cssi/SciSciGPT-SciSciNet huggingface dataset:
Transposition of the kanamycin-resistance transposon Tn903

The insertion of the kanamycin-resistance transposon, Tn903, into the Escherichia coli chromosome was studied. Tn903 is similar in structure to the well known transposons Tn5 and Tn10 in that it has a unique central sequence flanked by inverted repeat sequences extending more than a thousand base pairs. However, the central region of Tn903 has enough single-frame coding capacity only for the drug modifying enzyme, whereas Tn5 and Tn10 carry multigenic unique sequences. In this paper we demonstrate that two different classes of insertion event occur: (1) the first class is a complex event in which all or part of the genome of the bacteriophage lambda vector is co-inserted near the purE locus on the E. coli chromosome (11.7 min); (2) the second class appears to be a “simple” transposition event in which the transposon alone is inserted at relatively nonspecific sites in the chromosome, as has been described for Tn5 and Tn10. Furthermore both classes show dependency on homology-requiring recombination systems. We suggest that Tn903 transposes infrequently because it must utilize a recA-controlled host function, whereas Tn5 and Tn10 are recA-independent and encode similar but more active functions on the transposon DNA.
A Statewide Program to Stimulate Reporting of Adverse Drug Reactions

The purpose of a 26-month Food and Drug Administration sponsored study conducted in Mississippi was to determine how the reporting of adverse drug reactions (ADRs) might be stimulated. The program ...
The feasibility and acceptability of male circumcision among men, women, and health providers of the Altagracia Province, Dominican Republic

Abstract Background. Male circumcision (MC) is an effective strategy to reduce the risk of HIV acquisition in men. The objective of the present study was to evaluate the feasibility of introducing MC in the Altagracia Province and to qualitatively assess the knowledge and acceptability of MC among men, women, and health providers. Methods. Two surveys were administered to providers. The first, assessed their experience and knowledge of MC and the second, a “Health Facility Profile,” included an inventory of available surgical materials in the clinics. Fourteen focus group discussions were conducted to evaluate the acceptability of MC. Results. Forty-three providers were interviewed at 37 clinics. Median age was 33 years (range 23–55 years). Most were physicians (91%) employed by the government. Only 23% had experience with MC. Almost universally (95%), providers knew that MC has health benefits. All agreed that MC improves hygiene and 67% knew that MC decreases the risk of HIV infection. Only six clinics ...
Immobilization of Fertilizer Nitrogen in Rice

A recent transition in rice straw management, from open-field burning to soil incorporation in combination with winter-fallow flooding, has led to uncertainty in evaluating long-term N fertility. A 2-yr field study of 15 N-labeled fertilizer and crop residue was initiated in the fourth year of a rice straw management trial to examine the impacts of winter flooding and straw management on N fertilizer immobilization and crop uptake. After six seasons of residue incorporation and winter flooding, no effect on total soil C or N was observed. During the fifth and sixth year of the field study, microbial biomass C and N were greater for straw incorporation than for straw burned. Microbial biomass contained a sizable portion of soil-recovered 15 N fertilizer after the first (23%) and second (10%) crop season of the N study. The half-life of the 15 N in the biomass ranged from 0.55 to 0.87 yr. One year after 15 N-fertilizer application, greater recovery of 15 N in the soil from straw incorporation versus burning (22.2 versus 18.7%) resulted in a slight increase in residual fertilizer N recovery in grain in the second growing season of the 15 N study. Increased soil 15 N recovery 1 yr after fertilizer application in the straw incorporation treatment, however, was offset by higher grain recovery of 15 N in the burned treatment during the first growing season. Hence, the net result of these competing soil and plant sinks for fertilizer N led to similar 15 N losses after 2 yr (50.3 ± 2.2%) under burned and incorporated straw. The cumulative effects of straw incorporation resulted in greater net N mineralization, an increase in microbial biomass N, and greater recovery of 15 N in soil one year after application. Clearly, an active, labile N pool was formed when straw was incorporated that led to a reduction in fertilizer N dependency for rice.
Differential induction of regulatory genes during mesoderm formation in Xenopus laevis embryos.

Mesoderm development in Xenopus laevis depends on inductive cell interactions mediated by diffusible molecules. The mesoderm inducer activin is capable of redirecting the development of animal explants both morphologically and biochemically. We have studied the induction of four regulatory genes, Mix. 1, goosecoid (gsc), Xlim-1 and Xbra in such explants by activin, and the influence of other factors on this induction. Activin induction of gsc is strongly enhanced by dorsalization of the embryo by LiCl, while expression of the other genes is only slightly enhanced. The protein synthesis inhibitor cycloheximide (CHX) inhibits the activin-dependent induction of Xbra partially, while induction of Mix. 1 and Xlim- 1 is essentially unaffected. In contrast, gsc shows strong superinduction in the presence of activin and CHX, and can be induced in animal explants by CHX alone. Induction and superinduction by CHX have previously been observed for immediate early genes in a variety of systems, notably for the activation of c-fos expression by serum stimulation, but have not been reported in early amphibian embryos. © 1993Wiley-Liss, Inc.
Decision making in a sequential game: the case of pitting in NASCAR.

