cssi/SciSciGPT-SciSciNet huggingface dataset:
Twelve years in the evolution of the internet ecosystem

Our goal is to understand the evolution of the autonomous system (AS) ecosystem over the last 12 years. Instead of focusing on abstract topological properties, we classify ASs into a number of types depending on their function and business type. Furthermore, we consider the semantics of inter-AS links: customer-provider versus peering relations. We find that the available historic datasets from RouteViews and RIPE are not sufficient to infer the evolution of peering links, and so we restrict our focus to customer-provider links. Our findings highlight some important trends in the evolution of the Internet over the last 12 years and hint at what the Internet is heading toward. After an exponential increase phase until 2001, the Internet has settled into a slower exponential growth in terms of both ASs and inter-AS links. The growth is mostly due to enterprise networks and content/ access providers at the periphery of the Internet. The average path length remains almost constant, mostly due to the increasing multihoming degree of transit and content/access providers. The AS types differ significantly from each other with respect to their rewiring activity; content/access providers are the most active. A few large transit providers act as "attractors" or "repellers" of customers. For many providers, strong attractiveness precedes strong repulsiveness by 3-9 months. Finally, in terms of regional growth, we find that the AS ecosystem is now larger and more dynamic in Europe than in North America.
Who wants to be a cosmopolitan? Readings from the composite culture

This article explores two political discourses—composite culture and cosmopolitanism—as divergent, indeed competing, modes of advocating cultural pluralism. The first part of the article considers the genealogy of each construct and explores the theoretical differences between the two. The second part turns to the question of how composite culture and cosmopolitanism are configured in narrative terms in recent works of fiction and film. The primary focus is on Hindi author Manzoor Ahtesham’s 1986 novel Sukha Bargad (A Dying Banyan in English translation). The novel illustrates the withering of composite culture from the perspective of a brother and sister growing up in post-Independence Bhopal. To provide a comparative framework, two recent works of Anglophone fiction are drawn into the discussion: Aravind Adiga’s novel White Tiger (2008) and Vikas Swarup’s novel Q & A, the basis for the movie Slumdog Millionaire. These texts may be read as critiques of cosmopolitanism from the subaltern position. The art...
Polymerization control through the free-radical retrograde-precipitation polymerization process

In this article, we present results of our work in a novel polymerization process [called the free-radical retrograde-precipitation polymerization (or FRRPP) process] that occurs at temperatures above the lower critical solution temperature. In this process, conversion-time plots for styrene polymerization in ether show autoacceleration at the beginning, followed by a relatively long period of reduced conversion rate starting at conversions as low as 30% and at operating temperatures way below the glass transition of the reacting system. Molecular weight and polydispersity index data also indicate early autoacceleration (in the form of overshoots in these values), whereas the latter period of slow conversion rate is accompanied by stable levels of molecular weight and polydispersity index. Polymer radical concentration measurements show an initial sharp rise, followed by an asymptotic value, even after almost all the initiator molecules have already decomposed into radicals. With end-group analyses of product polystyrene and polymer radical data, we calculate a proportion of live polymeric radicals to asymptote at levels of 80–84% of all polymeric species, even after almost all initiator molecules have already decomposed into radicals. All the data presented herein verify the postulate of a controlled polymerization mechanism for the FRRPP process. Our results have become the basis for an anti-gel effect phenomenon that is derived from prior theoretical and experimental observations, in which phenomenological diffusivities vanish at the spinodal curve of the phase envelope. The universality of this behavior in FRRPP systems is manifested from similar observations in styrene polymerization in acetone and methacrylic acid polymerization in water. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 71: 761–774, 1999
C-H…X (X = N, O) hydrogen bond-mediated assembly of donors and acceptors : The crystal structures of phenazine complexes with 1,4-dinitrobenzene and TCNQ

Abstract The charge-transfer complexes of phenazine:1,4-dinitrobenzene ( 1 ) and phenazine:TCNQ ( 2 ) were crystallized from a 1:1 solution mixture of methanol:acetonitrile. The donor and acceptor molecules in 1 and 2 are stacked with centroid-centroid distances of 3.61 A and 4.24 A, respectively. The crystal packing analysis of these complexes reveal planar two-dimensional structures that are stabilized by numerous C-H⋯X (X = N, O) hydrogen bonds. Alignment of donor and acceptor molecules within the sheet structures of 1 and 2 is strikingly similar. A close analogue of complex 2 , the 1:1 charge transfer complex of anthracene:TCNQ exhibits an entirely different architecture from 2 due to differences in C-H⋯N hydrogen bonding preferences.
Protein kinase C–associated kinase is required for NF-κB signaling and survival in diffuse large B-cell lymphoma cells

