cssi/SciSciGPT-SciSciNet huggingface dataset:
Hierarchical Bayesian Markov switching models with application to predicting spawning success of shovelnose sturgeon.

Summary. The timing of spawning in fish is tightly linked to environmental factors; however, these factors are not very well understood for many species. Specifically, little information is available to guide recruitment efforts for endangered species such as the sturgeon. Therefore, we propose a Bayesian hierarchical model for predicting the success of spawning of the shovelnose sturgeon which uses both biological and behavioural (longitudinal) data. In particular, we use data that were produced from a tracking study that was conducted in the Lower Missouri River. The data that were produced from this study consist of biological variables associated with readiness to spawn along with longitudinal behavioural data collected by using telemetry and archival data storage tags. These high frequency data are complex both biologically and in the underlying behavioural process. To accommodate such complexity we developed a hierarchical linear regression model that uses an eigenvalue predictor, derived from the transition probability matrix of a two-state Markov switching model with generalized auto-regressive conditional heteroscedastic dynamics. Finally, to minimize the computational burden that is associated with estimation of this model, a parallel computing approach is proposed.
Studies of Phosphorus Pile‐Up at the Si ‐ SiO2 Interface Using Auger Sputter Profiling

We have used Auger sputter profiling to investigate in detail the pile‐up of phosphorus at the interface, which occurs during thermal oxidation of heavily doped silicon. We find that, in the early stages of oxidation, the interfacial region acts as a sink for phosphorus. As oxidation proceeds, the "pile‐up" within 50A of the interface saturates and the phosphorus concentration in the silicon near the interface begins to rise. High temperature nitrogen anneals had little effect on the pile‐up, indicating that existence of the pile‐up cannot be explained by a simple diffusion mechanism. We also observed the pile‐up to be greatly diminished in a heavily boron‐compensated sample. We discuss possible mechanisms which may be responsible for this effect.
Cryptic genetic and wing pattern diversity in a mimetic Heliconius butterfly

Despite rampant colour pattern diversity in South America, Heliconius erato exhibits a 'postman' wing pattern throughout most of Central America. We examined genetic variation across the range of H. erato, including dense sampling in Central America, and discovered a deep genetic break, centred on the mountain range that runs through Costa Rica. This break is characterized by a novel mitochondrial lineage, which is nearly fixed in northern Central America, that branches basal to all previously described mitochondrial diversity in the species. Strong genetic differentiation also appears in Z-linked and autosomal markers, and it is further associated with a distinct, but subtle, shift in wing pattern phenotype. Comparison of clines in wing phenotype, mtDNA and nuclear markers indicate they are all centred on the mountains dividing Costa Rica, but that cline width differs among data sets. Phylogeographical analyses, accounting for this new diversity, rewrite our understanding of mimicry evolution in this system. For instance, these results suggest that H. erato originated west of the Andes, perhaps in Central America, and as many as 1 million years before its co-mimic, H. melpomene. Overall our data indicate that neutral genetic markers and colour pattern loci are congruent and converge on the same hypothesis-H. erato originated in northwest South America or Central America with a 'postman' phenotype and then radiated into the wealth of colour patterns present today.
Physical Sequelae and Depressive Symptoms in Gynecologic Cancer Survivors: Meaning in Life as a Mediator

Background Continuing symptoms and poor health following cancer treatments may alter meaning in life for cancer survivors. Gynecologic cancer survivors are particularly troubled with physical sequelae. In addition, for the most common sites of disease, such as breast and gynecologic cancers, the prevalence of depression is also high.
Skill metrics for confronting global upper ocean ecosystem-biogeochemistry models against field and remote sensing data

Abstract We present a generalized framework for assessing the skill of global upper ocean ecosystem-biogeochemical models against in-situ field data and satellite observations. We illustrate the approach utilizing a multi-decade (1979–2004) hindcast experiment conducted with the Community Climate System Model (CCSM- 3 ) ocean carbon model. The CCSM-3 ocean carbon model incorporates a multi-nutrient, multi-phytoplankton functional group ecosystem module coupled with a carbon, oxygen, nitrogen, phosphorus, silicon, and iron biogeochemistry module embedded in a global, three-dimensional ocean general circulation model. The model is forced with physical climate forcing from atmospheric reanalysis and satellite data products and time-varying atmospheric dust deposition. Data-based skill metrics are used to evaluate the simulated time-mean spatial patterns, seasonal cycle amplitude and phase, and subannual to interannual variability. Evaluation data include: sea surface temperature and mixed layer depth; satellite-derived surface ocean chlorophyll, primary productivity, phytoplankton growth rate and carbon biomass; large-scale climatologies of surface nutrients, pCO2, and air–sea CO2 and O2 flux; and time-series data from the Joint Global Ocean Flux Study (JGOFS). Where the data is sufficient, we construct quantitative skill metrics using: model–data residuals, time–space correlation, root mean square error, and Taylor diagrams.
Time-resolved infrared study of reactive species produced by flash photolysis of the hydroformylation catalyst precursor Co2(CO)6(PMePh2)2