This article uses data from NASCAR to examine strategic decision making with professional players and high stakes. The authors look at driver decisions to pit, enabling car performance to be improved at the cost of track position. Unlike other sports choices that have been used to test game-theoretic play, pitting decisions occur sequentially. Therefore, optimal decision making should result in the sub-game perfect equilibrium outcome. After estimating the likelihood of successfully passing another driver, the authors find some evidence that drivers make optimal decisions; however, driver behavior is also consistent with a simple heuristic of following the preceding car.
Two- and Three-Dimensional Divalent Metal Isophthalate Coordination Polymers Incorporating Flexible Bispyridylmethylpiperazine Tethers: Structure Direction through Coordination Geometry Preferences, Carboxylate Binding Mode, and Ligand Conformation

Hydrothermal synthesis has afforded a family of divalent metal coordination polymers incorporating both the isophthalate dianion (ip) and the flexible organodiimine N,N′-bis(4-pyridylmethyl)piperazine (bpmp). The compounds of type {[M(ip)(bpmp)]·H2O} (M = Co, 1; M = Cd, 2) are isomorphous, possessing puckered two dimensional (2D) rectangular grid layers built from the linkage of [M2(ip)2] double chains through bpmp tethers. In contrast, the nickel congener {[Ni(ip)(bpmp)(H2O)]·H2O} (3) displays a corrugated, interpenetrated 2D structure. {[Zn(ip)(bpmp)]·H2O} (4) adopts a 5-fold interpenetrated three-dimensional diamondoid topology due to the tetrahedral coordination at Zn. Analysis of the variable temperature magnetic susceptibility of 1 indicated the presence of ferromagnetic coupling and zero-field splitting effects within the dinuclear subunits along with possible long-range ferromagnetic interactions transmitted through the ip ligands. The d10 derivatives 2 and 4 exhibited blue-violet luminescence upo...
The Landau-Ginzburg-Wilson model in 2 and 2+ϵ dimensions at low temperatures

Abstract By introducing a collective variable the two-dimensional Landau-Ginzburg-Wilson model (classical order parameter of non-rigid magnitude) may, if the order parameter dimension exceeds one, be solved at absolute zero. A low temperature expansion about this solution is developed. The low temperature expansion supports the hypothesis that d = 2 systems with a two-component order parameter will have a non-zero critical point, below which the susceptibility diverges, although no symmetry breaking occurs. The leading order temperature dependence of η is determined. In addition an ϵ expansion for systems of spatial dimension 2 + ϵ is developed. The critical exponents, calculated here to lowest order in ϵ, agree with those found for stiff spins.
Dislocation halos in an irradiated nickel-base alloy

Abstract Transmission electron microscopy has been used to examine a neutron irradiated nickel-base alloy which had been doped with boron enriched in the 10B isotope. These observations show concentric circular halos of dislocations, many of them loops, surrounding some of the carbide precipitates in the specimens. These halos are believed to be planar segments of spherical damage shells surrounding regions of 10B concentration, and to represent the resting points of helium and lithium atoms produced by the 10B(n, α)7Li reaction.
Development of a Jet Noise Prediction Method for Installed Jet Configurations

This paper describes development of the Jet3D noise prediction method and its application to heated jets with complex three-dimensional flow fields and installation effects. Noise predictions were made for four separate flow bypass ratio five nozzle configurations tested in the NASA Langley Jet Noise Laboratory. These configurations consist of a round core and fan nozzle with and without pylon, and an eight chevron core nozzle and round fan nozzle with and without pylon. Predicted SPL data were in good agreement with experimental noise measurements up to 121 inlet angle, beyond which Jet3D under predicted low frequency levels. This is due to inherent limitations in the formulation of Lighthill's Acoustic Analogy used in Jet3D, and will be corrected in ongoing development. Jet3D did an excellent job predicting full scale EPNL for nonchevron configurations, and captured the effect of the pylon, correctly predicting a reduction in EPNL. EPNL predictions for chevron configurations were not in good agreement with measured data, likely due to the lower mixing and longer potential cores in the CFD simulations of these cases.
The Crossing Guard

The hero is entrusted with but one unyielding duty: To protect and preserve the lives of children. There are but three things he must battle while endlessly fighting to perform his calling... One, he's only a crossing guard. Two, the traffic is heavy. Three, he's an armadillo.Hardware: HP Visualize WorkstationsSoftware: Alias/Wavefront Maya3.0, DeepPaint, Premiere. Copyright held by creator.
Influence of Antibiotics and Hemorrhage upon Serum Properdin Titers.