Diffuse large B-cell lymphoma (DLBCL) is an aggressive and the most common type of non-Hodgkin lymphoma. Despite recent advances in treatment, less than 50% of the patients are cured with current multiagent chemotherapy. Abnormal NF-κB activity not only contributes to tumor development but also renders cancer cells resistant to chemotherapeutic agents. Identifying and targeting signaling molecules that control NF-κB activation in cancer cells may thus yield more effective therapy for DLBCL. Here, we show that while overexpression of protein kinase C–associated kinase (PKK) activates NF-κB signaling in DLBCL cells, suppression of PKK expression inhibits NF-κB activity in these cells. In addition, we show that NF-κB activation induced by B cell–activating factor of tumor necrosis factor family (BAFF) in DLBCL cells requires PKK. Importantly, we show that knockdown of PKK impairs the survival of DLBCL cells in vitro and inhibits tumor growth of xenografted DLBCL cells in mice. Suppression of PKK expression also sensitizes DLBCL cells to treatment with chemotherapeutic agents. Together, these results indicate that PKK plays a pivotal role in the survival of human DLBCL cells and represents a potential target for DLBCL therapy.
A comparison of companion matrix methods to find roots of a trigonometric polynomial

Abstract A trigonometric polynomial is a truncated Fourier series of the form f N ( t ) ≡ ∑ j = 0 N a j cos ( jt ) + ∑ j = 1 N b j sin ( jt ) . It has been previously shown by the author that zeros of such a polynomial can be computed as the eigenvalues of a companion matrix with elements which are complex valued combinations of the Fourier coefficients, the “CCM” method. However, previous work provided no examples, so one goal of this new work is to experimentally test the CCM method. A second goal is introduce a new alternative, the elimination/Chebyshev algorithm, and experimentally compare it with the CCM scheme. The elimination/Chebyshev matrix (ECM) algorithm yields a companion matrix with real-valued elements, albeit at the price of usefulness only for real roots. The new elimination scheme first converts the trigonometric rootfinding problem to a pair of polynomial equations in the variables ( c , s ) where c ≡ cos ( t ) and s ≡ sin ( t ) . The elimination method next reduces the system to a single univariate polynomial P ( c ) . We show that this same polynomial is the resultant of the system and is also a generator of the Groebner basis with lexicographic ordering for the system. Both methods give very high numerical accuracy for real-valued roots, typically at least 11 decimal places in Matlab/IEEE 754 16 digit floating point arithmetic. The CCM algorithm is typically one or two decimal places more accurate, though these differences disappear if the roots are “Newton-polished” by a single Newton’s iteration. The complex-valued matrix is accurate for complex-valued roots, too, though accuracy decreases with the magnitude of the imaginary part of the root. The cost of both methods scales as O ( N 3 ) floating point operations. In spite of intimate connections of the elimination/Chebyshev scheme to two well-established technologies for solving systems of equations, resultants and Groebner bases, and the advantages of using only real-valued arithmetic to obtain a companion matrix with real-valued elements, the ECM algorithm is noticeably inferior to the complex-valued companion matrix in simplicity, ease of programming, and accuracy.
Neurobiological studies of chronic pain and analgesia: Rationale and refinements

Chronic pain is a complex condition for which the need for specialized research and therapies has been recognized internationally. This review summarizes the context for the international call for expansion of pain research to improve our understanding of the mechanisms underlying pain in order to achieve improvements in pain management. The methods for conducting sensory assessment in animal models are discussed and the development of animal models of chronic pain is specifically reviewed, with an emphasis on ongoing refinements to more closely mimic a variety of human pain conditions. Pharmacological correspondences between pre-clinical pain models and the human clinical experience are noted. A discussion of the 3Rs Framework (Replacement, Reduction, Refinement) and how each may be considered in pain research is featured. Finally, suggestions are provided for engaging principal investigators, IACUC reviewers, and institutions in the development of strong partnerships to simultaneously expand our knowledge of the mechanisms underlying pain and analgesia while ensuring the humane use of animals in research.
Stimulation of protein synthesis by internalized insulin.

Previous studies showed that microinjected insulin stimulates transcription and translation in Stage IV Xenopus oocytes by acting at nuclear and cytoplasmic sites (Miller, D.S., 1988, 1989). The present report is concerned with the question of whether hormone, internalized from an external medium, can act on those sites to alter cell function. Both intracellular accumulation of undegraded 125I-insulin and insulin-stimulated 35S-methionine incorporation into oocyte protein were measured. Anti-insulin antiserum and purified anti-insulin antibody were microinjected into the cytoplasm of insulin-exposed cells to determine if insulin derived from the medium acted through internal sites. In cells exposed for 2 h to 7 or 70 nM external insulin, methionine incorporation was stimulated, but intracellular hormone accumulation was minimal and microinjected antibody was without effect. In cells exposed for 24 h, methionine incorporation again increased, but now accumulation of undegraded, intracellular hormone was substantial (2.6 and 25.3 fmol with 7 and 70 nM, respectively), and microinjected anti-insulin antibody significantly reduced the insulin-stimulated component of incorporation; basal incorporation was not affected. For cells exposed to 70 nM insulin for 24 h, inhibition of the insulin-stimulated component was maximal at 39%. Thus under those conditions, about 40% of insulin's effects were mediated by the internal sites. Together, the data show that inhibition of insulin-stimulated protein synthesis by microinjected antibody was associated with the intracellular accumulation of insulin. They indicate that when oocytes are exposed to external insulin, hormone eventually gains access to intracellular sites of action and through these stimulates translation. Control of translation appears to be shared between the internal sites and the surface receptor.
Surfactant-enhanced liquid–liquid extraction in microfluidic channels with inline electric-field enhanced coalescence

