bluuebunny/crossref_metadata_2025 huggingface dataset:
The transition disc frequency in M stars
Authors: Ercolano B. , Clarke C. J. , Robitaille T. P.
Published: February 2009

We re-examine the recent suggestion of a high fraction of transition discs (i.e. those with a cleared inner hole) in M stars, motivated by the fact that we expect that, for M stars, even discs without inner holes should exhibit very weak excess shortwards of around 10 μm. Our analysis of spectral energy distribution models suggests that this indeed means that M stars where a detectable excess begins at around 6 μm may be misclassified as transition discs when in fact they have optically thick dust extending in to the dust sublimation radius. Consequently, we estimate that the transition disc fraction among M stars in the Coronet cluster is ∼15 ± 10 per cent (rather than the recently claimed value of 50 per cent). This revised figure would imply that the transition disc fraction is not after all markedly higher in later type stars. We suggest that, for M stars, transition discs can only be readily identified if they have emission that is close to photospheric out to >10 μm.
The Reliability of Difference Scores in Populations and Samples
Authors: Zimmerman Donald W.
Published: February 2009

This study was an investigation of the relation between the reliability of difference scores, considered as a parameter characterizing a population of examinees, and the reliability estimates obtained from random samples from the population. The parameters in familiar equations for the reliability of difference scores were redefined in such a way that determinants of reliability in both populations and samples become more transparent. Computer simulation was used to find sample values and to plot frequency distributions of various correlations and variance ratios relevant to the reliability of differences. The shape of frequency distributions resulting from the simulations and the means and standard deviations of these distributions reveal the extent to which reliability estimates based on sample data can be expected to meaningfully represent population reliability.
Convergent Radial Tracing of Viral and Solute Transport in Gneiss Saprolite
Authors: Taylor Richard , Tindimugaya Callist , Barker John , Macdonald David , Kulabako Robinah
Published: February 2009

Deeply weathered crystalline rock aquifer systems comprising unconsolidated saprolite and underlying fractured bedrock (saprock) underlie 40% of sub‐Saharan Africa. The vulnerability of this aquifer system to contamination, particularly in rapidly urbanizing areas, remains poorly understood. In order to assess solute and viral transport in saprolite derived from Precambrian gneiss, forced‐gradient tracer experiments using chloride and Escherichia coli phage ΦX174 were conducted in southeastern Uganda. The bacteriophage tracer was largely unrecovered; adsorption to the weathered crystalline rock matrix is inferred and enabled by the low pH (5.7) of site ground water and the bacteriophage's relatively high isoelectric point (pI = 6.6). Detection of the applied ΦX174 phage in the pumping well discharge at early times during the experiment traces showed, however, that average ground water flow velocities exceed that of the inert solute tracer, chloride. This latter finding is consistent with observations in other hydrogeological environments where statistically extreme sets of microscopic flow velocities are considered to transport low numbers of fecal pathogens and their proxies along a selected range of linked ground water pathways. Application of a radial advection‐dispersion model with an exponentially decaying source term to the recovered chloride tracer estimates a dispersivity (α) of 0.8 ± 0.1 m over a distance of 4.15 m. Specific yield (Sy) is estimated to be 0.02 from volume balance calculations based on tracer experiments. As single‐site observations, our estimates of saprolite Sy and α are tentative but provide a starting point for assessing the vulnerability of saprolite aquifers in sub‐Saharan Africa to contamination and estimating quantitatively the impact of climate and abstraction on ground water storage.
Modeled Ground Water Age Distributions
Authors: Woolfenden Linda R. , Ginn Timothy R.
Published: February 2009

The age of ground water in any given sample is a distributed quantity representing distributed provenance (in space and time) of the water. Conventional analysis of tracers such as unstable isotopes or anthropogenic chemical species gives discrete or binary measures of the presence of water of a given age. Modeled ground water age distributions provide a continuous measure of contributions from different recharge sources to aquifers. A numerical solution of the ground water age equation of Ginn (1999) was tested both on a hypothetical simplified one‐dimensional flow system and under real world conditions. Results from these simulations yield the first continuous distributions of ground water age using this model. Complete age distributions as a function of one and two space dimensions were obtained from both numerical experiments. Simulations in the test problem produced mean ages that were consistent with the expected value at the end of the model domain for all dispersivity values tested, although the mean ages for the two highest dispersivity values deviated slightly from the expected value. Mean ages in the dispersionless case also were consistent with the expected mean ages throughout the physical model domain. Simulations under real world conditions for three dispersivity values resulted in decreasing mean age with increasing dispersivity. This likely is a consequence of an edge effect. However, simulations for all three dispersivity values tested were mass balanced and stable demonstrating that the solution of the ground water age equation can provide estimates of water mass density distributions over age under real world conditions.
AMP‐activated protein kinase in contraction regulation of skeletal muscle metabolism: necessary and/or sufficient?
Authors: Jensen T. E. , Wojtaszewski J. F. P. , Richter E. A.
Published: February 2009

