published: November 2004

An old phosphate rock experiment was used to determine critical Colwell soil test phosphorus values for spring wheat (Triticum aestivum L.) and canola (rape, Brassica napus L.). Different amounts of phosphorus, applied to the soil 16 years previously as triple superphosphate and phosphate rock fertilisers, and different amounts of triple superphosphate applied in the current year, were used to generate soil with different P status. The phosphorus fertilisers contained different concentrations of cadmium as an impurity. The experiment was thus used to relate soil test cadmium, measured using 0.005 mol CaNO3/L, to cadmium concentration in grain. Colwell soil test phosphorus, related to 90% of the maximum grain yield (critical value), was 58 mg phosphorus/kg soil for wheat and 19 mg phosphorus/kg soil for canola. In soil with low Colwell phosphorus concentrations, canola efficiently used phosphorus that was banded with the seed while sowing (drilled phosphorus), requiring 15 kg phosphorus/ha as triple superphosphate to achieve 90% of the maximum yield, compared to 65–70 kg phosphorus/ha for wheat. Soil test cadmium was highly correlated with grain cadmium in both wheat (R2 = 0.89) and canola (R2 = 0.96), suggesting soil testing for cadmium may be used to predict the likelihood of grain cadmium contamination.
Effects of age and liveweight of dairy heifers at first calving on multiple lactation production
Authors: Dobos R. C. , Nandra K. S. , Riley K. , Fulkerson W. J. , Alford A. , Lean I. J.
Published: November 2004

This paper reports on both the individual and combined effects of age and liveweight at first calving (AFC and LWFC, respectively) for Australian Holstein–Friesian heifers on multiple lactation production. One hundred and thirty-five heifers were allocated to 1 of 3 AFC treatments. Within each AFC treatment, heifers were randomly assigned to 1 of 3 LWFC treatments. From 16 weeks of age until first calving, heifers in all groups grazed pasture and were provided with supplementary feed when the quantity and quality of pasture was inadequate to meet growth requirements. Mean AFC and LWFC achieved were 25.1 ± 0.121, 29.9 ± 0.11 and 33.9 ± 0.09 months and 498 ± 4.09, 549 ± 5.40 and 595 ± 5.09 kg, respectively. As AFC increased, total production over the first 3 lactations increased. For each month's delay in AFC an extra 56.7 L milk, 1.78 kg milk fat, 1.45 kg milk protein and 3.23 kg fat + protein over the first 3 lactations was produced but by the third lactation the response was minimal. By end of third lactation the remaining heifers that calved at 25.1 months AFC were producing similar amounts to those that calved at the older AFC. As LWFC increased from 498 to 595 kg, production over the first 3 lactations increased. The response to an extra kilogram increase in LWFC was 4.82 L milk, 0.20 kg milk fat, 0.18 kg milk protein and 0.38 kg fat + protein over the first 3 lactations. The greatest benefit was when LWFC increased from 498 to 549 kg. Increasing LWFC from 549 to 595 kg did not significantly increase milk, milk fat and milk protein yields from the second to third lactation. The combined effects of AFC and LWFC indicated that to reduce the negative effects on production due to decreasing AFC, LWFC would have to increase by 7.2, 2.9 and 2.2 kg for each month decrease in AFC (for milk, fat and protein production, respectively). By the end of the third lactation, only 58 heifers remained in the herd. The number of heifers remaining within the 9 groups ranged from 4 to 10. Increasing LWFC while decreasing AFC reduced the chances of a heifer remaining in the herd but this may have been biased by the feeding regime imposed during lactation. Responses to increasing AFC decreased as the number of lactations increased, indicating that heifers calving at younger AFC produce similar amounts to their older herd-mates by the end of third lactation. Increasing LWFC from 498 to 549 kg had the greatest benefits for yield, indicating a possible maximum LWFC of 549 kg for our study. Therefore, the negative effects due to decreasing AFC can be offset in part, by increasing LWFC. However, on-farm resources and ultimately milk price will determine the choice of combination of AFC and LWFC.
The role of applied science in helping farmers to make decisions about environmental sustainability
Authors: Ridley A.M.
Published: November 2004