Continuous microfluidic liquid–liquid extraction is realized in a microfluidic device by generating emulsions with large interfacial areas for mass transfer, and subsequently breaking these emulsions using electric fields into easily separated segments of immiscible liquids (plugs). The microfluidic device employs insulated electrodes in a potassium hydroxide-etched channel to create large electric fields (100 kV m−1) that drive coalescence of the emulsion phase. The result is a transition from disperse to slug flow that can then readily be separated by gravity. Extractions of phenol and p-nitrophenol from an aqueous to hexane–surfactant solution serve as model systems. In addition to the increased surface area in the emulsion, extraction efficiency is enhanced by reverse micelles resulting from the presence of surfactants. The surfactant concentration is varied ∼1–10 wt% and a general two-parameter model is developed to quantify the extraction behavior and demonstrate the effectiveness of reverse micelle enhanced extraction.
Anthracene Fibers Grown in a Microstructured Optical Fiber for X-ray Detection

Anthracene fibers are grown inside a microstructured quartz matrix to form a multicore optical fiber for X-ray detection. A modified fiber growth method for single crystal anthracene from the melt via the Bridgman-Stockbarger technique is presented. The anthracene fiber is characterized by using spectrophotometry, Raman spectroscopy, and X-ray diffraction. These results show the anthracene grown in fiber has high purity and a crystal structure similar to anthracene grown from liquid, vapor, and melt techniques. As an X-ray detector, the output is 12%-16% efficient between the energy ranges of 40 and 10 keV. The effect of materials and fiber processing are discussed.
Exhaustive construction of (255, 127, 63)-cyclic difference sets

Abstract Here, (255, 127, 63)-cyclic difference sets are exhaustively constructed. There are, in total, 64 distinct (255, 127, 63)-cyclic difference sets. They include one Singer's type and three miscellaneous types. These cyclic difference sets of miscellaneous types also provide new examples of Hadamard matrixs of order 256 and two-level autocorrelation sequences of length 255.
Theoretical Considerations Associated with the Production of Negative Ions in Sputter-Type Ion Sources

Processes which are important to the optimum formation of negative ions by sputtering in the presence of an alkali metal are discussed. Negative ion generation probabilities calculated from several theoretical models including the tunneling, Norskov and Lundqvist, "freezing" approximation of Overbosch and Los as well as modified surface ionization theories are compared with experimental observation. An analytical expression is introduced which reproduces with good accuracy observed maximum work function changes for electropositive adsorbates on metallic adsorbants. The expression is extremely useful for computing the value of the work function at its minimum which in turn can be used in the appropriate model for computing optimum negative ionization probabilities.
Reading and critically appraising systematic reviews and meta-analyses: A short primer with a focus on hepatology

Systematic review and meta-analysis are fundamental to evidence-based health practice. Their development has paralleled the rapid growth of the biomedical literature and the need to make inferences from an often varied and complex body of knowledge. Identifying and correctly interpreting a body of evidence relevant to a particular clinical question is a daunting challenge for busy clinicians. By contrast, a carefully conducted systematic review can greatly facilitate an understanding of the available evidence. The purpose of this review is to inform the reader about the basics of how systematic reviews are conducted and how to interpret their results. We summarize the major methodologies used in systematic reviews (Table 1) and the issues related to their conduct and interpretation. Systematic review is a rigorous process designed to comprehensively identify eligible studies pertaining to a specific question, appraise them, and present key findings and limitations [1–3]. It provides a framework to scrutinize a body of knowledge and describe in detail the variability in results and factors that may account for it. Meta-analysis, which is commonly included in systematic reviews, is a process where results from different studies are combined quantitatively. It can provide an overall estimate of the net benefit or harms, even when these may not have been apparent in individual studies [4]. Systematic reviews contrast with traditional ‘narrative’ reviews and textbook chapters, which, generally, do not exhaustively review the literature, may be biased or lack transparency in the selection and interpretation of supporting evidence, and usually do not provide a quantitative synthesis of the data [5].
Modes of Metabolic Compensation during Mitochondrial Disease Using the Drosophila Model of ATP6 Dysfunction