In skeletal muscle, the contraction‐activated heterotrimeric 5′‐AMP‐activated protein kinase (AMPK) protein is proposed to regulate the balance between anabolic and catabolic processes by increasing substrate uptake and turnover in addition to regulating the transcription of proteins involved in mitochondrial biogenesis and other aspects of promoting an oxidative muscle phenotype. Here, the current knowledge on the expression of AMPK subunits in human quadriceps muscle and evidence from rodent studies suggesting distinct AMPK subunit expression pattern in different muscle types is reviewed. Then, the intensity and time dependence of AMPK activation in human quadriceps and rodent muscle are evaluated. Subsequently, a major part of this review critically examines the evidence supporting a necessary and/or sufficient role of AMPK in a broad spectrum of skeletal muscle contraction‐relevant processes. These include glucose uptake, glycogen synthesis, post‐exercise insulin sensitivity, fatty acid (FA) uptake, intramuscular triacylglyceride hydrolysis, FA oxidation, suppression of protein synthesis, proteolysis, autophagy and transcriptional regulation of genes relevant to promoting an oxidative phenotype.
AMP‐activated protein kinase and cancer
Authors: Wang W. , Guan K.‐L.
Published: February 2009

AMP‐activated protein kinase (AMPK) is a cellular energy sensor that is conserved in eukaryotes. Elevated AMP/ATP ratio activates AMPK, which inhibits energy‐consuming processes and activates energy‐producing processes to restore the energy homeostasis inside the cell. AMPK activators, metformin and thiazolidinediones, are used for the treatment of type II diabetes. Recently, reports have indicated that AMPK may also be a beneficial target for cancer treatment. Cancer cells have characteristic metabolic changes different from normal cells and, being a key metabolic regulator, AMPK may regulate the switch. AMPK may act to inhibit tumorigenesis through regulation of cell growth, cell proliferation, autophagy, stress responses and cell polarity.
Vulnerability as a Regulatory Category in Human Subject Research
Authors: Coleman Carl H.
Published: February 2009

The concept of vulnerability has long played a central role in discussions of research ethics. In addition to its rhetorical use, vulnerability has become a term of art in U.S. and international research regulations and guidelines, many of which contain specific provisions applicable to research with vulnerable subjects. Yet, despite the frequency with which the term vulnerability is used, little consensus exists on what it actually means in the context of human subject protection or, more importantly, on how a finding of vulnerability should affect the process of research ethics review.

The Common Rule, the centerpiece of the U.S. human subject protection regulations, uses the word vulnerable three times. First, it provides that institutional review boards (IRBs) that regularly review research involving a vulnerable category of subjects should consider including one or more individuals who are knowledgeable about and experienced in working with these subjects.
Limited English Proficiency and Disparities in Clinical Research
Authors: Bustillos Dan
Published: February 2009

Imagine that you possess an indicator for a disease or illness that has nothing to do with your body. It is not a genetic predisposition to acquire cancer or a vice that raises the probability of contracting some dread disease, though estimates of its health risks have placed it on par with having diabetes. It has nothing to do with the environmental pollutants you are exposed to or whether you can afford health care. It is not a physical susceptibility that renders you more easily reachable by the clutches of pathology. No, this indicator of health hinges on certain learned abilities and skills, and it is a barrier to health that is totally within the health field's power and resources to lift.

The condition hinted at above is the inability to speak English proficiently in the United States. Today, more than one-sixth of the United States population speaks a language other than Englishat home,and this number (approximately 50 million people) is increasing rapidly.
Vulnerability in Clinical Research with Patients in Pain: A Risk Analysis
Authors: Tait Raymond C.
Published: February 2009

The concept of vulnerability has been the topic of considerable discussion in research bioethics, largely because of dissatisfaction with early constructions of the concept that were based on subpopulations of research subjects. These subpopulations have attributes likely to undermine their capacity to provide autonomous informed consent: persons who are relatively or absolutely incapable of protecting their own interests through negotiations for informed consent. Several subpopulations were seen as requiring special protections, including children, pregnant women, prisoners, racial minorities, the economically disadvantaged, the very sick, and the institutionalized. Recent years have witnessed the identification of other subpopulations with attributes that could render them vulnerable, as well. For example, the Council for the International Organization of Medical Societies has named such potentially vulnerable groups as the homeless, nursing home residents, patients with incurable diseases, patients in the emergency department, employees, students, and members of communities who are unfamiliar with modern medicine.
Rhodopsin Activation Switches in a Native Membrane Environment†
Authors: Lüdeke Steffen , Mahalingam Mohana , Vogel Reiner
Published: February 2009