Decision making about environmental sustainability is complex, involving both factual and value-based judgements by farmers. Some of the factors involved in making these decisions, such as the financial implications and riskiness, the urgency of the problem, ease of implementation and trialling and compatibility have been addressed elsewhere. The current paper discusses a number of less-explored issues involved in this type of decision making, including the need for multiple sources of knowledge such as farmers’ values and goals, an understanding of social and demographic issues, and consideration of the catchment or landscape context in which farmers live. It highlights scientific knowledge as only one of these knowledge sources, with other sources also needed in complex decision making. Evidence from a Western Australian case study suggests that there has been a shift in farmers’ values over the past few decades and that there is now a greater responsiveness to management solutions which include environmental considerations, even among the 40% of farmers driven primarily by monetary goals. Changing social conditions, particularly the roles of women on farms and of off-farm income, suggest greater potential for the incorporation of environmental considerations into farm management. However, demographic issues, particularly issues such as limited employment opportunities, the declining provision of services in areas dominated by an agricultural economy, and the trend of increasing privatisation of extension services, suggest that there remains potential for greater environmental exploitation in some areas. The role of scientists in helping farmers to address environmental sustainability is discussed, with an acknowledgment that there are insufficient scientists with the required skills available. Scientists need to work in teams with local people to develop a sufficient depth of understanding to translate abstract research findings into solutions that are relevant at the farm level. Highly participatory approaches (which empower farmers rather merely inform them) can help scientists to understand farmers’ needs and motivations, but involve losing control of highly focused research agendas. Environmental Management Systems are one way in which scientific research and group learning can help empower farmers to understand and make better decisions about the environment.
Potassium deficiency, and molybdenum deficiency and aluminium toxicity due to soil acidification, have become problems for cropping sandy soils in south-western Australia
Authors: Brennan R. F. , Bolland M. D. A. , Bowden J. W.
Published: November 2004

Nutrient omission experiments determined the cause of ‘waves’ of good and bad growth in wheat and barley crops following burning of swathed canola crop residues on acidified sandy soils in south-western Australia. Potassium deficiency, and molybdenum deficiency and aluminium toxicity induced by soil acidification, were identified as major problems. Burning canola swaths increased bicarbonate-extractable soil potassium by 20–100 mg/kg, and as measured in 0.01 mol/L CaCl2, increased soil pH by 0.3–0.8 of a pH unit and decreased aluminium extracted from soil by 1–6 mg/kg. These changes in soil chemistry were shown to be responsible for waves of better crop growth under the burnt swaths. Root lesion nematodes were shown not to be related to the problem.
Sustaining productivity of a Vertosol at Warra, Queensland, with fertilisers, no-tillage or legumes. 8. Effect of duration of lucerne ley on soil nitrogen and water, wheat yield and protein
Authors: Dalal R. C. , Weston E. J. , Strong W. M. , Probert M. E. , Lehane K. J. , Cooper J. E. , King A. J. , Holmes C. J.
Published: November 2004