Numerous mitochondrial DNA mutations cause mitochondrial encephalomyopathy: a collection of related diseases for which there exists no effective treatment. Mitochondrial encephalomyopathies are complex multisystem diseases that exhibit a relentless progression of severity, making them both difficult to treat and study. The pathogenic and compensatory metabolic changes that are associated with chronic mitochondrial dysfunction are not well understood. The Drosophila ATP6(1) mutant models human mitochondrial encephalomyopathy and allows the study of metabolic changes and compensation that occur throughout the lifetime of an affected animal. ATP6(1)animals have a nearly complete loss of ATP synthase activity and an acute bioenergetic deficit when they are asymptomatic, but surprisingly we discovered no chronic bioenergetic deficit in these animals during their symptomatic period. Our data demonstrate dynamic metabolic compensatory mechanisms that sustain normal energy availability and activity despite chronic mitochondrial complex V dysfunction resulting from an endogenous mutation in the mitochondrial DNA. ATP6(1)animals compensate for their loss of oxidative phosphorylation through increases in glycolytic flux, ketogenesis and Kreb's cycle activity early during pathogenesis. However, succinate dehydrogenase activity is reduced and mitochondrial supercomplex formation is severely disrupted contributing to the pathogenesis seen in ATP6(1) animals. These studies demonstrate the dynamic nature of metabolic compensatory mechanisms and emphasize the need for time course studies in tractable animal systems to elucidate disease pathogenesis and novel therapeutic avenues.
Termination of parental rights: Which foster care children are affected?

Abstract In 1997, the Adoption and Safe Families Act (ASFA) was passed with a primary goal of expediting the process of placing foster children with permanent or adoptive families. In order to meet this goal, ASFA requires states to terminate parental rights if a child has been in foster care for 15 of the most recent 22 months. Prior empirical research on foster care dependence supports the provision in ASFA to expedite the discharge process because over time children are progressively less likely to be discharged from foster care. However, very little research has examined what impact terminating parental rights will have on this goal. One of the first steps is to examine which children are most likely to see the rights of their parents terminated and how these children differ from those children who are returned home. Using a competing risks hazard model we find many differences between the children who are sent home and those children whose parents have their rights terminated.
Extended wearing trial of Trifield lens device for tunnel vision

Severe visual field constriction (tunnel vision) impairs the ability to navigate and walk safely. We evaluated Trifield glasses as a mobility rehabilitation device for tunnel vision in an extended wearing trial. Twelve patients with tunnel vision (5‐22� wide) due to retinitis pigmentosa or choroideremia participated in the 5-visit wearing trial. To expand the horizontal visual field, one spectacle lens was fitted with two apex-to-apex prisms that vertically bisected the pupil on primary gaze. This provides visual field expansion at the expense of visual confusion (two objects with the same visual direction). Patients were asked to wear these spectacles as much as possible for the duration of the wearing trial (median 8, range 6‐60 weeks). Clinical success (continued wear, indicating perceived overall benefit), visual field expansion, perceived direction and perceived visual ability were measured. Of 12 patients, nine chose to continue wearing the Trifield glasses at the end of the wearing trial. Of those nine patients, at long-term follow-up (35‐78 weeks), three reported still wearing the Trifield glasses. Visual field expansion (median 18, range 9‐38� ) was demonstrated for all patients. No patient demonstrated adaptation to the change in visual direction produced by the Trifield glasses (prisms). For reported difficulty with obstacles, some differences between successful and non-successful wearers were found. Trifield glasses provided reported benefits in obstacle avoidance to 7 of the 12 patients completing the wearing trial. Crowded environments were particularly difficult for most wearers. Possible reasons for long-term discontinuation and lack of adaptation to perceived direction are discussed.
Narrow-band, slowly varying decimetric radiation from the dwarf M flare star YZ Canis Minoris

Observations of slowly varying radiation from the dwarf M star YZ Canis Minoris with a maximum flux density of 20 mJy and narrow-band frequency structure at frequencies near 1465 MHz are presented. Possible explanations for this radiation are examined. Thermal gyroresonant radiation would require impossibly large coronal loops and magnetic field strengths. The narrow-band structure cannot be explained by continuum emission processes such as thermal bremsstrahlung, thermal gyroresonant radiation, or nonthermal gyrosynchrotron radiation. Coherent burst mechanisms seem to be required.
Measurements of the pons as a biomarker of progression for pediatric DIPG

Treatment of pediatric diffuse intrinsic pontine glioma (DIPG) remains challenging, and reliable biomarkers of response are lacking. Radiographic response is a primary endpoint in many investigational studies of brain tumors, but there is no standard method of tumor measurement for DIPG, significant inter-observer variability exists given the invasive nature of these tumors, and tumor measurements are not predictive of outcome. Because DIPGs involve a significant portion of the pons, we evaluated the reliability and prognostic value of one-dimensional (1D) and two-dimensional (2D) pons measurements using anatomical landmarks rather than tumor boundaries. Patients with DIPG (n = 75) were evaluated longitudinally at our institution using MRI. Four readers independently performed 1D and 2D measurements of the pons using FLAIR images. Agreement and inter-reader variability were evaluated using differences among the six reader pairs and the coefficient of variation (CV). Prognostic value of pons measurements was calculated using Cox proportional hazards models, where relative hazard (RH) represents risk of death. Readers evaluated 384 exams. Agreement of readers’ 1D and 2D measurements was strong (median difference between reader pairs 3.1 and 5.4 %, respectively), with low inter-reader variability (median CV = 3.1 % and median CV = 4.8 %, respectively). Increases in 1D and 2D pons measurements over time indicated poorer prognosis (RH = 2.29, p = 0.0025 and RH = 1.13, p = 0.0016, respectively), with shorter overall survival. Pons measurements had low inter-reader variability compared to previously reported tumor measurement techniques and correlated with outcome in children with DIPG. Measurements of the pons (as opposed to direct measurements of tumor) are a viable in vivo biomarker for DIPG.
Funding Poverty Law in an Era of Decentralization