The elucidation of structure–function relationships of membrane proteins still poses a considerable challenge due to the sometimes profound influence of the lipid bilayer on the functional properties of the protein. The visual pigment rhodopsin is a prototype of the family of G protein‐coupled transmembrane receptors and a considerable part of our knowledge on its activation mechanisms has been derived from studies on detergent‐solubilized proteins. This includes in particular the events associated with the conformational transitions of the receptor from the still inactive Meta I to the Meta II photoproduct states, which are involved in signaling. These events involve disruption of an internal salt bridge of the retinal protonated Schiff base, movement of helices and proton uptake from the solvent by the conserved cytoplasmic E(D)RY network around Glu134. As the equilibria associated with these events are considerably altered by the detergent environment, we set out to investigate these equilibria in the native membrane environment and to develop a coherent thermodynamic model of these activating steps using UV–visible and Fourier‐transform infrared spectroscopy as complementary techniques. Particular emphasis is put on the role of protonation of Glu134 from the solvent, which is a thermodynamic prerequisite for full receptor activation in membranes, but not in detergent. In view of the conservation of this carboxylate group in family A G protein‐coupled receptors, it may also play a similar role in the activation of other family members.
pH‐dependent Interaction of Rhodopsin with Cyanidin‐3‐glucoside. 2. Functional Aspects†
Authors: Tirupula Kalyan C. , Balem Fernanda , Yanamala Naveena , Klein‐Seetharaman Judith
Published: February 2009

Anthocyanins are a class of phytochemicals that confer color to flowers, fruits, vegetables and leaves. They are part of our regular diet and serve as dietary supplements because of numerous health benefits, including improved vision. Recent studies have shown that the anthocyanin cyanidin‐3‐O‐glucoside (C3G) increased regeneration of the dim‐light photoreceptor rhodopsin (Matsumotoet al. [2003]J.Agric.Food Chem.,51, 3560–3563). In an accompanying study (Yanamalaet al. [2009]Photochem.Photobiol.), we show that C3G directly binds to rhodopsin in a pH‐dependent manner. In this study, we investigated the functional consequences of C3G binding to rhodopsin. As observed previously in rod outer segments, regeneration of purified rhodopsin in detergent micelles is also accelerated in the presence of C3G. Thermal denaturation and stability studies using circular dichroism, fluorescence and UV/visible absorbance spectroscopy show that C3G exerts a destabilizing effect on rhodopsin structure while it only modestly alters G‐protein activation and the rates at which the light‐activated Metarhodopsin II state decays to opsin and free retinal. These results indicate that the mechanism of C3G‐enhanced regeneration may be based on changes in opsin structure promoting access to the retinal binding pocket.
Role of Arg123 in Light‐driven Anion Pump Mechanisms of pharaonis Halorhodopsin†
Authors: Kubo Megumi , Kikukawa Takashi , Miyauchi Seiji , Seki Akiteru , Kamiya Masakatsu , Aizawa Tomoyasu , Kawano Keiichi , Kamo Naoki , Demura Makoto
Published: February 2009

Halorhodopsin (HR) acts as a light‐driven chloride pump which transports a chloride ion from the extracellular (EC) to the cytoplasmic space during a photocycle reaction that includes some photointermediates initiated by illumination. To understand the chloride uptake mechanisms, we focused on a basic residue Arg123 of HR from Natronomonas pharaonis (NpHR), which is the only basic residue located in the EC half ion channel. By the measurements of the visible absorption spectra in the dark and the light‐induced inward current through the membrane, it was shown that the chloride binding and transport ability of NpHR completely disappeared by the change of arginine to glutamine. From flashphotolysis analysis, the photocycle of R123Q differed from that of wildtype NpHR completely. The response of the R123H mutant depended on pH. These facts imply that the positive charge at position 123 is essential for chloride binding in the ground state and for the chloride uptake under illumination. On the basis of the molecular structures of HR and the anion‐transportable mutants of bacteriorhodopsin, the effects of the positive charge and the conformational change of the Arg123 side chain as well as the chloride‐pumping mechanism are discussed.
Additive Effects of Chlorin E6 and Metal Ion Binding on the Thermal Stability of RhodopsinIn Vitro†
Authors: Balem Fernanda , Yanamala Naveena , Klein‐Seetharaman Judith
Published: February 2009

Zinc (Zn2+) deficiency causes retinal dysfunctions such as night blindness and neurodegeneration. Because Zn2+binds directly to the photoreceptor rhodopsin and alters its stability, the stabilization of rhodopsin may be key to prevention and treatment of retinal dysfunctions. In this paper, we investigated if not only trace metals but also other nutrients may stabilize rhodopsin structurein vitro. Detailed studies of the thermal stability of secondary and tertiary structure of rhodopsin in the presence and absence of the chlorophyll derivative chlorin e6 alone and together with bivalent metal ions Zn2+, Cu2+, Fe2+, Ni2+, Mg2+and Mn2+over a temperature range 5–100°C were conducted using circular dichroism and fluorescence spectroscopy. When both chlorin e6 and Zn2+are present, a pronounced increase in the thermal stability of overall secondary structure content is observed compared to either compound alone. This additive capacity is also noted with Cu2+, but not when other metal ions and chlorin e6 are combined.
Geology and Origin of Supergene Ore at the Lavrion Pb‐Ag‐Zn Deposit, Attica, Greece
Authors: Skarpelis Nikos , Argyraki Ariadne
Published: February 2009