Soil nitrogen (N) supply in the Vertosols of southern Queensland, Australia has steadily declined as a result of long-term cereal cropping without N fertiliser application or rotations with legumes. Nitrogen-fixing legumes such as lucerne may enhance soil N supply and therefore could be used in lucerne–wheat rotations. However, lucerne leys in this subtropical environment can create a soil moisture deficit, which may persist for a number of seasons. Therefore, we evaluated the effect of varying the duration of a lucerne ley (for up to 4 years) on soil N increase, N supply to wheat, soil water changes, wheat yields and wheat protein on a fertility-depleted Vertosol in a field experiment between 1989 and 1996 at Warra (26°47′S, 150°53′E), southern Queensland. The experiment consisted of a wheat–wheat rotation, and 8 treatments of lucerne leys starting in 1989 (phase 1) or 1990 (phase 2) for 1, 2, 3 or 4 years duration, followed by wheat cropping. Lucerne DM yield and N yield increased with increasing duration of lucerne leys. Soil N increased over time following 2 years of lucerne but there was no further significant increase after 3 or 4 years of lucerne ley. Soil nitrate concentrations increased significantly with all lucerne leys and moved progressively downward in the soil profile from 1992 to 1995. Soil water, especially at 0.9–1.2 m depth, remained significantly lower for the next 3 years after the termination of the 4-year lucerne ley than under continuous wheat. No significant increase in wheat yields was observed from 1992 to 1995, irrespective of the lucerne ley. However, wheat grain protein concentrations were significantly higher under lucerne–wheat than under wheat–wheat rotations for 3–5 years. The lucerne yield and soil water and nitrate-N concentrations were satisfactorily simulated with the APSIM model. Although significant N accretion occurred in the soil following lucerne leys, in drier seasons, recharge of the drier soil profile following long duration lucerne occurred after 3 years. Consequently, 3- and 4-year lucerne–wheat rotations resulted in more variable wheat yields than wheat–wheat rotations in this region. The remaining challenge in using lucerne–wheat rotations is balancing the N accretion benefits with plant-available water deficits, which are most likely to occur in the highly variable rainfall conditions of this region.
The high- and low-affinity receptor binding sites of growth hormone are allosterically coupled
Authors: Walsh Scott T. R. , Sylvester Juliesta E. , Kossiakoff Anthony A.
Published: November 2004

Growth hormone regulates its biological properties via a sequential hormone-induced receptor homodimerization mechanism. Using a mutagenesis-scanning analysis of 81 single and 32 pairwise double mutations, we show that the hormone's two spatially distal receptor binding sites (Site1 and Site2) are allosterically coupled. These allosteric effects are focused among a relatively few residues centered around the interaction between Asp-116 of the hormone and Trp-169 of the receptor in Site2. A rearrangement of this interaction triggered by mutations in Site1 produces both a major conformation and energetic reorganization of Site2, surprisingly without a reduction in overall binding affinity. Additionally, the data suggest a change in the conformational dynamics of several groups in Site2 that appear to be important in defining the Site2 interaction. Changes in binding energy of the affected Site2 residues usually range in magnitude from 3- to 60-fold, but in one case are as large as 10
4
.
A digital technique for art authentication
Authors: Lyu Siwei , Rockmore Daniel , Farid Hany
Published: November 2004

We describe a computational technique for authenticating works of art, specifically paintings and drawings, from high-resolution digital scans of the original works. This approach builds a statistical model of an artist from the scans of a set of authenticated works against which new works then are compared. The statistical model consists of first- and higher-order wavelet statistics. We show preliminary results from our analysis of 13 drawings that at various times have been attributed to Pieter Bruegel the Elder; these results confirm expert authentications. We also apply these techniques to the problem of determining the number of artists that may have contributed to a painting attributed to Pietro Perugino and again achieve an analysis agreeing with expert opinion.
Coordinated assembly of human translation initiation complexes by the hepatitis C virus internal ribosome entry site RNA
Authors: Ji Hong , Fraser Christopher S. , Yu Yonghao , Leary Julie , Doudna Jennifer A.
Published: November 2004

Protein synthesis in all cells begins with recruitment of the small ribosomal subunit to the initiation codon in a messenger RNA. In some eukaryotic viruses, RNA upstream of the coding region forms an internal ribosome entry site (IRES) that directly binds to the 40S ribosomal subunit and enables translation initiation in the absence of many canonical translation initiation factors. The hepatitis C virus (HCV) IRES RNA requires just two initiation factors, eukaryotic initiation factor (eIF) 2 and eIF3, to form preinitiation 48S ribosomal complexes that subsequently assemble into translation-competent ribosomes. Using an RNA-based affinity purification approach, we show here that HCV IRES RNA facilitates eIF2 function through its interactions with eIF3 and the 40S ribosomal subunit. Although the wild-type IRES assembles normally into 48S and 80S ribosomal complexes in human cell extract, mutant IRES RNAs become trapped at the 48S assembly stage. Trapped 48S complexes formed by IRES mutants with reduced eIF3 binding affinity nonetheless contain eIF3, consistent with inherent eIF3–40S subunit affinity. Intriguingly, however, one of these IRES mutants prevents stable association of both eIF3 and eIF2, preventing initiator tRNA deposition and explaining the block in 80S assembly. In contrast, an IRES mutant unable to induce a conformational change in the 40S subunit, as observed previously by single-particle cryoelectron microscopy, blocks 80S formation at a later stage in assembly. These data suggest that the IRES RNA coordinates interactions of eIF3 and eIF2 on the ribosome required to position the initiator tRNA on the mRNA in the ribosomal peptidyl-tRNA site (P site).
Imaging of receptor trafficking by using α-bungarotoxin-binding-site-tagged receptors
Authors: Sekine-Aizawa Yoko , Huganir Richard L.
Published: November 2004