ConclusionIn dogs subjected to a standard hemorrhagic hypotension. survival rate was significantly increased by prior treatment with antibiotics. This regimen eliminated typical E. coli, and markedly reduced the Gram–negative fecal flora. Seven of 8 of these survivors had significantly increased properdin titers following antibiotic administration. In a group of dogs treated with milk of magnesia, though the survival rate was not increased, the survivors all had significantly increased properdin titers. The pre–treatment properdin titers were not significantly related to subsequent survival from standard hemorrhagic hypotension.
SU‐FF‐T‐167: Digital Data Integrity QA for Multi‐Institutional Clinical Trials

Purpose: The Image‐guided Therapy QA Center (ITC) as part of the NCI‐sponsored Advanced Technology QA Consortium (ATC) has nearly 15 years experience in performing data integrity QA review for multi‐institutional advanced technology clinical trials that require digital data submission. This presentation will report on that experience. Method and Materials: Participants in some advanced technology multi‐institutional clinical trials must be able to submit imaging data as well as RT objects (CT, RT Structure Set, RT Dose, and RT Plan) to the ITC for protocol compliance QA review of contoured volumes and dose coverage/heterogeneity. Data are sent via FTP or on media. However, prior to that QA review, experienced personnel at the ITC carefully review each digital data set in regard to completeness of protocol required elements, format of data, and possible data corruption. Results: Thus far over 3000 data sets have been submitted to ITC. Unfortunately, data often need resubmission due to problems discovered by ITC. Errors in submission can be divided into five categories: 1) misuse of UI of treatment planning system (TPS), 2) misunderstanding of protocol requirements, 3) non‐uniformity of DICOM export implementations by TPS vendors, 4) user error with digital data transfer software, and 5) updated TPS software, whose data export feature no longer is ATC compliant. Statistics of number of resubmissions required as well as specific details of these problems will be presented. Conclusion: Digital data submission of complete 3D data set is essential for QA of advanced technology clinical trials. However, collection of these data requires review and troubleshooting by experienced personnel to ensure subsequent protocol compliance QA and later still, quality data analysis. A significant portion of the ITC workload involves digital data integrity QA to ensure quality of submitted digital data. Support: NIH U24 Grant CA81647.
Multicast routing for multimedia collaborative applications

This paper introduces a multicast routing technique that is suitable for multimedia collaborative applications. Typically, the multicast groups for such applications are small and of slow membership dynamics. Moreover, the group members are not assumed to be located in a single domain; rather, they may span a global inter-network. An important requirement for multimedia collaborative applications is the delivery time-a shortest path delivery tree is of a major interest in constructing the multicast tree. Our routing technique constructs a distribution tree per source and it uses explicit membership messages to build and maintain the tree. Thus, it combines the advantages of both broadcast and prune (BAP) and shared tree techniques; that is, it produces shortest path trees, yet the bandwidth consumed in building and maintaining such trees is minimal. We present a simulation study to compare the performance of our technique against BAP and shared tree techniques. Results of the simulation show that our technique outperforms previous ones.
On complex waves

A widely used approximate technique for treating radiation problems involving a source-excited interface is derived from a saddle-point evaluation of the inverse transform-integral representation of the solution. The total solution is approximated to by the first saddle-point term plus residue terms in their respective wedges of contribution, i.e. space wave plus complex waves. The paper considers the well known approximation of space wave plus complex waves in the light of the modified saddle-point technique. The condition for validity of this approximation is shown to be that the numerical distance, a quantity involving both the distance from pole to saddle point and the distance from origin to observation point, should be greater in magnitude than ten. The discussion is numerically illustrated using the example of unidirectional travelling-leaky-wave and surface-wave aperture distributions. For these examples, graphs are compared of the approximate solutions and of solutions including the correction terms. Diagrams which show where in space the complex wave is a valid and significant part of the total solution are also constructed. The leaky-wave case is particularly interesting, since the correction terms are required in a rather large region of space.
Axon-mediated gene transfer of retinal ganglion cells in vivo.

Modification of the intracellular functions of mature neurons through specific gene transfer has many potential applications. Here we present a new methodology for the successful transfection of retinal ganglion cells by administration of plasmid at the cut end of the optic nerve, or at their intact axon terminals; the latter is significantly more efficient. Plasmids contained either the SV40 promoter linked to the luciferase gene, or the CMV or RSV promoter linked to the lacZ gene. Assays for both reporter genes demonstrated significant expression of exogenous DNA in the retina for at least 10 days after retrograde transport. Duration of expression was extended to 20 days or more (duration of the experiment) when plasmid DNA was condensed with poly(L-lysine). β-Galactosidase analysis revealed transfection of ganglion cells in high numbers. Such an approach for gene delivery to specific subpopulations of neurons might be useful in studies of molecular functions in vivo and as an experimental therapeutic strategy to extend survival and restore their function. © 1997 John Wiley & Sons, Inc. J Neurobiol 32: 111–122, 1997.
Marketing as a Pluralistic Discipline: The Forestalling of an Identity Crisis:

Most scholars of marketing have argued explicitly or implicitly in favor of unidimensional perspectives in the discipline. As a discipline matures, however, it must branch out into several identities lest repression of the natural manifestations of a field causes an identity crisis. In scratching an intellectual itch concerning some major debates about the identity of marketing, this article proposes a pluralistic perspective to clarify the nature and scope of marketing, and hence deter an identity crisis.
Plasma corticosterone of city and desert Curve-billed Thrashers, Toxostoma curvirostre, in response to stress-related peptide administration