This article explores intergovernmental relations, discretionary authority and the effect of state political ideology on the nature of civil legal representation in the United States. I examine support for legal services from 1996 to 1999 using data gathered by the federal Legal Services Corporation (LSC). A Heckman (1976) selection model is employed to test several hypotheses regarding states' decisions to supplement the federal funding for legal services. I find that state citizen political ideology, economic capacity of the state, and institutional design shape the decision-making environment for civil legal services. In addition, I find evidence that suggests that states are sensitive to shifts in intergovernmental relations in the area of legal services.
Pulmonary function tests at work.

Abstract Occupational exposures remain an important cause of lung disease. A number of PFTs are used in the occupational setting, including spirometry, PEF recordings, methacholine challenge testing, lung volume, and DL(CO). These tests are used in a number of situations, including the clinical evaluation and management of patients with possible occupational lung disorders, preplacement and fitness-for-duty examinations, medical screening of exposed workers, impairment and disability evaluations, and research. The diagnosis of occupational lung disease has serious consequences for a worker and, in addition to a careful occupational history, usually requires objective assessment using PFTs. Serial PFTs are useful in following such patients and screening exposed populations of workers for respiratory conditions.
Differential scanning calorimetric study of rat brain hexokinase: domain structure and stability.

Rat brain hexokinase (ATP:d-hexose 6-phosphotransferase, EC 2.7.1.1) has been studied by differential scanning calorimetry. In “high-ionic-strength” buffer (50 mm Tris-Cl, 0.5 mm EDTA, 10 mm monothioglycerol, pH 8.5), and assuming two-state behavior with calorimetric enthalpy equal to van't Hoff enthalpy, the endotherm could be deconvoluted into two transitions with Tm values of about 48 and 51 °C and enthalpies of about 109 and 112 kcal/mol, respectively. A similar endotherm was seen when glucose or glucose 6-phosphate was present, except that Tm values for both transitions were increased. The glucose analog, N-acetylglucosamine, had no observable effect on the endotherm, which is in agreement with previous studies indicating that this ligand, unlike glucose and glucose 6-phosphate, does not induce conformational changes that lead to increased stability of the enzyme. In “low-ionic-strength” buffer (5 mm Tris-Cl, 0.5 mm EDTA, 10 mm monothioglycerol, pH 8.5), the transitions were partially resolved even in the absence of ligands, with Tm values of about 49 and 55 °C. Due to difficulties with erratic baseline behavior under the low-ionic-strength conditions, enthalpies were not routinely determined, but these appeared to be similar to those seen in high-ionic-strength buffer. Also similar was the increase in stability, as reflected by the increase in Tm for both transitions, when glucose or glucose 6-phosphate was present. Correlation of these transitions with specific regions of the molecule was established by analysis of enzyme in which the domain corresponding to the first transition was selectively denatured by a partial scan in the calorimeter. Subsequent rescanning of these samples showed only the second transition, confirming the selective denaturation of the domain corresponding to the first transition and retention of the folded structure of the second domain. Discrimination between denatured (first transition) and undenatured (second transition) domains was based on the markedly increased susceptibility of the denatured region to tryptic digestion; regions of the molecule that retained their folded structure and resistance to proteolysis were identified by immunoblotting techniques using monoclonal antibodies recognizing epitopes having defined locations within the overall sequence. Based on this analysis, the first transition corresponds to unfolding of the C-terminal half of the molecule, with the second transition resulting from unfolding of the more stable N-terminal half. The order of unfolding could be reversed in the presence of ATP-Mg2+ and N-acetylglucosamine, conditions which have been shown to result in selective stabilization of the C-terminal domain (T. K. White and J. E. Wilson, Arch. Biochem. Biophys. 274, 375–393 (1989).
The production and use of prospective radionuclides for radioimmunotherapy

The potential of utilizing monoclonal antibodies (Mab) as carriers of radionuclides for the selective destruction of tumors has stimulated much research activity. The approach should be most beneficial for treatment of tumors not easily amenable to surgical control, for treatment of early recurrence and of distant metastases. Even though significant progress has been made, more work will be necessary to understand the various chemical and biological factors which can influence antibody specificity, stability and kinetics, as well as dosimetric considerations for effective therapy. The choice of radiolabel is an important factor that needs to be optimized to allow the modality to fulfill its potential. For immunoscintigraphy, I-123, I-131, In-111, and Tc-99m have all been used with some success. However, almost all therapeutic trials have utilized I-131. This is largely due to its ready availability at moderate cost, the ease of halogenation techniques for proteins, and its long history of use in treating thyroid malignancy, rather than any careful analysis of its suitability for radioimmunotherapy.
Optical guiding in a Raman free-electron laser

A theoretical and computational study of optical guiding in a Raman free-electron laser (of wavelength ≃ 2 mm) is given. A set of basic dynamical equations is given, including the effects of space-charge and two-dimensional diffraction, both with and without a waveguide. The results from a computer code based on these equations are reported, showing optical guiding. An experiment is proposed in the Columbia free-electron laser to measure optical guiding.
Myeloperoxidase singlet molecular oxygen generation detected by direct infrared electronic emission.