The Lavrion carbonate‐hosted Pb‐Ag‐Zn deposit in southeast Attica, Greece, consisted of significant non‐sulfide ore bodies. The polymetallic sulfide mineralization was subjected to supergene oxidation, giving rise to gossan. The principal non‐sulfide minerals of past economic importance were smithsonite, goethite and hematite. The supergene mineral assemblages occupy secondary open spaces and occur as replacement pods within marble. Calamine and iron ore mainly filled open fractures. X‐ray diffraction and scanning electron microscopy of samples of oxidized ore indicate complex gossan mineralogy depending on the hypogene mineralogy, the degree of oxidation and leaching of elements, and the local hydrologic conditions. Bulk chemical analysis of the samples indicated high ore‐grade variability of the supergene mineralization. On multivariate cluster analysis of geochemical data the elements were classified into groups providing evidence for their differential mobilization during dissolution, transport and re‐precipitation. The mode of occurrence, textures, mineralogy and geochemistry of the non‐sulfide mineralization confirm that it is undoubtedly of supergene origin: the product of influx into open fractures in the country rock of highly acidic, metal‐rich water resulting from the oxidation of pyrite‐rich sulfide protore. Dissolution of carbonates led to opening of the fractures. Mineral deposition in the supergene ore took place under near‐neutral to mildly acidic conditions. The supergene dissolution and re‐precipitation of Fe and Zn in the host marble increased metal grades and separated iron and zinc from lead, thereby producing economically attractive deposits; it further contributed to minimization of pollution impact on both soil and ground water.
FeO*‐Al2O3‐TiO2‐Rich Rocks of the Tertiary Bana Igneous Complex, West Cameroon
Authors: Kuepouo Gilbert , Sato Hiroaki , Tchouankoue Jean‐Pierre , Murata Mamoru
Published: February 2009

FeO*‐Al2O3‐TiO2‐rich rocks are found associated with transitional tholeiitic lava flows in the Tertiary Bana plutono‐volcanic complex in the continental sector of the Cameroon Line. These peculiar rocks consist principally of iron‐titanium oxides, aluminosilicates and phosphates, and occur as layers 1–3 m thick occupying the upper part of lava flows on the southwest (site 1) and northwest (site 2) sites of the complex. Mineral constituents of the rocks include magnetite, ilmenite, hematite, rutile, corundum, andalusite, sillimanite, cordierite, quartz, plagioclase, alkali feldspar, apatite, Fe‐Mn phosphate, Al phosphate, micas and fine mixtures of sericite and silica. Texturally and compositionally, the rocks can be subdivided into globular type, banded type, and Al‐rich fine‐gained massive type. The first two types consist of dark globule or band enriched in Fe‐Ti oxides and apatite and lighter colored groundmass or bands enriched in aluminosilicates and quartz, respectively. The occurrence of andalusite and sillimanite and the compositional relations of magnetite and ilmenite in the FeO*‐Al2O3‐TiO2‐rich rocks suggest temperatures of crystallization in a range of 690–830°C at low pressures. The Bana FeO*‐Al2O3‐TiO2‐rich rocks are characterized by low concentrations of SiO2 (25–54.2 wt%), Na2O + K2O (0–1%), CaO (0–2%) and MgO (0–0.5%), and high concentrations of FeO* (total iron as FeO, 20–42%), Al2O3 (20–42%), TiO2 (3–9.2%), and P2O5 (0.26–1.30%). TiO2 is positively correlated with Al2O3 and inversely correlated with FeO*. The bulk rock compositions cannot be derived from the associated basaltic magma by crystal fractionation or by partial melting of the mantle or lower crustal materials. In ternary diagrams of (Al2O3)−(CaO + Na2O + K2O)−(FeO*+ MnO + MgO) and (SiO2)−(FeO*)−(Al2O3), the compositional field of the rocks is close to that of laterite and is distinct from the common volcanic rocks, suggesting that the rocks are derived from lateritic materials by recrystallization when the materials are heated by the basaltic magmas. A hydrothermal origin is discounted because the rocks contain high‐temperature mineral assemblages and lack sulfide minerals. It is proposed that the FeO*‐Al2O3‐TiO2‐rich rocks of the Bana complex were formed by pyrometamorphism of laterite by the heat of basaltic magmas.
Isolation of polymorphic microsatellite loci from the Chinese alligator (Alligator sinensis)
Authors: ZHU HAITAO , WU XIAOBING , XUE HUI , WEI LEI , HU YULING
Published: February 2009

Ten microsatellite loci were isolated from the Chinese alligator (Alligator sinensis), using a partial genomic DNA library and an enrichment method. Fifty microsatellite repeats were screened from the library of 888 positive clones, 10 of which were polymorphic. These microsatellite loci developed here are another set of novel molecular markers for A. sinensis, and they will be suitable for population genetic studies as well as for kinship analysis.
Microsatellite markers for the silver arowana (Osteoglossum bicirrhosum, Osteoglossidae, Osteoglossiformes)
Authors: DE JESUS DA SILVA THEMIS , HRBEK TOMAS , FARIAS IZENI P.
Published: February 2009