We compared the activity and responsiveness of the hypothalamo-pituitary-adrenal (HPA) axis of an urban (Phoenix, Arizona) and desert population of a male songbird species (Curve-billed Thrasher, Toxostoma curvirostre), by measuring plasma corticosterone in response to acute administration of corticotropin-releasing factor, arginine vasotocin, or adrenocorticotropin hormone. Urban adult male thrashers showed greater responsiveness than desert birds to an injection of arginine vasotocin or adrenocorticotropin hormone, suggesting a population difference in pituitary and adrenal gland sensitivity. Plasma corticosterone in response to corticotropin-releasing factor injection did, however, not differ between populations. The differential corticosterone response to arginine vasotocin and corticotropin-releasing factor may reflect effects of chronic stress or habituation, which are known to favor arginine vasotocin over corticotropin-releasing factor sensitivity. Efficacy of HPA negative feedback by glucocorticoids was determined by measuring plasma corticosterone in response to acute administration of the synthetic glucocorticoid dexamethasone. This administration decreased plasma corticosterone similarly in urban and desert thrashers, suggesting that the negative feedback of glucocorticoids on the HPA axis in the two populations was equally effective. The higher sensitivity of urban than desert thrashers to adrenocorticotropin hormone and arginine vasotocin may result from up-regulation of the HPA axis in urban birds. This up-regulation may in turn make it easier for city birds to cope with urban environment-associated stressors.
pH Dependent Transfer of Nano-pores into Membrane of Cancer Cells to Induce Apoptosis

Proper balance of ions in intracellular and extracellular space is the key for normal cell functioning. Changes in the conductance of membranes for ions will lead to cell death. One of the main differences between normal and cancerous cells is the low extracellular pHe and the reverse pH gradient: intracellular pHi is higher than extracellular pHe. We report here pH-selective transfer of nano-pores to cancer cells for the dis-regulation of balance of monovalent cations to induce cell death at mildly acidic pHe as it is in most solid tumors. Our approach is based on the pH-sensitive fusion of cellular membrane with the liposomes containing gramicidin A forming cation-conductive β-helix in the membrane. Fusion is promoted only at low extracellular pH by the pH (Low) Insertion Peptide (pHLIP®) attached to the liposomes. Gramicidin channels inserted into the cancer cells open flux of protons into the cytoplasm and disrupt balance of other monovalent cations, which induces cell apoptosis.
Movement and Mobility as Essentials for Daily Living: Preface

The articles in this issue of Quest are “The Academy Papers,” which are based on invited presentations at the 2004 annual meeting of the American Academy of Kinesiology and Physical Education in Oak Brook, Illinois. The theme for this meeting was “Movement and Mobility: Essentials for Daily Living.” It is widely accepted that quality of life is in large part dependent on one’s capability to engage in coordinated movement in all aspects of daily life. Whether the daily task involves getting out of one’s bed and walking to the bathroom, keyboarding at a computer at work, or riding a bicycle as a means of transportation or exercise, movement and mobility serve as key factors in determining the level of success and independence one can achieve at home, work, or play. The goal of the Academy meeting was to establish the importance of movement and mobility for all people and its prevalence in daily living. It is from this perspective that the articles in this issue derive their purpose. The articles discuss research and professional practice issues that reflect the multidisciplinary nature of movement and mobility in our daily lives. The opening article provides an appropriate foundation for what follows. It is based on the keynote presentation by Wojtek Chodzko-Zajko of the University of Illinois, Urbana-Champaign, and founding editor of the Journal of Aging and Physical Activity. The article presents a broad overview of how efforts are being taken to address physical activity needs for senior citizens in the United States. Articles that follow discuss movement and mobility issues as they relate to various areas of research and professional interests for kinesiology and physical education. These include research perspectives as they relate to public health, self-efficacy beliefs, infant motor development, successful aging, motor skill learning, and various issues in motor control (Parkinson’s Disease, gait control, and artificial limb control). In addition, the implications for professional applications are considered for physical education, dance education, physical rehabilitation, and fitness/wellness programs. The article on motor skill learning by Timothy Lee and Laurie Wishart is based on the 2004 Vendien International Lecture by Timothy Lee, who is at McMaster University in Ontario, Canada. The final article presents the meeting’s capstone summation by Scott Kretchmar, professor of sport philosophy at Penn State University. Kretchmar presents a fascinating discussion in which he relates two metaphors, jigsaw puzzles and river banks, to illustrate the importance of interdisciplinary research as well as the need for cooperation, unity, and mutual appreciation by researchers from multiple disciplines who investigate common issues such as the one represented by the theme of this year’s Academy meeting.
An Algorithm for the Oversight of Field Trials in Economically Developing Countries

A risk-based proposal for regulating field trials—of any kind of organism—that is adaptable to any form of government regulation or institutional oversight
THz for space: The golden age