Myeloperoxidase in micromolar concentrations reacting with half-millimolar stock solution H2O2 in acetate buffer containing KBr and in 50% D2O (pH + pD = 4.5) at 298 K is shown to generate singlet delta molecular oxygen efficiently. The near infrared electronic emission of singlet oxygen at 1268 nm is detected directly by novel ultrasensitive IR spectrophotometer equipment. The quantum efficiency of singlet oxygen generation by the MPO·Br−·H2O2 reaction is shown to be comparable with that of the standard chemical reaction OCl−·H2O2 at identical peroxide concentrations.
Intrinsic Disorder, Epigenetics, and Leukemia - the MLL-AF9 SAGA

The MLL gene is a target of chromosomal translocations found in human leukemia. One of the translocation partners is AF9. The portion of AF9 fused to MLL is the C-terminal ANC1 homology domain (AHD) of AF9. We have shown that this domain is intrinsically disordered. Upon interaction with its binding partners, it undergoes coupled binding and folding. Intriguingly, this domain has been shown to bind four different partners: AF4 (PolII phosphorylation, productive transcriptional elongation), DOT1L (catalyzes H3K79 methylation, gene activation), as well as BCoR and hPC3 (CBX8) which are transcriptional repressors. The binding of both activating and repressing partners suggests that this domain acts as a multi-functional switch. We have used NMR spectroscopy to solve structures of AF9 with all four binding partners, showing they all bind in a similar manner to AF9, leading to questions about how binding to specific partners is regulated and/or orchestrated.Interestingly, we found a linear repeat motif in DOT1L to which AF9 binds with high affinity. Such repeat motifs are seen frequently in intrinsically disordered proteins, but the functional consequences of binding to such elements has not been clear. We created point mutations in AF9 which disrupt binding to only one site or to both sites and incorporated these into MLL-AF9 for functional characterization. DOT1L is a non-processive enzyme, i.e. the local concentration of enzyme will define the level of H3K79 methylation, so we hypothesized that a mutation disrupting one binding site will impact H3K79me3 levels but not H3K79me2 levels whereas one affecting both sites will impact both. Indeed, this is what we observed in our ChIP-Seq analysis. This suggests, at least in some cases, these repeat motifs are a clever way to regulate the degree of enzymatic activity by increasing the local effective concentration.
Systematic design for task related multimedia interfaces

Abstract Multimedia interfaces are currently created primarily by intuition. Development of a method for analysis and design of multimedia presentation interfaces is described. The study investigates task based information analysis, persistence of information, selection attention and concurrency in presentation. The method gives an agenda of issues, diagrams and techniques for specification, with guidelines for media selection and presentation scripting. Use of the method is illustrated with an example interface from a shipboard emergency management system.
Demonstration of neurofibrillary tangles in the indusium griseum and of axonal disturbances in sagittal sulcal lesions of the corpus callosum: An immunohistochemical investigation

This is an immunohistochemical investigation of the indusium griseum (supracommissural hippocampus) of the brains of control subjects and patients with Alzheimer's disease (AD). Our assays revealed the presence of fine deposits of synaptophysin-positive dots in the neuropil and around neurons in the indusium griseum of control subjects. By using an antibody to Alzheimer neurofibrillary tangles (NFT) we identified NFT and neuropil thread-like structures in the indusium griseum of AD patients; no β-amyloid protein-containing senile plaques were seen. To our knowledge, this is the first documentation of the occurrence of NFT in the indusium griseum. We also performed immunohistochemical assays on anterior sagittal sulcal lesions of the corpus callosum (ASSLCC), also known as surface lesions of the corpus callosum. These studies revealed a uniformly increased expression of the 200 kDa phosphorylated neurofilament protein by the axons in the pale myelin areas around the zonal depressions caused by the mechanical pressure of the anterior pericallosal artery. By contrast, immunoreactivity with an antibody to glial fibrillary acidic protein was either unchanged or reduced in the ASSLCC.
TAMARIN AND MARMOSET MATING SYSTEMS - UNUSUAL FLEXIBILITY

Recent studies of wild tamarins and marmosets have shown that at least one species exhibits variable mating patterns, including cooperative polyandry, monogamy and, more rarely, polygyny. Polyandry is thought to occur because the high frequency of twinning and the relatively high weights of infants in these species make the rearing of infants unusually difficult. Nonreproductive helpers (older offspring) and polyandrous males may serve as alternative sources of the extra help needed with infant care. The apparent causes of facultative polyandry in saddle-back tamarins are quite different from those of the cooperative polyandry that has been studied in some bird species.
An event-driven multithreaded dynamic optimization framework