Abstract Flash photolysis with time-resolved infrared (TRIR) spectroscopy was used to elucidate the photochemical reactivity of the hydroformylation catalyst precursor Co 2 (CO) 6 (PMePh 2 ) 2 . Depending on reaction conditions, the net products of photolysis varied significantly. A model is presented that accounts for the net reactivity with two initial photoproducts, the 17-electron species Co(CO) 3 (PMePh 2 ) and the coordinatively unsaturated dimer Co 2 (CO) 5 (PMePh 2 ) 2 . No evidence was found for photochemical formation of Co 2 (CO) 6 (PMePh 2 ). Time-resolved spectroscopic studies allowed for the direct observation of transient species and for kinetics studies of certain reactions; for example, the reactions of Co(CO) 3 PMePh 2 with CO and with PMePh 2 gave the respective rate constants 1.5 × 10 5 and 1.2 × 10 7 M −1 s −1 , while the analogous reactions with Co 2 (CO) 5 (PMePh 2 ) 2 gave the rate constants of 2.6 × 10 6 M −1 s −1 and 3.9 × 10 7 M −1 s −1 .
Interaction of penicillin and pentobarbital with inhibitory synaptic mechanisms in neocortex.

1. In this study we characterized the responses of neocortical neurons to iontophoretically appliedγ-aminobutyric acid (GABA) and examined how these GABA responses as well as the inhibitory postsynaptic potentials (IPSPs) were affected by the presence of penicillin or pentobarbital. Intracellular recordings were obtained from slices of rat neocortex maintainedin vitro; injection of the dye Lucifer yellow indicated that recordings were primarily from pyramidal neurons. 2. Orthodromically evoked responses were always depolarizing at the cell's resting membrane potential. Such depolarizing responses could easily be reversed in polarity by depolarizing the cell 10–15 mV, suggesting that the response consisted partly of an IPSP. In some cases, depolarization unmasked a small, short-latency excitatory postsynaptic potential (EPSP). Responses to iontophoretically applied GABA were also depolarizing at rest. Biphasic hyperpolarizing-depolarizing responses were occasionally observed upon depolarization of the neuron. 3. Bath application of penicillin (1.7–3.4 mM) decreased the amplitude of the IPSPs and increased their time to peak, an effect associated with the development of epileptiform activity. Penicillin also reduced the maximum response to iontophoretically applied GABA without affecting the dose required to obtain a half-maximal response, suggesting a noncompetitive antagonism. 4. Pentobarbital (100–200µM) prolonged the time course and increased the amplitude of the IPSPs while producing a leftward shift in the GABA charge-response relation. These results suggest that the convulsant penicillin and the anticonvulsant pentobarbital have opposing actions on GABAergic inhibition in the neocortex.
Detection of Visible Implant Elastomer in Fingerling and Yearling Rainbow Trout

Abstract Visible implant elastomer (VIE) was evaluated for marking yearling rainbow trout Oncorhynchus mykiss. The rate of tag detection after the yearlings had been at large for 35 months was also compared with the detection rate found in a subsequent year-class that had been marked as fingerlings and had been at large for 29 months. Fish were marked in the postocular adipose eyelid tissue and on the ventral surface of the lower jaw and examined in the dark under ultraviolet light. Detection rates for both year-classes ranged from 29% to 33%, based on the proportion of fish with two detectable marks. Because the marks were not easily recognized, we believe the detection rates were overestimated. We conclude that detection of VIE at the sites we chose was problematic for the strain of rainbow trout we marked. More favorable long-term detection rates in other species suggest that poor detection rates may be unique to heavily pigmented strains of rainbow trout.
Herpetofaunal and vegetational characterization of a thermally-impacted stream at the beginning of restoration

Abstract Pen Branch, a third order stream on the Savannah River Site (SRS), located near Aiken, SC, USA, received thermal effluents from the cooling system of a nuclear production reactor from 1954 to 1988. The thermal effluent and increased flow destroyed vegetation in the stream corridor (i.e. impacted portion of the floodplain), and subsequent erosion created a braided stream system with a greatly expanded delta. Restoration of the area began with planting of bottomland hardwood species in 1993. Occurrence of amphibians and reptiles was monitored by daily sampling from 1 January 1995 through 30 September 1996 to characterize the course of the restoration. Vegetation was sampled in the summer of 1996 to characterize the habitats in the unimpacted riparian zone and the impacted stream corridor. A total of 12 580 individuals representing 72 species of herpetofauna were captured. There were no significant differences in relative abundance or diversity of herpetofauna in unplanted versus planted zones within the impacted corridor 3 years after planting. Likewise, there were no significant differences in abundance or diversity of herpetofauna in the upper and lower corridor areas, which differed in site preparation before planting, or in riparian zones of different widths. However, species diversity of amphibians and reptiles in the unimpacted riparian zone was significantly higher than on vegetated islands located between stream braids within the impacted floodplain corridor. There were also significantly more species and individuals within the riparian zone than in the corridor, and the species assemblage within the riparian zone differed from that of the corridor. Woody vegetation within the unimpacted riparian zone was significantly higher in basal area than on islands within the corridor.
Reverse Engineering Molecular Hypergraphs