Over the past three decades interest in the unique spectral measurements offered by terahertz instruments operat-ing outside the Earth's atmosphere has grown enormously. Since the historic flight of Cosmos 669 in 1974, and the first THz telescope with cryo-cooled detectors operated on board Salyut 6 in 1978, satellite instruments have performed both direct detection and heterodyne spectroscopy measurements in the interstellar medium, in external galaxies, in the atmospheres of planets and comets and in the Earth's stratosphere. Seven-teen orbital instruments containing THz sensors or sources have either completed their mission objectives or are currently operational. They originate in Russia, Japan, Europe and the US and cover applications in astrophysics and cosmology; planetary and small solar system body science; and pollution, ozone and climate monitoring on the Earth. At least a dozen serious future mission proposals are under consideration, including new areas of meteorology, terrestrial planet finding and planetary radar spectroscopy. It is truly a golden age for THz space science and applications. This talk will review past, present and future space instruments carrying infrared, millimeter wave and terahertz components and their science objectives.
Abstract 3752: Nanoparticles delivery of a novel AKT/PDK1 inhibitor inhibits pancreatic cancer tumor growth

AKT (protein kinase B), a pleckstrin homology (PH) lipid binding domain and a serine/threonine kinase containing protein is a key component of the phophatidylinositol-3-kinase (PtdIns3-K) cell survival signaling pathway which is activated in pancreatic cancers. In this study, we describe the effects of a novel inhibitor of AKT/PDK1 (PH-427) that binds to the PH domain of AKT (K i = 2.67 ± 0.37 μM) and PDK1 (K i = 5.20 ± 0.45 μM) [1] thus preventing its binding to PtIns-(3,4,5)P 3 at the plasma membrane and subsequent activation of both kinases. PH-427 inhibits AKT/PDK1 activities at low micromolar concentrations in BxPC-3 (wt-KRAS) and not in MiaPaCa2 (mt-KRAS) human pancreatic cancer cell lines. Accordingly, we have shown that in vivo, PH-427 is poorly efficient in MiaPaCa2 xenografts as compared to BxPC-3 xenografts. In order to increase the potency and delivery of PH-427 to the tumor, we have encapsulated the compound (>10% of the compound) into (poly-d, l-lactide-co-glycolide) (PLGA) nanoparticles (PNP). We demonstrate that PH-427 incorporates well in the nanoparticles (PH-427-PNP) ( 3 ). In conclusion, PH-427 alone did not alter tumor growth in MiaPaCa-2-Luc but was able to reduce tumor growth significantly when encapsulated in PNP. Finally and interestingly, metastasis to the liver and other organs was also significantly inhibited by PH-427-PNP as compared to PNP or PH-427 alone. [1]. Meuillet EJ, Ihle N, Lemos R, Moses SA, Song Z, Zhang S, Mash EA, Powis G (2010). Mol Cancer Ther 9(3):706-717. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3752. doi:1538-7445.AM2012-3752
A vulnerability study of geographic routing in Underwater Acoustic Networks

Underwater Acoustic Networks (UANs) are utilized in many sensitive commercial, scientific and military applications. However, current network protocols have not been designed to defend against security attacks that can block or degrade network communication and performance. Geographic routing is an essential service used in UANs and current protocols are quite vulnerable. In this paper we call attention to unique factors of UANs that need to be considered when designing secure network protocols and study the vulnerabilities of geographic routing in UANs. We investigate the effects of location spoofing on a standard UAN geographic routing protocol, Depth-Based Routing (DBR), as a case study. We provide a preliminary spoofing attack that can stop network traffic from reaching its destination. Attack performance is given using detailed simulation analysis. Lastly, we improve our attack by using a placement scheme to sample positions in the deployment area in order to increase the attack effectiveness while meeting energy constraints. Our attack is tested on both static and mobile UANs.
Atyid shrimps (Decapoda: Atyidae) influence the spatial heterogeneity of algal communities over different scales in tropical montane streams, Puerto Rico

1. Atyid (Decapoda: Atyidae) shrimps influence the distribution of algal communities over different scales in tropical montane streams of Puerto Rico. Within pools of an atyid-dominated stream, atyid shrimps enhanced patchiness in algal communities along the depth gradient. Algal bands occurred in shallow pool margins where atyids did not forage (< 3 cm below water surface), with significantly greater standing crop, taxon richness, and structural complexity than deeper areas. In deeper water, atyids reduced small-scale patchiness in algal community composition and maintained a low-growing understorey turf dominated by sessile diatoms (Bacillariophyta) and, sometimes, closely cropped, filamentous blue-greens (Cyanophyta). 2. Among pools of the atyid-dominated stream, atyids interacted with light to determine algal patchiness between stream margins and deeper areas. In sunny pools, algal standing crop was 140-fold greater in pool margins than in deeper areas where atyids foraged. In shaded pools, however, standing crop in pool margins was only 5-fold greater than in deeper areas. Effects of light on algal standing crop were greater outside atyid foraging areas than within, indicating that shrimp grazing overrides the positive effects of light. 3. In contrast to the atyid-dominated stream, algal communities in an atyid-poor stream were characterized by a high biomass of loosely attached epipelic diatoms and no depth zonation. Interstream rock and shrimp transplant experiments indicated that atyids significantly reduced algal standing crop and altered community composition on rocks from atyid-poor streams within 24 h. Results support the hypothesis that atyid shrimps play a major role in determining observed interstream differences in algal communities.
Entropy-enthalpy compensation in ionic interactions probed in a zinc finger peptide.