Osteoglossum bicirrhosum (silver arowana) is an important fish for the economy of the Amazon region, both as an ornamental fish and as a food fish. To provide tools for addressing ecological and genetic questions, we developed 19 polymorphic microsatellite markers that had between 2 and 7 alleles per locus in the 24 tested individuals. The transferability of many of the loci was confirmed for Osteoglossum ferreirai (black arowana) and Arapaima gigas, and for three African osteoglossiform species.
FLOCK: a method for quick mapping of admixture without source samples
Authors: DUCHESNE P. , TURGEON J.
Published: February 2009

Identifying and estimating individual and/or population admixture is a very common objective in evolution and conservation biology. There are many situations where samples from one or many of the putatively hybridizing entities are not available or easily identified. Here we describe FLOCK, a new method especially designed to provide spatial and/or temporal admixture maps in the absence of one or several source samples. FLOCK is a non‐Bayesian method and therefore differs substantially from previous clustering algorithms. Its working principle is repeated re‐allocation of all collected specimens (total sample) to the k subsamples, each re‐allocation being more effective than the previous one in attracting genetically similar individuals. This snowball effect, more formally referred to as a positive feedback mechanism, makes FLOCK an efficient and quick sorting process. The usage of FLOCK is illustrated with two empirical situations which have been thoroughly analysed previously with other approaches. A number of simulations were run to better assess the power of the FLOCK algorithm. Performance comparisons were made between the FLOCK and Structure algorithms. When non‐negligible numbers of pure genotypes were present, the two performed equally well. However, FLOCK proved significantly more powerful in the absence of pure genotypes. Moreover, FLOCK showed more potential for fast processing. Run times were shown to increase linearly with size of total sample and with size of k, the number of reference samples from which admixture mapping is performed.
DNA barcoding Central Asian butterflies: increasing geographical dimension does not significantly reduce the success of species identification
Authors: LUKHTANOV VLADIMIR A , SOURAKOV ANDREI , ZAKHAROV EVGENY V. , HEBERT PAUL D. N.
Published: February 2009

DNA barcoding employs short, standardized gene regions (5’ segment of mitochondrial cytochrome oxidase subunit I for animals) as an internal tag to enable species identification. Prior studies have indicated that it performs this task well, because interspecific variation at cytochrome oxidase subunit I is typically much greater than intraspecific variation. However, most previous studies have focused on local faunas only, and critics have suggested two reasons why barcoding should be less effective in species identification when the geographical coverage is expanded. They suggested that many recently diverged taxa will be excluded from local analyses because they are allopatric. Second, intraspecific variation may be seriously underestimated by local studies, because geographical variation in the barcode region is not considered. In this paper, we analyse how adding a geographical dimension affects barcode resolution, examining 353 butterfly species from Central Asia. Despite predictions, we found that geographically separated and recently diverged allopatric species did not show, on average, less sequence differentiation than recently diverged sympatric taxa. Although expanded geographical coverage did substantially increase intraspecific variation reducing the barcoding gap between species, this did not decrease species identification using neighbour‐joining clustering. The inclusion of additional populations increased the number of paraphyletic entities, but did not impede species‐level identification, because paraphyletic species were separated from their monophyletic relatives by substantial sequence divergence. Thus, this study demonstrates that DNA barcoding remains an effective identification tool even when taxa are sampled from a large geographical area.
Polymorphic microsatellite loci for primitively eusocial wasp Ropalidia marginata
Authors: JOHNY S. , CHAKRABORTY S. , GADAGKAR R. , NAGARAJU J.
Published: February 2009

We report here development and characterization of 48 novel microsatellite markers for Ropalidia marginata, a tropical, primitively eusocial polistine wasp from peninsular India. Thirty‐two microsatellites showed polymorphism in a wild population of R. marginata (N = 38) collected from Bangalore, India. These markers will facilitate answering some interesting questions in ecology and evolutionary biology of this wasp, such as population structure, serial polygyny, intra‐colony genetic relatedness and the pattern of queen succession.
Is the distribution of nitrogen‐fixing cyanobacteria in the oceans related to temperature?
Authors: Stal Lucas J.
Published: February 2009

Approximately 50% of the global natural fixation of nitrogen occurs in the oceans supporting a considerable part of the new primary production. Virtually all nitrogen fixation in the ocean occurs in the tropics and subtropics where the surface water temperature is 25°C or higher. It is attributed almost exclusively to cyanobacteria. This is remarkable firstly because diazotrophic cyanobacteria are found in other environments irrespective of temperature and secondly because primary production in temperate and cold oceans is generally limited by nitrogen. Cyanobacteria are oxygenic phototrophic organisms that evolved a variety of strategies protecting nitrogenase from oxygen inactivation. Free‐living diazotrophic cyanobacteria in the ocean are of the non‐heterocystous type, namely the filamentous Trichodesmium and the unicellular groups A–C. I will argue that warm water is a prerequisite for these diazotrophic organisms because of the low‐oxygen solubility and high rates of respiration allowing the organism to maintain anoxic conditions in the nitrogen‐fixing cell. Heterocystous cyanobacteria are abundant in freshwater and brackish environments in all climatic zones. The heterocyst cell envelope is a tuneable gas diffusion barrier that optimizes the influx of both oxygen and nitrogen, while maintaining anoxic conditions inside the cell. It is not known why heterocystous cyanobacteria are absent from the temperate and cold oceans and seas.
When Best Theories Go Bad1
Authors: MANLEY DAVID
Published: February 2009