Analysis of molecular interaction networks is pervasive in systems biology. This research relies almost entirely on graphs for modeling interactions. However, edges in graphs cannot represent multiway interactions among molecules, which occur very often within cells. Hypergraphs may be better representations for networks having such interactions, since hyperedges can naturally represent relationships among multiple molecules. Here, we propose using hypergraphs to capture the uncertainty inherent in reverse engineering gene-gene networks. Some subsets of nodes may induce highly varying subgraphs across an ensemble of networks inferred by a reverse engineering algorithm. We provide a novel formulation of hyperedges to capture this uncertainty in network topology. We propose a clustering-based approach to discover hyperedges. We show that our approach can recover hyperedges planted in synthetic data sets with high precision and recall, even for moderate amount of noise. We apply our techniques to a data set of pathways inferred from genetic interaction data in S. cerevisiae related to the unfolded protein response. Our approach discovers several hyperedges that capture the uncertain connectivity of genes in relevant protein complexes, suggesting that further experiments may be required to precisely discern their interaction patterns. We also show that these complexes are not discovered by an algorithm that computes frequent and dense subgraphs.
Exposure of hematopoietic stem cells to benzene or 1,4-benzoquinone induces gender-specific gene expression.

Chronic exposure to benzene results in progressive decline of hematopoietic function and may lead to the onset of various disorders, including aplastic anemia, myelodysplastic syndrome, and leukemia. Damage to macromolecules resulting from benzene metabolites and misrepair of DNA lesions may lead to changes in hematopoietic stem cells (HSCs) that give rise to leukemic clones. We have shown previously that male mice exposed to benzene by inhalation were significantly more susceptible to benzene-induced toxicities than females. Because HSCs are targets for benzene-induced cytotoxicity and genotoxicity, we investigated DNA damage responses in HSC from both genders of 129/SvJ mice after exposure to 1,4-benzoquinone (BQ) in vitro or benzene in vivo. 1,4-BQ is a highly reactive metabolite of benzene that can cause cellular damage by forming protein and DNA adducts and producing reactive oxygen species. HSCs cultured in the presence of 1,4-BQ for 24 hours showed a gender-independent, dose-dependent cytotoxic response. RNA isolated from 1,4-BQ–treated HSCs and HSCs from mice exposed to 100 ppm benzene by inhalation showed altered expression of apoptosis, DNA repair, cell cycle, and growth control genes compared with unexposed HSCs. Rad51, xpc, and mdm-2 transcript levels were increased in male but not female HSCs exposed to 1,4-BQ. Males exposed to benzene exhibited higher mRNA levels for xpc, ku80, ccng, and wig1. These gene expression differences may partially explain the gender disparity in benzene susceptibility. HSC culture systems such as the one used here will be useful for testing the hematotoxicity of various substances, including other benzene metabolites.
Linear and circular unidimensional scaling for symmetric proximity matrices

The tasks of linear and circular unidimensional scaling can be characterized by the attempt to represent the entries in a symmetric proximity matrix through distances among a set of object locations defined either along a linear continuum or around a closed, circular continuum. These two scaling tasks are approached through a least-squares optimization strategy based on a combination of combinatorial search and iterative projection techniques. Extensions are provided for considering multiple linear or circular unidimensional structures, and to the inclusion of several representational alternatives offered by (restricted) additive tree models. Two published data sets are used to illustrate the results obtainable from the optimization method being proposed.
A method for the description and analysis of complex software systems

This paper outlines a modeling scheme and associated method of analysis which are particularly useful during the design of complex software systems since they facilitate an iterative design methodology and provide feedback to help guide the creation of the final design. The process oriented modeling scheme is outlined first and a brief indication is given of how it may be easily and naturally used in a top-down elaboration of a system's design. Then the method of analysis is outlined and shown to provide a procedure for deriving algebraic descriptions of a system's internal behavior which may be used to check whether or not the system is correct in the sense that it exhibits desirable behavior and does not exhibit undesirable behavior. This paper necessarily gives only a brief overview of the description shceme and method of analysis and full details may be found in [1] and [2].
State observability and condition observability for a class of interacting discrete event systems

This paper introduces the concepts of state observability and condition observability for condition systems, a class of systems composed of discrete state components which interact via discrete binary signals called conditions. Given a set of externally observed conditions, state observability implies that the state of the system can be determined from the observations, and condition observability implies that all unobserved input and output conditions of the system can be determined from the observations. In this paper, we present a class of systems which is state observable and condition observable. We present a method to synthesize an observer system to provide state and condition signal estimates for a single component subsystem.
Si heterojunction diodes with a thin β-SiC layer prepared with gas layer source molecular beam epitaxy