Zinc(II) and cobalt(II) binding to a series of zinc finger peptides with different charged residue pairs across from one another in a β-sheet were examined. Previous studies revealed a narrow range of interaction free energies (<0.5 kcal/mol) between these residues. Here, isothermal titration calorimetry studies were performed, revealing a range of over 3 kcal/mol in relative binding enthalpies. Double mutant cycle analysis revealed a range of interaction enthalpies ranging from −3.1 to −3.4 kcal/mol for the Arg−Asp pair to −0.8 kcal/mol for the Lys−Glu pair. The large range of interaction enthalpies coupled with the small range of interaction free energies reveals substantial entropy−enthalpy compensation. The magnitudes of the effects are consistent with the formation of a structurally rigid Arg−Asp contact ion pair but less direct and more mobile interactions involving the other combinations.
A multi-objective variable-fidelity optimization method for genetic algorithms

A novel variable-fidelity optimization (VFO) scheme is presented for multi-objective genetic algorithms. The technique uses a low- and high-fidelity version of the objective function with a Kriging scaling model to interpolate between them. The Kriging model is constructed online through a fixed updating schedule. Results for three standard genetic algorithm test cases and a two-objective stiffened panel optimization problem are presented. For the stiffened panel problem, statistical analysis of four performance metrics are used to compare the Pareto fronts between the VFO method, full high-fidelity optimizer runs, and Pareto fronts developed by enumeration. The fixed updating approach is shown to reduce the number of high-fidelity calls significantly while approximating the Pareto front in an efficient manner.
Hedonic housing prices and the demand for clean air

This paper investigates the methodological problems associated with the use of housing market data to measure the willingness to pay for clean air. With the use of a hedonic housing price model and data for the Boston metropolitan area, quantitative estimates of the willingness to pay for air quality improvements are generated. Marginal air pollution damages (as revealed in the housing market) are found to increase with the level of air pollution and with household income. The results are relatively sensitive to the specification of the hedonic housing price equation, but insensitive to the specification of the air quality demand equation.
Unusual Knoevenagel condensations of 16a-substituted-16-methylene-17-keto-steroids

Abstract A Knoevenagel condensation between 3β-acetoxy-16-pyrrolidinylmethylenandrost-5-en-17-one ( 8c ) and an excess of malononitrile led unexpectedly to 3β-acetoxyandrost-5-eno-[17,16-c]-1′,6′-dicyanoaniline ( 12a ) as the major product and 3β-acetoxy-16-pyrrolidinylmethylen-17-dicyanomethylenandrost-5-ene ( 11a ) as the minor product. Knoevenagel reactions of other 16a-substituted-16-methylen-17-keto steroids were studied to evaluate the scope and mechanism of the reaction.
Coulomb scattering of dirac particles

Abstract The continuum Coulomb wave function in the Johnson and Deck form—a matrix operator acting on a plane wave spinor—is discussed. General relations for the elastic differential cross section, the asymmetry parameters, and the precession and nutation of polarization are developed. An expansion of the asymptotic wave function correct to third order in λ = αZ for all Born parameters ν = αZ β is obtained. This expansion involves a two parameter function T(θ, ν) which in turn may be expanded for small ν to give results previously obtained by Johnson, Weber, and Mullin. On the other hand, a large ν asymptotic expansion of T(θ, ν) valid for |2πν| > 1 permits a discussion of the non-relativistic limit. Both the small and large approximations substantially agree for |ν| ⋍ 1 2 . Consequently, these two approximations may be used to span the whole range of Born parameters. The asymptotic Born parameter approximation predicts markedly different scattering behavior for electrons and positrons. A striking feature is that functions pertaining to electron scattering are oscillatory in the scattering angle θ while the positron functions are not. In particular, the oscillations in the asymmetry parameter for electron scattering obtained numerically by Sherman are contained in the analytical approximate form. Also, the approach to the Rutherford cross section is different than that quoted by Mott and Massey.
The Arabidopsis thaliana ortholog of a purported maize cholinesterase gene encodes a GDSL-lipase

Acetylcholinesterase is an enzyme that is intimately associated with regulation of synaptic transmission in the cholinergic nervous system and in neuromuscular junctions of animals. However the presence of cholinesterase activity has been described also in non-metazoan organisms such as slime molds, fungi and plants. More recently, a gene purportedly encoding for acetylcholinesterase was cloned from maize. We have cloned the Arabidopsis thaliana homolog of the Zea mays gene, At3g26430, and studied its biochemical properties. Our results indicate that the protein encoded by the gene exhibited lipase activity with preference to long chain substrates but did not hydrolyze choline esters. The At3g26430 protein belongs to the SGNH clan of serine hydrolases, and more specifically to the GDS(L) lipase family.
Dynamic dysfunction in dihydrofolate reductase results from antifolate drug binding: modulation of dynamics within a structural state