Dynamic optimization has the potential to adapt the program's behavior at run-time to deliver performance improvements over static optimization. Dynamic optimization systems usually perform their optimization in series with the application's execution. This incurs overhead which reduces the benefit of dynamic optimization, and prevents some aggressive optimizations from being performed. In this paper we propose a new dynamic optimization framework called Trident. Concurrent with the program's execution, the framework uses hardware support to identify optimization opportunities, and uses spare threads on a multithreaded processor to perform dynamic optimizations for these optimization events. We evaluate the benefit of using Trident to guide code layout, basic compiler optimizations, and value specialization. Our results show that using Trident with these optimizations achieves an average 20% speedup, and is complementary with other memory latency tolerant techniques, such as prefetching.
Ultrasound simulation in bone

The manner in which ultrasound interacts with bone is of key interest in therapy and diagnosis alike. These may include applications directly to bone, as, for example, in treatment to accelerate the healing of bone fractures and in assessment of bone density in osteoporosis, or indirectly in diagnostic imaging of soft tissue with interest in assessing exposure levels to nearby bone. Because of the lack of analytic solutions to virtually every "practical problem" encountered clinically, ultrasound simulation has become a widely used technique for evaluating ultrasound interactions in bone. This paper provides an overview of the use of ultrasound simulation in bone. A brief description of the mathematical model used to characterize ultrasound propagation in bone is first provided. A number of simulation examples are then presented that explain how simulation may be utilized in a variety of practical configurations. The focus of this paper in terms of examples presented is on diagnostic applications in bone, and, in particular, for assessment of osteoporosis. However, the use of simulation in other areas of interest can easily be extrapolated from the examples presented. In conclusion, this paper describes the use of ultrasound simulation in bone and demonstrates the power of computational methods for ultrasound research in general and tissue and bone applications in particular.
ORCHESTRA : Rapid, collaborative sharing of dynamic data

Conventional data integration techniques employ a “top-down” design philosophy, starting by assessing requirements and defining a global schema, and then mapping data sources to that schema. This works well if the problem domain is well-understood and relatively static, as with enterprise data. However, it is fundamentally mismatched with the “bottom-up”model of scientific data sharing, in which new data needs to be rapidly developed, published, and then assessed, filtered, and revised by others. We address the need for bottom-up collaborative data sharing, in which independent researchers or groups with different goals, schemas, and data can share information in the absence of global agreement. Each group independently curates, revises, and extends its data; eventually the groups compare and reconcile their changes, but they are not required to agree. This paper describes our initial design and prototype of the ORCHESTRA system, which focuses on managing disagreement among multiple data representations and instances. Our work represents an important evolution of the concepts of peer-to-peer data sharing [23], which considers revision, disagreement, authority, and intermittent participation.
Crystal structures of vegetative soybean lipoxygenase VLX‐B and VLX‐D, and comparisons with seed isoforms LOX‐1 and LOX‐3

The lipoxygenase family of lipid-peroxidizing, nonheme iron dioxygenases form products that are precursors for diverse physiological processes in both plants and animals. In soybean (Glycine max), five vegetative isoforms, VLX-A, VLX-B, VLX-C, VLX-D, VLX-E, and four seed isoforms LOX-1, LOX-2, LOX-3a, LOX-3b have been identified. In this study, we determined the crystal structures of the substrate-free forms of two major vegetative isoforms, with distinct enzymatic characteristics, VLX-B and VLX-D. Their structures are similar to the two seed isoforms, LOX-1 and LOX-3, having two domains with similar secondary structural elements: a beta-barrel N-terminal domain containing highly flexible loops and an alpha-helix-rich C-terminal catalytic domain. Detailed comparison of the structures of these two vegetative isoforms with the structures of LOX-1 and LOX-3 reveals important differences that help explain distinct aspects of the activity and positional specificity of these enzymes. In particular, the shape of the three branches of the internal subcavity, corresponding to substrate-binding and O(2) access, differs among the isoforms in a manner that reflects the differences in positional specificities.
Yeast dual-affinity biobricks: Progress towards renewable whole-cell biosensors

Point-of-care (POC) diagnostic biosensors offer a promising solution to improve healthcare, not only in developed parts of the world, but also in resource limited areas that lack adequate medical infrastructure and trained technicians. However, in remote and resource limited settings, cost and storage of traditional POC immunoassays often limit actual deployment. Synthetically engineered biological components ("BioBricks") provide an avenue to reduce costs and simplify assay procedures. In this article, the design and development of an ultra-low cost, whole-cell "renewable" capture reagent for use in POC diagnostic applications is described. Yeast cells were genetically modified to display both single chain variable fragment (scFv) antibodies and gold-binding peptide (GBP) on their surfaces for simple one step enrichment and surface functionalization. Electrochemical impedance spectroscopy (EIS) and fluorescent imaging were used to verify and characterize the binding of cells to gold electrodes. A complete electrochemical detection assay was then performed on screen-printed electrodes fixed with yeast displaying scFv directed to Salmonella outer membrane protein D (OmpD). Electrochemical assays were optimized and cross-validated with established fluorescence techniques. Nanomolar detection limits were observed for both formats.
Advanced electromagnetic design of cavities for high current accelerators