Abstract Recently we have achieved successful growth of thin β-SiC film on Si substrates using gas source molecular beam epitaxy (MBE) at low temperatures around 850°C. In this work, we have studied the growth of β-SiC film on Si substrate using C2H2 gas source MBE. The films grown with C2H2 gas were analysed using various in situ (Auger electron spectroscopy, reflected high energy electron diffraction) and ex situ analysis tools (secondary ion mass spectroscopy X-ray photoelectron spectroscopy, Fourier transform IR, ellipsometry). We also have studied the C2H2 gas reaction for potential SiC atomic layer epitaxy (ALE) applications. The C2H2 gas shows a useful self-limiting reaction for the ALE process, in that C2H2 gas reacts rapidly with the highly reactive Si surface; after forming β-SiC on the Si surface, the reaction of C2H2 gas with Si drops rapidly and further reaction of SiC is almost quenched. Finally, to study further these thin β-SiC films, Si heterojunction diodes with a thin β-SiC layer between heavily doped n+-type polysilicon and highly doped p-type Si layers were fabricated. The I–V curve of these diodes shows a reasonably good forward characteristic and an improved breakdown voltage compared with those of devices without the thin β-SiC film.
Combinatorial behavior of extreme points of perturbed polyhedra

Abstract Two polyhedral convex sets A and B are considered, where A and B have the same set of defining linear forms but differ in a least one right-hand-side resource. Upper bounds are established for the Euclidean distance between an extreme point of A and an extreme point of B, and then for the Hausdorff distance between sets A and B. Both bounds involve a scaler multiple of the Euclidean distance between the resource vectors. Combinatorial arguments are employed to establish the scalers. An application to stability theory for mathematical programming is given.
Polymer self assembly in semiconductor microelectronics

Integration of polymer self assembly with semiconductor processing enables sub-lithographic patterning of integrated circuit (IC) device elements and offers a non-traditional pathway to performance improvements (Black, 2005). We discuss target applications including surface-roughening for on-chip decoupling capacitors (Black et al., 2004), patterning nanocrystal floating gates for FLASH devices (Guarini et al., 2003), and defining FET channel arrays (Black, 2005)
RAPIDLY CONVERGENT ITERATION METHODS FOR QUANTUM OPTIMAL CONTROL OF POPULATION

A family of new iteration methods is presented for designing quantum optimal controls to manipulate the transition probability. Theoretical analysis shows that these new methods exhibit quadratic and monotonic convergence. Numerical calculations verify that for these new methods, within very few steps, the optimized objective functional comes close to its convergent limit.
Mechanisms of disease for the clinician: systemic lupus erythematosus.

Abstract Objective To review the complex interactions and processes in systemic lupus erythematosus (SLE). Data Sources Brief review of the important literature in peer-reviewed journals. Study Selection Studies on the clinical and immunologic features, pathogenesis, epidemiology, laboratory evaluation, and treatment of SLE are included in this review. Results SLE may include a variety of disease entities, such as isolated cutaneous lupus, undifferentiated connective tissue disease, mixed connective tissue disease, and drug-induced lupus. There are many ongoing clinical trials in SLE patients of therapeutics with different mechanisms of cellular action, such as classic immunosuppression, cell depletion, antigen-specific immunomodulation, and targeting of antigen-nonspecific, immune-activating molecules. New immune cell–targeted therapies are now available that are specifically designed to block cellular pathways involved in disease pathogenesis. Conclusion The practicing physician should understand the immunology, pathogenesis, laboratory evaluation, and updated treatment options when diagnosing SLE in their clinic or daily practice.
Professional Music Therapy Supervision: A Survey

Clinical supervision is regularly given to music therapy students and interns, but the need for professional music therapy supervision has largely not been discussed or explored. In order to better understand prevailing thoughts about professional music therapy supervision, music therapists were surveyed and asked if they participate in supervision and how important they think supervision is for professionals. The results indicated that almost two thirds of professional music therapists do not participate in supervision. Differences in participation and importance ratings were found between several demographic groupings including years of practice and level of education. Two-tailed t tests revealed a significant difference in importance rating between those who participate in supervision and those who do not, with those who participate giving a higher importance rating. However, the majority of all respondents indicated that they felt professional supervision is at least moderately important. These results are explored and discussed, and recommendations are given.
Cytoplasmic phospholipase A2 antagonists inhibit multiple endocytic membrane trafficking pathways.

Previous studies have suggested a role for cytosolic Ca 2+ -independent phospholipase A 2 (PLA 2 ) activity in the formation of endosome membrane tubules that participate in the export of transferrin (Tf) and transferrin receptors (TfR) from sorting endosomes (SEs) and the endocytic recycling compartment (ERC). Here we show that the PLA 2 requirement is a general feature of endocytic trafficking. The reversible cytoplasmic PLA 2 antagonist ONO-RS-082 (ONO) produced a concentration-dependent, differential block in the endocytic recycling of both low-density lipoprotein receptor (LDLR) and TfRs, and in the degradative pathways of LDL and epidermal growth factor (EGF). These results are consistent with the model that a cytoplasmic PLA 2 plays a general role in the export of cargo from multiple endocytic compartments by mediating the formation of membrane tubules.
GESIM: Image management system for TIFF structures