Summary The arduous task of rationally designing small-molecule enzyme inhibitors is complicated by the inherent flexibility of the protein scaffold. To gain insight into the changes in dynamics associated with small-molecule-based inhibition, we have characterized, using NMR spectroscopy, Escherichia coli dihydrofolate reductase in complex with two drugs: methotrexate and trimethoprim. The complexes allowed the intrinsic dynamic effects of drug binding to be revealed within the context of the "closed" structural ensemble. Binding of both drugs results in an identical decoupling of global motion on the micro- to millisecond timescale. Consistent with a change in overall dynamic character, the drugs' perturbations to pico- to nanosecond backbone and side-chain methyl dynamics are also highly similar. These data show that the inhibitors simultaneously modulate slow concerted switching and fast motions at distal regions of dihydrofolate reductase, providing a dynamic link between the substrate binding site and distal loop residues known to affect catalysis.
Coupling Capillary Zone Electrophoresis with Electron Transfer Dissociation and Activated Ion Electron Transfer Dissociation for Top-Down Proteomics

Top-down proteomics offers the potential for full protein characterization, but many challenges remain for this approach, including efficient protein separations and effective fragmentation of intact proteins. Capillary zone electrophoresis (CZE) has shown great potential for separation of intact proteins, especially for differentially modified proteoforms of the same gene product. To date, however, CZE has been used only with collision-based fragmentation methods. Here we report the first implementation of electron transfer dissociation (ETD) with online CZE separations for top-down proteomics, analyzing a mixture of four standard proteins and a complex protein mixture from the Mycobacterium marinum bacterial secretome. Using a multipurpose dissociation cell on an Orbitrap Elite system, we demonstrate that CZE is fully compatible with ETD as well as higher energy collisional dissociation (HCD), and that the two complementary fragmentation methods can be used in tandem on the electrophoretic time scale fo...
Spectroscopic ellipsometry study of novel nanostructured transparent conducting oxide structures

Spectroscopic ellipsometry has been used to find the optical constants, including refractive index, extinction coefficient, thickness and volume fraction of nanostructured transparent conducting oxides including indium tin oxide (ITO) and indium zinc oxide (IZO). We observed sharp features in the ellipsometry data, with the spectral peaks and positions depending on the nanostructure dimensions and material. A superposition of Lorentzian oscillators and the effective medium approximation has been applied to determine the volume ratio of voids and nanopillars, thereby providing the effective optical constants.
Reprogramming of the SWI/SNF complex for co-activation or co-repression in prohibitin-mediated estrogen receptor regulation

The SWI/SNF complex participates as a co-activator in the transcriptional regulation of certain genes. Conversely, we and others have recently established that Brg1 and Brm, the central components of SWI/SNF, act instead as co-repressors for E2F-mediated transcriptional repression, and for the transcription of certain other promoters. We report here that Brg-1 and Brm can switch their mode of function at same promoter between activation and repression by ligand-directed differential coordination with BAF155, BAF170, HDAC1, p300 and prohibitin. This ligand and context-dependent reprogramming of the SWI/SNF complex allows it to differentially serve as either a co-repressor or a co-activator of transcription at the same promoter.
Abstract 628: A novel SND1-BRAF fusion confers resistance to the cMet inhibitor PF-04217903 in GTL16 cells

The hepatocyte growth factor receptor (HGFR/cMET) signaling pathway is a driver of tumorigenesis in a variety of tumor types, and a number of agents targeting cMet, including PF-04217903, are under investigation in clinical trials. Tumor types exhibiting an amplified MET gene locus such as gastric, NSCLC, or esophageal cancers are of particular interest for clinical development of c-Met inhibitors. While inhibition of other receptor tyrosine kinases (RTKs) such as ErbB2, EGFR, or KIT have proven to be effective treatments for cancer patients, most tumors become refractory to respective targeted therapies due to the emergence of resistance mechanisms associated with drug targets or upregulation of compensatory pathways. To identify potential mechanisms of resistance to c-Met inhibitors, a gastric carcinoma line (GTL16) was placed under selective pressure by culturing cells in increasing concentrations of PF-0421703 in vitro and resistant clones were isolated. Resistant clones were characterized for changes in signaling, gene expression, and DNA copy number variation as compared to parental GTL16 cells. These studies resulted in the identification of genomic rearrangements at the 7q32 and 7q34 loci which produce a novel SND1-BRAF fusion protein in resistant cells. The fusion protein includes the BRAF kinase domain and is both constitutively active and overexpressed relative to parent cells as determined by gene expression array, immunoblot, and mass spectrometry. In addition, phosphoproteomic analyses demonstrated enrichment of phosphopeptides associated with the MAPK pathway signaling proteins relative to wildtype cells. Cells expressing the fusion protein exhibited resistance to multiple c-Met inhibitors whereas treatment of resistant cells with a combination of c-Met and BRAF inhibitors or a MEK inhibitor (PD325901) reversed the resistance phenotype by reestablishing inhibition of MAPK signaling and restoring growth inhibition. Together, these data provide an unique example of a mechanism where MAPK activation, through BRAF amplification/rearrangement, confers resistance to a RTK/cMET inhibitor. Furthermore, the results suggest the importance of MEK/ERK signaling downstream of c-Met and that a potential combination strategy for c-Met inhibitors with BRAF or MEK inhibitors could be employed to delay onset or circumvent potential resistance mechanisms. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 628.
Rabbit esophagus metabolizes arachidonic acid predominantly via a lipoxygenase pathway.