α-Amino-3-hydroxy-5-methyl-4-isoxazole-propionate (AMPA) receptors mediate excitatory synaptic transmission and are dynamically regulated during synaptic plasticity in the CNS. The membrane trafficking of AMPA receptors to synapses is critical for the regulation of the efficacy of excitatory synaptic transmission. Direct imaging of AMPA receptors in various cell compartments is important to dissecting the regulation of distinct steps in receptor membrane trafficking. In this study, we have developed an approach for the imaging of receptor trafficking with subunits tagged with a 13-aa α-bungarotoxin (BTX)-binding site (BBS). The small polypeptide neurotoxin BTX has been used for decades to study the nicotinic acetylcholine receptor. Similar high-affinity ligands are rarely available for most receptors. Engineering the BBS tag into receptor subunits allowed the high-affinity binding of fluorescent, radioactive, and biotinylated BTX to the tagged receptor subunits. By using this approach, the total receptor expression, surface expression, internalization, and insertion of receptors into the plasma membrane could be visualized and quantified in fixed or live cells including cultured neurons. The BBS tag is a flexible approach for labeling membrane proteins and studying their dynamic trafficking.
Critical roles for collagenase-3 (Mmp13) in development of growth plate cartilage and in endochondral ossification
Authors: Inada Masaki , Wang Yingmin , Byrne Michael H. , Rahman Mahboob U. , Miyaura Chisato , López-Otín Carlos , Krane Stephen M.
Published: November 2004

Collagenase-3 (MMP13), a member of the matrix metalloproteinase (MMP) family of neutral endopeptidases, is expressed in the skeleton during embryonic development and is highly overexpressed in human carcinomas and in chondrocytes and synovial cells in rheumatoid arthritis and osteoarthritis. To determine the functional roles of Mmp13, we generated
Mmp13
-null mice that showed profound defects in growth plate cartilage with markedly increased hypertrophic domains as well as delay in endochondral ossification and formation and vascularization of primary ossification centers. Absence of Mmp13 resulted in significant interstitial collagen accumulation due, in part, to the lack of appropriate collagenase-mediated cleavage that normally occurs in growth plates and primary ossification centers. Cartilaginous growth plate abnormalities persisted in adult mice and phenocopied defects observed in human hereditary chondrodysplasias. Our findings demonstrate a unique role of Mmp13 in skeletal development.
Glycine as a
d
-amino acid surrogate in the K
+
-selectivity filter
Authors: Valiyaveetil Francis I. , Sekedat Matthew , MacKinnon Roderick , Muir Tom W.
Published: November 2004

The K+ channel-selectivity filter consists of two absolutely conserved glycine residues. Crystal structures show that the first glycine in the selectivity filter, Gly-77 in KcsA, is in a left-handed helical conformation. Although the left-handed helical conformation is not favorable for the naturally occurring
l
-amino acids, it is favorable for the chirally opposite
d
-amino acids. Here, we demonstrate that Gly-77 can be replaced by
d
-Ala with almost complete retention of function. In contrast, substitution with an
l
-amino acid results in a nonfunctional channel. This finding suggests that glycine is used as a surrogate
d
-amino acid in the selectivity filter. The absolute conservation of glycine in the K
+
-selectivity filter can be explained as a result of glycine being the only natural amino acid that can play this role.
The Yeast Par-1 Homologs Kin1 and Kin2 Show Genetic and Physical Interactions with Components of the Exocytic Machinery
Authors: Elbert Maya , Rossi Guendalina , Brennwald Patrick
Published: November 2004