Abstract GESIM is a system for the storage and retrieval of a great amount of images. The images are stored with TIFF format as part of a database structure. This structure allows the organization and management of a great amount of TIFF images, maintaining the relationship between the different images. The simplicity of the structure and procedures incorporated by GESIM eases its use for the analysis and treatment of images and graphic software allowing integration with textual information databases. The system allows the retrieval of the images using as a selector any of the labels (tags) included in the TIFF format. Additionally, GESIM allows the grouping of related images in independent volumes within the same database. GESIM is a library of functions developed in Microsoft C and also has a user interface that allows the use of its functions through pop-up menus, which makes the procedure easier for non-expert users.
Interleukin-12 P40 induces the expression of TNF-α in microglia and macrophages

Recently, it has been found that overproduction of IL-12 can be dangerous to the host as it is involved in the pathogenesis of a number of autoimmune inflammatory diseases such as multiple sclerosis. It is composed of two different subunits – p40 and p35. Expression of p40 mRNA but not that of p35 mRNA in excessive amount in the CNS of patients with Multiple Sclerosis (MS) suggests that IL-12 p40 may have a role in the pathogenesis of the disease. The present study was undertaken to explore the role of p40 in the expression of TNF-α in microglia. Interestingly, we have found that IL-12 p70, p402 (the p40 homodimer) and p40 (the p40 monomer) dose-dependently induced the production of TNF-α in BV-2 microglial cells. This induction of TNF-α production was accompanied by an induction of TNF-α mRNA. In addition to BV-2 glial cells, p70, p402 and p40 also induced the production of TNF-α in mouse primary microglia and peritoneal macrophages. Since the activation of both NF-κB and C/EBPb is important for the expression of TNF-α in microglial cells, we investigated the effect of p40 on the activation of NF-κB as well as C/EBPb. Activation of NF-κB as well as C/EBPb by p40 and inhibition of p40-induced expression of TNF-α by Dp65, a dominant-negative mutant of p65, and DC/EBPb, a dominant-negative mutant of C/EBPb, suggests that p40 induces the expression of TNF-α through the activation of NF-κB and C/EBPb. This study delineates a novel role of IL-12 p40 in inducing the expression of TNF-α in microglial cells which may participate in the pathogenesis of neuroinflammatory diseases. Acknowledgements: This study was supported by NIH grants (NS39940 and AG19487).
AMP sensing by DEAD-box RNA helicases

In eukaryotes, cellular levels of adenosine monophosphate (AMP) signal the metabolic state of the cell. AMP concentrations increase significantly upon metabolic stress, such as glucose deprivation in yeast. Here, we show that several DEAD-box RNA helicases are sensitive to AMP, which is not produced during ATP hydrolysis by these enzymes. We find that AMP potently inhibits RNA binding and unwinding by the yeast DEAD-box helicases Ded1p, Mss116p, and eIF4A. However, the yeast DEAD-box helicases Sub2p and Dbp5p are not inhibited by AMP. Our observations identify a subset of DEAD-box helicases as enzymes with the capacity to directly link changes in AMP concentrations to RNA metabolism.
Divergence of visual channels in the inner retina.

Bipolar cells form parallel channels that carry visual signals from the outer to the inner retina. Each type of bipolar cell is thought to carry a distinct visual message to select types of amacrine cells and ganglion cells. However, the number of ganglion cell types exceeds that of the bipolar cells providing their input, suggesting that bipolar cell signals diversify on transmission to ganglion cells. We explored in the salamander retina how signals from individual bipolar cells feed into multiple ganglion cells and found that each bipolar cell was able to evoke distinct responses among ganglion cells, differing in kinetics, adaptation and rectification properties. This signal divergence resulted primarily from interactions with amacrine cells that allowed each bipolar cell to send distinct signals to its target ganglion cells. Our findings indicate that individual bipolar cell–ganglion cell connections have distinct transfer functions. This expands the number of visual channels in the inner retina and enhances the computational power and feature selectivity of early visual processing.
Evanescent Waves and the Electromagnetic Field of a Moving Charged Particle

An angular-spectrum representation is obtained of the electromagnetic field in a homogeneous medium, arising from any prescribed motion of a charged particle in a plane. The field on either side of the plane of motion is expressed as a superposition of monochromatic waves in general, homogeneous as well as evanescent ones. The homogeneous waves are propagated away from the plane of motion of the particle, the evanescent ones decay exponentially with increasing distance from this plane. For each plane wave, the appropriate dispersion relation is satisfied and hence the representation is a true mode expansion in each of the two half-spaces. The results are illustrated by considering the field of a uniformly moving charged particle. In free space, the Coulomb field of the particle, as would be observed in a fixed laboratory system, is shown to arise from the superposition of evanescent waves to which the moving particle gives rise. The main formulas relating to the Cerenkov field both above and below threshold are also obtained, as an illustration of this technique.
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation

Whole-genome mRNA quantitation can be used to identify the genes that are most responsive to environmental or genotypic change. By searching for mutually similar DNA elements among the upstream non-coding DNA sequences of these genes, we can identify candidate regulatory motifs and corresponding candidate sets of coregulated genes. We have tested this strategy by applying it to three extensively studied regulatory systems in the yeast Saccharomyces cerevisiae: galactose response, heat shock, and mating type. Galactose-response data yielded the known binding site of Gal4, and six of nine genes known to be induced by galactose. Heat shock data yielded the cell-cycle activation motif, which is known to mediate cell-cycle dependent activation, and a set of genes coding for all four nucleosomal proteins. Mating type α and a data yielded all of the four relevant DNA motifs and most of the known a- and α-specific genes.
Numerical Investigation of Ash Deposition on Nozzle Guide Vane Endwalls

A computational study was performed to determine the factors that affect ash deposition rates on the endwalls in a nozzle guide vane passage. Deposition tests were simulated in flow around a flat plate with a cylindrical leading edge, as well as through a modern, high performance turbine vane passage. The flow solution was first obtained independent of the presence of particulates, and individual ash particles were subsequently tracked using a Langrangian tracking model. Two turbulence models were applied and their differences were discussed. The critical viscosity model was used to determine particle deposition. Features that contribute to endwall deposition, such as secondary flows, turbulent dispersion, or ballistic trajectories, were discussed and deposition was quantified. Particle sizes were varied, to reflect Stokes numbers ranging from 0.01 to 1.0, to determine the effect on endwall deposition. Results showed that endwall deposition rates can be as high as deposition on the leading edge for particles with a Stokes number less than 0.1, but endwall deposition rates for a Stokes numbers of 1.0 were less than 25% of the deposition rates on the leading edge or pressure surface of the turbine vane. Deposition rates on endwalls were largest near the leading edge stagnation region on both the cylinder and vane geometries, with significant deposition rates downstream showing a strong correlation to the secondary flows.© 2012 ASME
Regulation and autoregulation by lexA protein

Resume La proteine lexA reprime de nombreux genes chez E. coli. Lorsque le DNA de la cellule est endommage, la proteine lexA est inactivee et ces genes sont induits. Nous passons en revue trois aspects de la fonction de represseur de la proteine lexA: comment elle regule les genes de la reponse SOS, comment elle regule sa propre synthese, et comment elle reconnait ses propres sites operateurs. Des etudes recentes de la fonction de represseur de la proteine lexA suggerent que la concentration de proteine lexA intacte apres induction pourrait determiner le controle minutieux de la reponse SOS.
Interfaces as rhetorical constructions: reddit and 4chan during the boston marathon bombings

In this paper, we describe the rhetorical construction of two community sites and analyze how these sites support the information sharing practices of these communities. By examining activity on web-based discussion boards reddit and 4chan, we show how these spaces are developed and shaped over time by participants making rhetorical moves in order to share content within these ecologies. During the 2013 Boston Marathon bombings, we show how these spaces can be altered, disregarding the more typical practices on these sites. When community members embrace or reject these uses, it is as much a reaction to the content as it is to the cultural misuse of the community. In the case of reddit and 4hcan, this acceptance and rejection is especially true when the makers and maintainers of the system are participants themselves. Through this examination, we conclude that it is important to understand the rhetorical construction of these systems as reflections of the cultures they support.
A general solid phase method for the synthesis of depsipeptides

Herein we describe the synthesis of depsipeptide sequences in which the backbone is composed of alternating esters and amides. Our methodology is based on the synthesis and protection of a depsidipeptide block, which is used as the growing unit for manual SPPS. We have explored Fmoc/OBzl and Fmoc/tBu SPPS strategies, and found the latter to be most compatible with our methodology.
Drug–Nutrient Interactions in Patients with Cancer

Nutrition has a major role in both cancer prevention and its therapy. In fact, dietary choices and physical activity are the two major modifiable determinants of cancer risk. The evidence suggests that one-third of the more than 500,000 cancer deaths in the United States can be attributed to these two factors each year (1). The recent observation of improved 5-yr survival rates for all cancers is encouraging because much of the research into early cancer detection and treatment appears to be invaluable (2). Unfortunately, the increase in 5-yr survival over time (1950 to 1990) had little relationship to changes in the mortality from cancer. There are several reasons that the 5-yr survival rates have increased. These include improvements in the treatment of established cancer, earlier identification of patients in their disease course, and early effective treatment regimens. Naturally, if more effective treatments of existing disease and more cancers are found early and treated, then mortality rates should decrease. The major explanation for improved 5-yr survival rates without improved mortality is simply changes in the diagnosis of cancer, including detection of subclinical cancers. However, epidemiological studies of populations whose diets are high in vegetables and fruits and low in animal fat, meat, and total calories have shown reduced risks for some of the most common types of cancer (3).
Evaluating the Effects of the Wendigo Lake Expedition Program on Young Offenders