Abstract Eicosanoids modulate the response of gastrointestinal mucosa to noxious stimuli. Though these compounds have been extensively investigated in the stomach, their role in the esophagus has received less attention. Thus, the metabolism of 14 C-arachidonic acid by homogenates of rabbit esophageal mucosa was investigated. The major metabolites formed and separated by TLC and HPLC had the chromatographic characteristics of (percent conversion follows each metabolite) 6-keto-prostaglandin F 1α (3.80 ± 1.15), prostaglandin F 2α (2.05 ± 0.37), prostaglandin E 2 (5.92 ± 1.65) and 12-hydroxyeicosatetraenoic acid (26.03 ± 4.58). Indomethacin, a cyclooxygenase inhibitor, caused a significant decrease in prostaglandin formation without affecting 12-hydroxyeicosatetraenoic acid. BW755C, a combined cyclooxygenase-lipoxygenase inhibitor, dramatically decreased formation of all metabolites. It is concluded that esophageal mucosa metabolizes arachidonic acid primarily to a lipoxygenase derived product. This is the most abundantly produced eicosanoid yet described in the gastrointestinal tract. The importance of this compound to esophageal function is unknown but its presence suggests that future studies of eicosanoids in the esophagus should focus on lipoxygenase metabolites.
Intermediate P* from soluble methane monooxygenase contains a diferrous cluster.

During a single turnover of the hydroxylase component (MMOH) of soluble methane monooxygenase from Methylosinus trichosporium OB3b, several discrete intermediates are formed. The diiron cluster of MMOH is first reduced to the FeIIFeII state (Hred). O2 binds rapidly at a site away from the cluster to form the FeIIFeII intermediate O, which converts to an FeIIIFeIII-peroxo intermediate P and finally to the FeIVFeIV intermediate Q. Q binds and reacts with methane to yield methanol and water. The rate constants for these steps are increased by a regulatory protein, MMOB. Previously reported transient kinetic studies have suggested that an intermediate P* forms between O and P in which the g = 16 EPR signal characteristic of the reduced diiron cluster of Hred and O is lost. This was interpreted as signaling oxidation of the cluster, but a low level of accumulation of P* prevented further characterization. In this study, three methods for directly detecting and trapping P* are applied together to allow its spec...
Water exchange between canals and surrounding aquifer and wetlands in the Southern Everglades, USA

Abstract Continuous volumetric discharge data was collected at six acoustic velocity meters (AVMs) installed in two canals along the eastern boundary of Everglades National Park (ENP) in Florida, USA. Discharge data from these six sites, and from two others monitored by state and federal government agencies, were used to compute the rate of water exchange ( Q g ) between six canal reaches and their surroundings (the unconfined Biscayne Aquifer and its overlying wetlands). Net water exchange ( Q g ) for the two northernmost canal reaches corresponded to groundwater, but further south in the study area Q g included a surface water component. While canal L-31W was built to supply water to ENP, data show that its primary (though unintended) function during the study period was redistribution of water from north to south within ENP. This “hydrologic short-circuiting” (where water flowed south in L-31W rather than in wetlands) is problematic for ecosystem restoration efforts. A similar short-circuiting operates on a larger spatial scale over the entire basin of the larger C-111 canal, the main flood control canal in the area. While this hydrologic regime does offer flood control benefits, changes in water management infrastructure and operations are needed to restore more natural spatial and temporal patterns of flow through wetlands in the area. Four of the AVM stations were located close to large water control structures on the canals. Agreement was generally good though slightly non-linear between daily average discharge ( Q ) values based on AVM data and those determined using hydraulic rating equations at nearby flow control structures. The AVMs used in this study required significant maintenance but provided sound data on discharge. They provided a good check on hydraulic rating equations at flow control structures, quantified rates of water leakage around and/or through these structures, allowed discharge measurements where there are no structures, and allowed calculation of rates of water exchange with canals.
Clinical characterization of idiopathic intracranial hypertension at the Detroit Medical Center.

Abstract Background : Idiopathic intracranial hypertension (IIH), also known as pseudotumor cerebri (PTC), is a condition characterized by increased intracranial pressure without clinical, laboratory or radiologic evidence of an intracranial space-occupying lesion, meningeal inflammation or venous outflow obstruction. Previous population-based studies evaluated the presenting clinical features of IIH in North-Eastern Libya, Iowa, Louisiana, Minnesota, Northern Ireland, Israel and Western Turkey. However, we report the demographic patterns of a metropolitan North American city. Methods : We performed a retrospective study of all patients with an initial IIH diagnosis and follow-up at the Detroit Medical Center (DMC), Michigan from 1985 to 2002. Medical records of 174 patients were reviewed, with 77 patients fitting the diagnostic criteria. Results : Seventy-seven patients, 71 females (92.2%) and 6 males (7.8%) were identified. Age ranged from 10 to 50 years, with a mean of 34 years. Fifty patients (65%) were African–American and 24 patients (31%) were Caucasian. The most common presentation was isolated headache (28.6%). Nineteen patients (24.7%) were asymptomatic. Obesity was described in 65 of 74 patients (87.8%) evaluated for body dimensions. Conclusions : We report an increased number of asymptomatic patients after routine ophthalmic examination. Obese females in metropolitan Detroit would benefit from routine eye evaluations to avoid potential visual loss related to papilledema.