For high-current accelerators such as those proposed for transmutation technologies or spallation sources, preconstruction numerical modeling has a high importance. Non axisymmetric cavities require a full 3-D modeling. A complex analysis of structures beyond tuning and the calculation of Q and shunt impedance is required and also the interaction with the mechanical properties of the structures has to be taken into account. This paper reports on recent work done at LANL for proposed beam funnels, a new normal-conducting medium-energy structure and superconducting cavities for medium energy. The electromagnetic calculations have been done with MAFIA, Rel 3.2 the thermal and stress analysis results reported come from the ABAQUS engineering code.
Experimental Methods for the Evaluation of Aggregate Resistance to Polishing, Abrasion, and Breakage

This paper presents the development of new methods for measuring aggregate resistance to polishing, and degradation. These are important properties that influence pavement skid resistance and resistance to distresses under traffic loading. The aggregate imaging system is used to measure aggregate surface texture after different polishing time intervals in the micro-Deval test. Mathematical functions are then used to describe the initial texture, rate of polishing, and final texture. Aggregate abrasion is quantified by the percent difference in surface angularity before and after the micro-Deval test, while aggregate breakage is described by the weight loss in this test. The efficacy of the new methods is demonstrated through the analysis of aggregates from different sources that exhibit a wide range of properties. In addition, the new methods are verified by comparing the measured aggregate properties to the degradation of these aggregates in hot mix asphalt mixtures due to compaction forces.
Humic Acid Interferes with Species Recognition in Zebrafish (Danio rerio)

Few studies have addressed how chemosensation may be impaired by chemical alterations of the environment and anthropogenic disturbance. Humic acid (HA) is a pervasive, naturally occurring organic derivative found in aquatic and terrestrial environments; human activity, however, can lead to elevated levels of HA. Recent studies suggest that environments that contain high levels of HA may hinder chemical communication. We tested the ability of adult zebrafish (Danio rerio) to discriminate between conspecific and heterospecific urinary chemical cues found in the presence and absence of HA. We show that high humic acid levels (200 mg/l) can impair the ability to differentiate conspecifics from heterospecifics. We also found that zebrafish prefer untreated water over HA-treated water. These findings suggest that, in addition to human-produced synthetic compounds, changes in the abundance of naturally occurring substances may also negatively impact natural behaviors in aquatic species by disturbing the sensory environment.
Scale-up of microbubble dispersion generator for aerobic fermentation

A laboratory-scale microbubble dispersion (MBD) generator was shown to improve oxygen transfer to aerobic microorganisms when coupled to the conventional air-sparger. However, the process was not demonstrated on a large scale to prove its practical application. We investigated the scale-up of a spinning-disk MBD generator for the aerobic fermentation of Saccharomyces cerevisiae (baker's yeast). A 1-L spinning-disk MBD generator was used to supply air for 1- and 50-L working volume fermentation of baker's yeast. For the two levels investigated, the MBD generator maintained an adequate supply of surfactant-stabilized air microbubbles to the microorganisms at a relatively low agitation rate (150 rpm). There was a significant improvement in oxygen transfer to the microorganism relative to the conventional sparger. The volumetric mass transfer coefficient, kLa, for the MBD system at 150 rpm was 765 h(-1) compared to 937 h(-1) for the conventional sparger at 500 rpm. It is plausible to surmise that fermentation using larger working volumes may further improve the kLa values and the dissolved oxygen (DO) levels because of longer hold-up times and, consequently, improve cell growth. There was no statistically significant difference between the cell mass yield on substrate (0.43 g/g) under the MBD regime at an agitation rate of 150 rpm and that achieved for the conventional air-sparged system (0.53 g/g) at an agitation rate of 500 rpm. The total power consumption per unit volume of broth in the 50-L conventional air-sparged system was threefold that for the MBD unit for a similar product yield. Practical application of the MBD technology can be expected to reduce power consumption and therefore operating costs for aerobic fermentation.
Cephalosporium maydis is a distinct species in the Gaeumannomyces- Harpophora species complex

Cephalosporium maydis is an important plant pathogen whose phylogenetic position relative to other fungi has not been established clearly. We compared strains of C. maydis, strains from several other plant-pathogenic Cephalosporium spp. and several possible relatives within the Gaeumannomyces-Harpophora species complex, to which C. maydis has been suggested to belong based on previous preliminary DNA sequence analyses. DNA sequences of the nuclear genes encoding the rDNA ITS region, β-tubulin, histone H3, and MAT-2 support the hypothesis that C. maydis is a distinct taxon within the Gaeumannomyces-Harpophora species complex. Based on amplified fragment length polymorphism (AFLP) profiles, C. maydis also is distinct from the other tested species of Cephalosporium, Phialophora sensu lato and members of Gaeumannomyces-Harpophora species complex, which supports its classification as Harpophora maydis. Oligonucleotide primers for H. maydis were developed that can be used in a PCR diagnostic protocol to rapidly and reliably detect and identify this pathogen. These diagnostic PCR primers will aid the detection of H. maydis in diseased maize because this fungus can be difficult to detect and isolate, and the movement of authentic cultures may be limited by quarantine restrictions.