This study reports an evaluative case study of Wendigo Lake Expeditions (WLE), a continuous intake, open custody program for young offenders that uses a positive youth development approach. Four objectives guided the case study: (a) describe and illustrate WLE's approach to working with adjudicated youth, (b) identify and report perceptions of the program and process, (c) assess changes in their well-being utilizing the Youth-Outcome Questionnaire (Y-OQ), and (d) track postprogram recidivism rates. Results indicated a significant improvement in youth well-being indicated by significant score reductions on the Y-OQ. Of the 40 youths contacted at the follow-up assessment, 21 (53%) had been charged with a criminal offense during this period, including those charged for administrative offences such as breaching conditions of probation, whereas 19 (47%) had not been charged. Implications of positive youth development programming for adjudicated youth are discussed.
The effects of topographically-controlled thermal tides in the martian upper atmosphere as seen by the MGS accelerometer

Abstract Mars Global Surveyor accelerometer observations of the martian upper atmosphere revealed large variations in density with longitude during northern hemisphere spring at altitudes of 130–160 km, all latitudes, and mid-afternoon local solar times (LSTs). This zonal structure is due to tides from the surface. The zonal structure is stable on timescales of weeks, decays with increasing altitude above 130 km, and is dominated by wave-3 (average amplitude 22% of mean density) and wave-2 (18%) harmonics. The phases of these harmonics are constant with both altitude and latitude, though their amplitudes change significantly with latitude. Near the South Pole, the phase of the wave-2 harmonic changes by 90° with a change of half a martian solar day while the wave-3 phase stays constant, suggesting diurnal and semidiurnal behaviour, respectively. We use a simple application of classical tidal theory to identify the dominant tidal modes and obtain results consistent with those of General Circulation Models. Our method is less rigorous, but simpler, than the General Circulation Models and hence complements them. Topography has a strong influence on the zonal structure.
Poststructuralism and GIS: Is There a ‘Disconnect’?

Human geography critiques of GIS are operationalized under a unique interpretation of ontology and epistemology. Internal to poststructuralism, this metaphysics collapses the traditional separation between ontology and epistemology, reducing ontological questions to epistemological constructs. Although critiques have moved beyond an initial fixation upon positivism, critical/cultural assessments of GIS tendered within the last ten years continue to motivate epistemology as a basis for its deconstruction. The epistemological reductionism of such a reading of the technology inappropriately abstracts GIS from its ontic basis in computing, giving rise to a fundamental ‘disconnect’ of poststructuralist metaphysics to the technology. This disconnect is identified in terms of (1) the epistemic fallacy, which, underwritten by (2) an ‘undoing’ of the metaphysics of presence, culminates in (3) an effective ‘deontologization’ of an immediately ontic entity. This does not negate the poststructuralist critique of GIS,...
THE REDUCTION AND QUENCHING OF PHOTOEXCITED FLAVINS BY EDTA

— Riboflavin was irradiated anaerobically in aqueous EDTA solutions over the pH range 2.5–10. In other dye systems (Bonneau and Pereyre, 1975), only the trivalent anion of EDTA was found to have significant reactivity for photoreduction. For riboflavin, the reactivity begins with monoanionic EDTA, and the reactivity is markedly increased as the charge increases. This suggests that the charge on the reductant is more important to the electron transfer process for riboflavin than the formation of a nonhydrogen bonded nitrogen site on EDTA. At high concentrations of EDTA in the pH range 4–8, quenching of the photoreduction occurs, which can be explained by an energy transfer between the excited singlet state of riboflavin and trianionic EDTA, possibly as an association complex. The rate constants for the photoreduction of riboflavin by the monovalent, divalent, and trivalent anions of EDTA are 1.0 times 107M-1 s-l, 4.8 times 10′M-1 s-l, and 2.0 times 108M-1s-1, respectively. The rate constant for the singlet state quenching by trianionic EDTA is 3 times 109M-l s-1, and the limiting quantum yield for intersystem crossing for riboflavin in aqueous solution is 0.50 ± 0.05.
The strength of chemical linkage as a criterion for pruning metabolic graphs

Motivation: A metabolic graph represents the connectivity patterns of a metabolic system, and provides a powerful framework within which the organization of metabolic reactions can be analyzed and elucidated. A common practice is to prune (i.e. remove nodes and edges) the metabolic graph prior to any analysis in order to eliminate confounding signals from the representation. Currently, this pruning process is carried out in an ad hoc fashion, resulting in discrepancies and ambiguities across studies. Results: We propose a biochemically informative criterion, the strength of chemical linkage (SCL), for a systematic pruning of metabolic graphs. By analyzing the metabolic graph of Escherichia coli, we show that thresholding SCL is powerful in selecting the conventional pathways' connectivity out of the raw network connectivity when the network is restricted to the reactions collected from these pathways. Further, we argue that the root of ambiguity in pruning metabolic graphs is in the continuity of the amount of chemical content that can be conserved in reaction transformation patterns. Finally, we demonstrate how biochemical pathways can be inferred efficiently if the search procedure is guided by SCL. Contact:wz4@rice.edu; nakhleh@rice.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Promoting international digital government research collaboration: an experiment in community building