Kin1 and Kin2 are Saccharomyces cerevisiae counterparts of Par-1, the Caenorhabditis elegans kinase essential for the establishment of polarity in the one cell embryo. Here, we present evidence for a novel link between Kin1, Kin2, and the secretory machinery of the budding yeast. We isolated KIN1 and KIN2 as suppressors of a mutant form of Rho3, a Rho-GTPase acting in polarized trafficking. Genetic analysis suggests that KIN1 and KIN2 act downstream of the Rab-GTPase Sec4, its exchange factor Sec2, and several components of the vesicle tethering complex, the Exocyst. We show that Kin1 and Kin2 physically interact with the t-SNARE Sec9 and the Lgl homologue Sro7, proteins acting at the final stage of exocytosis. Structural analysis of Kin2 reveals that its catalytic activity is essential for its function in the secretory pathway and implicates the conserved 42-amino acid tail at the carboxy terminal of the kinase in autoinhibition. Finally, we find that Kin1 and Kin2 induce phosphorylation of t-SNARE Sec9 in vivo and stimulate its release from the plasma membrane. In summary, we report the finding that yeast Par-1 counterparts are associated with and regulate the function of the exocytic apparatus via phosphorylation of Sec9.
Fibronectin Matrix Turnover Occurs through a Caveolin-1–dependent Process
Authors: Sottile Jane , Chandler Jennifer
Published: November 2004

Extracellular matrix remodeling occurs during development, tissue repair, and in a number of pathologies, including fibrotic disorders, hypertension, and atherosclerosis. Extracellular matrix remodeling involves the complex interplay between extracellular matrix synthesis, deposition, and degradation. Factors that control these processes are likely to play key roles in regulating physiological and pathological extracellular matrix remodeling. Our data show that fibronectin polymerization into the extracellular matrix regulates the deposition and stability of other extracellular matrix proteins, including collagen I and thrombospondin-1 ( Sottile and Hocking, 2002 . Mol. Biol. Cell 13, 3546). In the absence of continual fibronectin polymerization, there is a loss of fibronectin matrix fibrils, and increased levels of fibronectin degradation. Fibronectin degradation occurs intracellularly after endocytosis and can be inhibited by chloroquine, an inhibitor of lysosomal degradation, and by caveolae-disrupting agents. Down-regulation of caveolin-1 by RNAi inhibits loss of fibronectin matrix fibrils, fibronectin internalization, and fibronectin degradation; these processes can be restored by reexpression of caveolin-1. These data show that fibronectin matrix turnover occurs through a caveolin-1–dependent process. Caveolin-1 regulation of fibronectin matrix turnover is a novel mechanism regulating extracellular matrix remodeling.
Munc18-1 Regulates Early and Late Stages of Exocytosis via Syntaxin-independent Protein Interactions
Authors: Ciufo Leonora F. , Barclay Jeff W. , Burgoyne Robert D. , Morgan Alan
Published: November 2004

Sec1/Munc18 (SM) proteins are involved in various intracellular membrane trafficking steps. Many SM proteins bind to appropriate syntaxin homologues involved in these steps, suggesting that SM proteins function as syntaxin chaperones. Organisms with mutations in SM genes, however, exhibit defects in either early (docking) or late (fusion) stages of exocytosis, implying that SM proteins may have multiple functions. To gain insight into the role of SM proteins, we introduced mutations modeled on those identified in Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae into mammalian Munc18-1. As expected, several mutants exhibited reduced binding to syntaxin1A. However, three mutants displayed wild-type syntaxin binding affinities, indicating syntaxin-independent defects. Expression of these mutants in chromaffin cells either increased the rate and extent of exocytosis or altered the kinetics of individual release events. This latter effect was associated with a reduced Mint binding affinity in one mutant, implying a potential mechanism for the observed alteration in release kinetics. Furthermore, this phenotype persisted when the mutation was combined with a second mutation that greatly reduced syntaxin binding affinity. These results clarify the data on the function of SM proteins in mutant organisms and indicate that Munc18-1 controls multiple stages of exocytosis via both syntaxin-dependent and -independent protein interactions.
A Sorting Nexin PpAtg24 Regulates Vacuolar Membrane Dynamics during Pexophagy via Binding to Phosphatidylinositol-3-Phosphate
Authors: Ano Yoshitaka , Hattori Takeshi , Oku Masahide , Mukaiyama Hiroyuki , Baba Misuzu , Ohsumi Yoshinori , Kato Nobuo , Sakai Yasuyoshi
Published: November 2004