It is common for contemporary metaphysical realists to adopt Quine’s criterion of ontological commitment while at the same time repudiating his ontological pragmatism.2Drawing heavily from the work of others—especially Joseph Melia and Stephen Yablo—I will argue that the resulting approach to meta‐ontology is unstable. In particular, if we are metaphysical realists, we need not accept ontological commitment to whatever is quantified over by our best first‐order theories.
What Mary Did Yesterday: Reflections on Knowledge‐wh
Authors: BROGAARD BERIT
Published: February 2009

Reductionists about knowledge‐whhold that “sknows‐wh” (e.g. “John knows who stole his car”) is reducible to “there is a propositionpsuch thatsknows thatp, andpanswers the indirect question of thewh‐clause.” Anti‐reductionists hold that “sknows‐wh” is reducible to “sknows thatp,asthe true answer to the indirect question of thewh‐clause.” I argue that both of these positions are defective. I then offer a new analysis of knowledge‐whas a special kind of de re knowledge.
Knowledge‐wh and the Problem of Convergent Knowledge
Authors: KALLESTRUP JESPER
Published: February 2009

Call knowledge where so‐and‐so, knowledge who so‐and‐so, etc., knowledge‐wh. The reductive view says that knowledge‐wh reduces to the two‐place knowledge relation Ksp. Schaffer (2007) argues that this view has no viable response to the problem of convergent knowledge: how can a knowing‐wh ascription be reduced to a Ksp ascription if a second knowing‐wh ascription intuitively inequivalent to the first can be reduced to the same Ksp ascription? Instead he suggests that knowledge‐wh be understood as a three‐place knowledge relation Kspq, where q is a contextually salient contrast proposition. I argue firstly that once we realise that wh‐questions can have more than one true answer, the reductivist has an obvious response to this problem. Secondly, I pose a revenge problem for Schaffer’s contrastivist alternative: how can a knowing‐wh ascription be reduced to a Kspq ascription if a second knowing‐wh ascription intuitively equivalent to the first can be reduced to a distinct Kspq ascription?
Measuring the Impact of Increased Product Substitution on Pricing and Capacity Decisions Under Linear Demand Models
Authors: Lus Betul , Muriel Ana
Published: February 2009

We consider two substitutable products and compare two alternative measures of product substitutability for linear demand functions that are commonly used in the literature. While one leads to unrealistically high prices and profits as products become more substitutable, the results obtained using the other measure are in line with intuition. Using the more appropriate measure of product substitutability, we study the optimal investment mix in flexible and dedicated capacities in both monopoly and oligopoly settings. We find that the optimal investment in manufacturing flexibility tends to decrease as the products become closer substitutes; this is because (1) pricing can be used more effectively to balance supply and demand, and (2) the gains obtained by shifting production to the more profitable product are reduced due to increased correlation between the price potentials of the substitutable products. The value of flexibility always increases with demand variability. We also show that, as long as the optimal investments in dedicated capacity for both products are positive, the optimal expected prices and production quantities do not depend on the cost of the flexible capacity. Manufacturing flexibility simply allows the firm to achieve those expected values with lower capacity, while leading to higher expected profits.
Workload Balancing Through Recurrent Subcontracting
Authors: Bichescu Bogdan C. , Fry Michael J. , Polak George G.
Published: February 2009

We model a situation where a firm wishes to balance workload requirements by creating a portfolio of recurrent insourcing and outsourcing contracts. We use harmonic analysis to decompose an input workload profile into a portfolio of insourcing and outsourcing contracts using rectangular‐wave basis functions to better achieve some desired constant workload level. However, this initial selection of contracts may result in impractical options. Therefore, we also develop mathematical programs using principles from goal programming and integer programming to refine the portfolio of contracts to more accurately reflect a realistic environment by placing constraints on the available contracts and explicitly considering operational costs. We consider several modeling extensions including the ability to hold limited amounts of inventory and the use of one‐shot contracts to supplement our portfolio of recurrent contracts.
Influence of Thermomigration on Lead-Free Solder Joint Mechanical Properties
Authors: Abdulhamid Mohd F. , Basaran Cemal
Published: February 2009