Global issues present many opportunities for digital government (DG) researchers to form long-lasting relationships that lead to shared research agendas focused on questions of international importance. However, the relatively young DG community has little experience and few guiding strategies or methods for encouraging these kinds of investigations. As a result, the practical feasibility of international DG research partnerships is of interest for both investigators and funders. This paper reports the evaluation of an experiment to create sustainable international digital government research collaborations by providing legitimacy and modest funding within a minimal set of structural and management requirements. Participants rated the experience as highly positive, contributing substantially to their research productivity, community building, international awareness, and professional growth. While the working group strategy is not a substitute for direct research support, it is a readily replicable method to build international research communities, and to stimulate and enhance their scholarly work.
Aggregating Ordinal Labels from Crowds by Minimax Conditional Entropy

We propose a method to aggregate noisy ordinal labels collected from a crowd of workers or annotators. Eliciting ordinal labels is important in tasks such as judging web search quality and rating products. Our method is motivated by the observation that workers usually have difficulty distinguishing between two adjacent ordinal classes whereas distinguishing between two classes which are far away from each other is much easier. We formulate our method as minimax conditional entropy subject to constraints which encode this observation. Empirical evaluations on real datasets demonstrate significant improvements over existing methods.
Automatic word sense discrimination

This paper presents context-group discrimination, a disambiguation algorithm based on clustering. Senses are interpreted as groups (or clusters) of similar contexts of the ambiguous word. Words, contexts, and senses are represented in Word Space, a high-dimensional, real-valued space in which closeness corresponds to semantic similarity. Similarity in Word Space is based on second-order co-occurrence: two tokens (or contexts) of the ambiguous word are assigned to the same sense cluster if the words they co-occur with in turn occur with similar words in a training corpus. The algorithm is automatic and unsupervised in both training and application: senses are induced from a corpus without labeled training instances or other external knowledge sources. The paper demonstrates good performance of context-group discrimination for a sample of natural and artificial ambiguous words.
A low-power Viterbi decoder design for wireless communications applications

Viterbi decoders employed in digital wireless communications are complex and dissipate large amount of power. In this paper, we investigate power dissipation for three different implementations of the Viterbi algorithm for wireless communications applications, including our proposed low-power Viterbi decoder. The schemes employed in our low-power design are clock-gating and toggle filtering. We described the behavior of three Viterbi decoders in VHDL and synthesized using a synthesis tool. The synthesized circuits were placed and routed in the standard cell design environment. Power estimation obtained through gate level simulations indicates that the proposed design reduces the power dissipation of an original Viterbi decoder design by 55%.
Unusual positioning of a central venous catheter

Central venous cannulation, with or without a flow-directed pulmonary artery catheter, is commonly performed in patients undergoing cardiac surgery to measure central filling pressure and cardiac output, and to administer medications and fluids. The complications of central venous cannulation are numerous and include malposition, arterial puncture, pneumothorax, hemothorax, chylothorax, extravasation of infusate, thrombophlebitis, and infection. We describe a single-lumen catheter that was placed through the hemostatic valve of a 9F percutaneous introducer, which inadvertently entered the left internal mammary (internal thoracic) vein. The current case is unique in that it was diagnosed by visualization of the catheter during surgical dissection.
Intolerance of Uncertainty and Immediate Decision-Making in High-Risk Situations:

Given evidence that individuals high in intolerance of uncertainty (IU; the tendency to experience unknown outcomes as unacceptably threatening) exhibit poorer decision-making strategies and are mo...
Crosstalk and microlens study in a color CMOS image sensor

The paper describes results of crosstalk investigations and microlens (/spl mu/-lens) scan experiments in a color CMOS image sensor with active pixel structure . The investigation of optical and electrical crosstalk was made on 7.8- and 5.6-/spl mu/m pixels by using samples with continuous shift of color filter (CF ) and /spl mu/-lens across the array. As a result of this investigation, the distribution of sensitivity inside a pixel has been determined. By using minimum crosstalk criteria, the optimum parameters of the /spl mu/-lens manufacturing process and optimum position of the /spl mu/-lens was determined. The paper presents color maps of pixel sensitivity and crosstalk criteria as well as snapshots illustrating sensitivity distribution and collection area. The paper presents spectral characteristics measured at different relative apertures (f-number) as well. The quantitative analysis of spectral responses allowed us to determine the contribution of each component to the overall crosstalk.
Photoyellowing of poly(4,4′-diphenylolpropane isophthalate): A novel polymer photorearrangement

The photoyellowing of 4,4′-diphenylolpropane isophthalate (DPP-I) was attributed to a photochemical rearrangement resulting in a polymer containing o-hydroxybenzophenones as part of the chain structure. Chain cleavage by photolysis was an accompanying side reaction. o-Hydroxybenzophenone derivatives of DPP were prepared to serve as model compounds to confirm the structure of the photorearrangement product. Additional confirmation of the mechanism was obtained by solid phase or solution photorearrangement of the model ester, DPP dibenzoate to its monohydroxybenzophenone derivative. Kinetics of the DPP-I photorearrangement exposed to a xenon high pressure lamp and a carbon are lamp gave rates of 3.9 × 10−2 and 3.8 × 10−3 mole/1.-hr., respectively. The rate of yellowing in Florida sunlight, open exposure in April, was 1.5 × 10−2 mole/1.-hr.