Diverse cellular processes such as autophagic protein degradation require phosphoinositide signaling in eukaryotic cells. In the methylotrophic yeast Pichia pastoris, peroxisomes can be selectively degraded via two types of pexophagic pathways, macropexophagy and micropexophagy. Both involve membrane fusion events at the vacuolar surface that are characterized by internalization of the boundary domain of the fusion complex, indicating that fusion occurs at the vertex. Here, we show that PpAtg24, a molecule with a phosphatidylinositol 3-phosphate-binding module (PX domain) that is indispensable for pexophagy, functions in membrane fusion at the vacuolar surface. CFP-tagged PpAtg24 localized to the vertex and boundary region of the pexophagosome-vacuole fusion complex during macropexophagy. Depletion of PpAtg24 resulted in the blockage of macropexophagy after pexophagosome formation and before the fusion stage. These and other results suggest that PpAtg24 is involved in the spatiotemporal regulation of membrane fusion at the vacuolar surface during pexophagy via binding to phosphatidylinositol 3-phosphate, rather than the previously suggested function in formation of the pexophagosome.
ATP-2 Interacts with the PLAT Domain of LOV-1 and Is Involved inCaenorhabditis elegansPolycystin Signaling
Authors: Hu Jinghua , Barr Maureen M.
Published: November 2004

Caenorhabditis elegans is a powerful model to study the molecular basis of autosomal dominant polycystic kidney disease (ADPKD). ADPKD is caused by mutations in the polycystic kidney disease (PKD)1 or PKD2 gene, encoding polycystin (PC)-1 or PC-2, respectively. The C. elegans polycystins LOV-1 and PKD-2 are required for male mating behaviors and are localized to sensory cilia. The function of the evolutionarily conserved polycystin/lipoxygenase/α-toxin (PLAT) domain found in all PC-1 family members remains an enigma. Here, we report that ATP-2, the β subunit of the ATP synthase, physically associates with the LOV-1 PLAT domain and that this interaction is evolutionarily conserved. In addition to the expected mitochondria localization, ATP-2 and other ATP synthase components colocalize with LOV-1 and PKD-2 in cilia. Disrupting the function of the ATP synthase or overexpression of atp-2 results in a male mating behavior defect. We further show that atp-2, lov-1, and pkd-2 act in the same molecular pathway. We propose that the ciliary localized ATP synthase may play a previously unsuspected role in polycystin signaling.
COLONY AND FRUSTULE MORPHOLOGY OF THREE TUBE‐DWELLING DIATOMS FROM EASTERN CANADA1
Authors: Lobban Christopher S.
Published: November 2004

Three species of Navicula are described from light and scanning electron microscopy. Navicula bottnica Grunow, has not previously been illustrated at the SEM level, nor has it previously been reported to form colonies, but the cells appear to be identical to Schizonema smithii C. Agardh (sensu van Heurck) and the name is amended to Navicula smithii (C. Ag.) van Heurck. The colonies are irregularly branched, the cells within forming strands which frequently appear braided. Material of N. delognei van Heurck differs in several points from typical material and a new form, elliptica is proposed. Observations on the third species, N. pseudocomoides corroborate recent work by Cox in Britain.
THE OCCURRENCE OF CHLOROPHYLLS C1 AND C2 IN THE CHRYSOPHYCEAE1
Authors: Andersen Robert A. , Mulkey Timothy J.
Published: November 2004