Thermomigration experiments were conducted to study the change in mechanical properties of 95.5Sn–4Ag–0.5Cu (SAC405) lead-free solder joint under high temperature gradients. This paper presents some observations on samples that were subjected to 1000°C/cm thermal gradient (TG) for 286 h, 712 h, and 1156 h. It was observed that samples subjected to thermal gradient did not develop a Cu3Sn intermetallic compound (IMC) layer, and we observed disintegration of Cu6Sn5 IMC. On the other hand, samples subjected to isothermal annealing exhibited IMC growth. In samples subjected to thermomigration, near the cold side the Cu concentration is significantly higher compared with hot side. Extensive surface hardness testing showed an increase in hardness from the hot to cold sides, which possibly indicates that Sn grain coarsening is in the same direction.
Detection of Solder Bump Defects in Electronic Packages Using Local Temporal Coherence Analysis of Laser Ultrasonic Signals
Authors: Yang Jin , Ume I. Charles
Published: February 2009

Microelectronics packaging technology has evolved from through-hole and bulk configurations to surface-mount and small-profile configurations. Surface mount devices, such as flip chip packages, chip scale packages, and ball grid arrays, use solder bump interconnections between them and substrates/printed wiring boards. Solder bumps, which are hidden between the device and the substrate/board, are difficult to inspect. A solder bump inspection system was developed using laser ultrasound and interferometric techniques. This system has been successfully applied to detect solder joint/bump defects, including missing, misaligned, open, and cracked solder joints/bumps in flip chips, chip scale packages, and multilayer ceramic capacitors. This system uses a pulsed Nd:YAG laser to induce ultrasound in the electronic packages in the thermoelastic regime; it then measures the transient out-of-plane displacement response on the package surface using the interferometric technique. This paper presents a local temporal coherence (LTC) analysis of laser ultrasound signals and compares it to previous signal-processing methods, including error ratio and correlation coefficient methods. The results showed that LTC analysis increased measurement accuracy and sensitivity for inspecting solder bump defects in electronic packages. Laser ultrasound inspection results are also compared with X-ray and C-mode scanning acoustic microscopy results. In particular, this paper discusses defect detection for 6.35×6.35×0.6 mm3 flip chips and flip chips (“SiMAF;” Siemens AG) with lead-free solder bumps.
Development of Analytical Model to a Temperature Distribution of a First Level Package With a Nonuniformly Powered Die
Authors: Kaisare Abhijit , Agonafer Dereje , Haji-Sheikh A. , Chrysler Greg , Mahajan Ravi
Published: February 2009

Microprocessors continue to grow in capabilities, complexity, and performance. Microprocessors typically integrate functional components such as logic and level two cache memory in their architecture. This functional integration of logic and memory results in improved performance of the microprocessor. However, the integration also introduces a layer of complexity in the thermal design and management of microprocessors. As a direct result of functional integration, the power map on a microprocessor is typically highly nonuniform, and the assumption of a uniform heat flux across the die surface has been shown to be invalid post Pentium II architecture. The active side of the die is divided into several functional blocks with distinct power assigned to each functional block. Previous work (Kaisare et al., 2005, “Thermal Based Optimization of Functional Block Distributions in a Non-Uniformly Powered Die,” InterPACK 2005, San Francisco, CA, Jul. 17–22) has been done, which includes numerical analysis and thermal based optimization of a typical package consisting of a nonuniformly powered die, heat spreader, thermal interface materials I and II, and the base of the heat sink. In this paper, an analytical approach to temperature distribution of a first level package with a nonuniformly powered die is carried out for the first time. The analytical model for two-layer bodies developed by Haji-Sheikh et al. (2003, “Steady-State Heat Conduction in Multi-Layer Bodies,” Int. J. Heat Mass Transfer, 46(13), pp. 2363–2379) is extended to this typical package, which is a multilayer body. The solution is to begin by designating each surface heat flux as a volumetric heat source. An inverse methodology is applied to solve the equations for various surfaces to calculate the maximum junction temperature for a given multilayer body. Finally validation of the analytical solution is carried out using previously developed numerical model.
Analysis and Limit State Design of Stiffened Plates and Shells: A World View
Authors: Bedair Osama
Published: February 2009

Stiffened plates and shells are encountered in many engineering applications. Several analytical and numerical procedures were developed over the past decades for analysis of these structures. Empirical and simplified analytical models were also developed to estimate their ultimate strength for various limit states. The paper reviews and pieces together engineering work developed for all the applications. The first part reviews the analytical, numerical, and orthotropic plate procedures that were developed for analysis of stiffened plates and shells. The structural idealization, the theoretical basis, and the merits of each method are also discussed. The second part of the paper reviews the design philosophies that were developed to predict the ultimate strength of these structures. The influence of various parameters affecting the structural performance, such as geometric and material imperfections, stiffener profile, etc., is discussed. The optimization procedures to minimize the weight of the structure are also reviewed. The paper offers a comprehensive and unique “reference-manual” for all types of stiffened plate applications.
Air kerma standard for calibration of well‐type chambers in Brazil using HDR sources and its traceability
Authors: Di Prinzio Renato , deAlmeida Carlos Eduardo
Published: February 2009