We analyzed 34 strains representing 25 species of Chrysophyceae for chlorophylls c1 and c2 using thin‐layer chromatography. Most organisms had both chlorophylls c1 and c2 in addition to chlorophyll a but 17 strains of 9 species of Synura and Mallomonas possessed only chlorophylls a and c1. These are the first chlorophyll c‐bearing algae which lack chlorophyll c2. We postulate that at least some of the silica‐scaled algae including Mallomonas and Synura may be distinct from other Chrysophyceae based upon pigmentation and other characters described in the literature.
DIATOM MINERALIZATION OF SILICIC ACID. VII. INFLUENCE OF MICROTUBULE DRUGS ON SYMMETRY AND PATTERN FORMATION IN VALVES OF NAVICULA SAPROPHILA DURING MORPHOGENESIS1
Authors: Blank Gregory S. , Sullivan Cornelius W.
Published: November 2004

Microtubule involvement in diatom valve symmetry and pattern formation was investigated using cells synchronized subsequent to mitosis and cytokinesis but prior to cell wall formation. Two analog drug pairs, each consisting of an active and an inactive microtubule drug, were used to distinguish inhibitory effects related or unrelated to microtubule disruption. The active anti‐microtubule drug of each analog pair produced significantly higher percentages of aberrant valves than did the respective inactive analogs. High frequencies of aberrant valves also were caused by N‐isophenlpropylcarbamate, which disorganizes rather than disrupts microtubules. Valves could be placed into different classes based upon characteristic aberrations. Formation of these classes was not random but was instead a function of both the drug and the drug concentration. The central nodule and the raphe were the principal valve components affected by anti‐microtubule drugs. Stria alterations appeared as a secondary result of alterations in the central nodule/raphe. Valve aberrations occurred at very low drug concentrations in the range 1 × 10−6 to 1 × 10−9M.
LIGHT AND NUTRIENT DEPENDENCE OF PHOTOSYNTHESIS BY ALGAE1
Authors: Smith Val H.
Published: November 2004

The validity of a recent nutrient‐based modal of algal photosynthesis was tested using phosphorus‐limited semi‐continuous cultures of the green alga, Scenedesmus quadricauda. The data suggest that light‐saturate photosynthesis (P opt, mg C · mg chla−1· h−1) is a hyperbolic function of cellular phosphorus quota (Qp), whether Qp is expressed per unit cellular chlorophyll a, per unit dry weight, or per cell number. Furthermore, the light availability during growth appears to have little effect on these hyperbolic relationships over the range of light intensities studied here (65–110 μE · m−2· s−1). These data, and data presented from other published studies, suggest that the cell quota model is a valid empirical description of the photosynthetic behavior of nutrient‐limited cells.
DIATOM COLONIZATION ON ARTIFICIAL SUBSTRATA IN POOL AND RIFFLE ZONES STUDIED BY LIGHT AND SCANNING ELECTRON MICROSCOPY1
Authors: Korte Virginia L. , Blinn Dean W.
Published: November 2004

Light and scanning electron microscopy were utilized to quality diatom colonization in Oak Creek, Arizona. Aluminum SEM stubs with and without plexiglass discs were anchored into rocks. Early colonization on five stub microzones was examined at hourly intervals; weekly intervals of up to 3 wk were employed to record community development in pool find riffle. Plexiglass was more suitable for microbial colonization than aluminum. Organic matter and bacteria were important surface pre‐conditioning agents while fungi were instrumental in trap/ting cells during early stages of colonization in the riffle. Diatom colonization was initialed within 1 h on the upstream side of substrata in riffles, while the tap face was colonized first in pools. Colonization moved rapidly to the perimeter in each system. Early colonization of‐side microzones was considerably more asymmetric in the riffle than, pool. At Idler stages (2 wk) diatoms with their associated mucilage and algal filaments contributed to the stability of the microbial communities. Horizontally positioned species(Achnanthes, Cocconeis)were early colonizers in both systems while vertically positioned species(Gomphonema, Nitzschia)were more important in later successional stages (3 wk) in the riffle. Horizontally positioned species remained dominant throughout the 3 wk period in the pool. After 3 wk, diversity was normally greater in the pool while density was higher in the riffle. Detrital microcosms containing viable microbiol assemblages frequently collected on tin‐upstream face of substrata in the riffle. The random nature by which these detrital microcoms contact downstream substrata greatly contribute to the spatial variation of periphyton in streams. These detrital microcosms expedite repeated colonization in lotic systems.