In Brazil there are over 100 high dose rate (HDR) brachytherapy facilities using well‐type chambers for the determination of the air kerma rate of sources. This paper presents the methodology developed and extensively tested by the Laboratorio de Ciencias Radiologicas (LCR) and presently in use to calibrate those types of chambers. The system was initially used to calibrate six well‐type chambers of brachytherapy services, and the maximum deviation of only 1.0% was observed between the calibration coefficients obtained and the ones in the calibration certificate provided by the UWADCL. In addition to its traceability to the Brazilian National Standards, the whole system was taken to the University of Wisconsin Accredited Dosimetry Calibration Laboratory (UWADCL) for a direct comparison and the same formalism to calculate the air kerma was used. The comparison results between the two laboratories show an agreement of 0.9% for the calibration coefficients. Three Brazilian well‐type chambers were calibrated at the UWADCL, and by LCR, in Brazil, using the developed system and a clinical HDR machine. The results of the calibration of three well chambers have shown an agreement better than 1.0%. Uncertainty analyses involving the measurements made both at the UWADCL and LCR laboratories are discussed.
Portal dose image prediction for in vivo treatment verification completely based on EPID measurements
Authors: van Zijtveld Mathilda , Dirkx Maarten , Breuers Marcel , de Boer Hans , Heijmen Ben
Published: February 2009

A high dosimetric accuracy is required for radiotherapy treatments where IMRT in combination with narrow treatment margins is applied to achieve optimally conformal dose distributions. In order to routinely verify the in vivo fluence delivery (i.e., during the actual patient treatment), our method for predicting portal dose images with a patient in the beam was validated. A unique feature of this method is that it is fully based on calibration measurements with an EPID. The portal dose image (PDI) behind a patient is dependent on the transmission of primary radiation through the patient and a contribution of scattered radiation from the patient. To derive both components, the patient geometry as observed in the planning CT scan is converted into an equivalent homogeneous phantom. A limited set of EPID measurements is required to derive the input parameters of this model. The accuracy of the in vivo PDI prediction was verified using measurements behind phantoms and four prostate cancer patients treated with IMRT. Behind homogeneous slab phantoms, the local differences between measured and predicted PDIs were within 2% inside the field, while behind a lung and a pelvic phantom, the agreement was within 3% or within 3 mm in regions with steep gradients. Outside the fields, the PDIs agreed within 2% of the global dose maximum. Evaluation of the in vivo PDI measurements behind patients showed that, on average, 87% of the pixels inside the field fulfilled the 3% local dose and 3 mm distance‐to‐agreement criteria. For half of the failing pixels the differences occurred due to changes in patient geometry with respect to the planning CT or due to beam attenuation by the treatment couch that was not accounted for. A fully EPID‐based method for predicting portal dose images using the planning CT scan has been implemented and validated for phantoms and clinical patients.
Determination of electron energy, spectral width, and beam divergence at the exit window for clinical megavoltage x‐ray beams
Authors: Sawkey D. L. , Faddegon B. A.
Published: February 2009

Monte Carlo simulations of x‐ray beams typically take parameters of the electron beam in the accelerating waveguide to be free parameters. In this paper, a methodology is proposed and implemented to determine the energy, spectral width, and beam divergence of the electron source. All treatment head components were removed from the beam path, leaving only the exit window. With the x‐ray target and flattener out of the beam, uncertainties in physical characteristics and relative position of the target and flattening filter, and in spot size, did not contribute to uncertainty in the energy. Beam current was lowered to reduce recombination effects. The measured dose distributions were compared with Monte Carlo simulation of the electron beam through the treatment head to extract the electron source characteristics. For the nominal 6 and x‐ray beams, the energies were and , respectively, with the uncertainties resulting from uncertainties in the detector position in the measurement and in the stopping power in the simulations. Gaussian spectral distributions were used, with full widths at half maximum ranging from at to at required to match the fall‐off portion of the percent‐depth ionization curve. Profiles at the depth of maximum dose from simulations that used the manufacturer‐specified exit window geometry and no beam divergence were narrower than measured profiles. Two simulation configurations yielding the measured profile width were the manufacturer‐specified exit window thickness with electron source divergences of 3.3° at and 1.8° at and an exit window 40% thicker than the manufacturer's specification with no beam divergence. With the x‐ray target in place (and no flattener), comparison of measured to simulated profiles sets upper limits on the electron source divergences of 0.2° at and 0.1° at . A method of determining source characteristics without mechanical modification of the treatment head, and therefore feasible in clinics, is presented. The energies and spectral widths determined using this method agree with those determined with only the exit window in the beam path.
Calculation of the biological effective dose for piecewise defined dose‐rate fits
Authors: Hobbs Robert F. , Sgouros George
Published: February 2009

An algorithmic solution to the biological effective dose (BED) calculation from the Lea–Catcheside formula for a piecewise defined function is presented. Data from patients treated for metastatic thyroid cancer were used to illustrate the solution. The Lea–Catcheside formula for the ‐factor of the BED is integrated numerically using a large number of small trapezoidal fits to each integral. The algorithmically calculated BED is compatible with an analytic calculation for a similarly valued exponentially fitted dose‐rate plot and is the only resolution for piecewise defined dose‐rate functions.