cssi/SciSciGPT-SciSciNet huggingface dataset:
Formation of plagioclase-bearing peridotite and plagioclase-bearing wehrlite and gabbro suite through reactive crystallization: an experimental study

Plagioclase-bearing peridotites are commonly associated with gabbroic rocks sampled around the Moho Transition Zone. Based on mineral chemistry, texture, and spatial relations, the formation of plagioclase-bearing peridotites has been attributed to impregnation of basalt into residual peridotites. We conducted reactive dissolution and crystallization experiments to test this hypothesis by reacting a primitive mid-ocean ridge basalt with a melt-impregnated lherzolite at 1,300 °C and 1 GPa and then cooling to 1,050 °C as pressure decreased to 0.7 GPa. Crystallization during cooling produced lithologic sequences of gabbro–wehrlite or gabbro–wehrlite–peridotite, depending on reaction time. Wehrlitic and peridotitic sections contain significant amounts of plagioclase interstitial to olivine and clinopyroxene and plagioclase compositions are spatially homogeneous. Clinopyroxene in the wehrlite–peridotite section is reprecipitated from the melt and exhibits poikilitic texture with small rounded olivine chadacrysts. Mineral composition in olivine and clinopyroxene varies spatially, both at the scale of the sample and within individual grains. Olivine grains that crystallized close to the melt–peridotite interface are enriched in iron due to their proximity to the basaltic melt reservoir. Consistent with many field studies, we observed gradual spatial variation in olivine and clinopyroxene composition across a lithologically sharp boundary between the gabbro and wehrlite–peridotite. Plagioclase compositions show no obvious dependence on distance from the melt–rock interface and were precipitated from late-stage trapped melts. Compositional trends of olivine, pyroxene, and plagioclase are consistent with previous experimental results and natural observations of the Moho Transition Zone. Different lithological sequences form based primarily on the melt–rock ratio, composition of the melt and host peridotite, and thermochemical conditions, but are expected to grade from gabbro to wehrlite or troctolite to peridotite. Plagioclase-bearing peridotite represents the low melt–rock ratio end member where pyroxene is only partially replaced by olivine and melt, whereas dunite is expected to form where melts overwhelm and consume all other phases. This study confirms that under nominally anhydrous conditions, the gabbro–wehrlite–plagioclase-peridotite sequence can be formed by reaction between basalt and lherzolite and subsequent crystallization at intermediate to low pressures. Melt–rock reaction is a fundamental process in the formation of new crust at the shallowest part of the melting column where pyroxene-undersaturated melts percolate through depleted peridotite.
Base-group specificity at the primary recognition site of ribonuclease T1 for minimal RNA substrates

Abstract Kinetic studies on the RNase T 1 -catalyzed transesterification of 12 dinucleoside monophosphates, N p 1 N 2 (N 1 = A, C, and U; N 2 = A, C, G, and U) at pH 5, 25 °C, and 0.2 m ionic strength, revealed that the catalytic efficiency ( k cat K m ) for GpN substrates (H. L. Osterman, and F. G. Walz, Jr., 1978, Biochemistry , 17 , 4142) was ~10 6 -fold greater than corresponding ApNs and at least 10 8 -fold greater than corresponding CpNs and UpNs. The catalytic activity with ApN substrates survives phenol extraction which indicates (along with other criteria) that it is intrinsic to RNase T 1 and is not due to trace contamination by other nucleases. Circumstantial evidence is presented which suggests that homologous GpN and ApN substrates bind productively at different sites on the enzyme. The results of steady-state kinetic studies of RNase T 1 with IpNs (N = C and U) were compared with those for GpNs and indicated that the primary effect of the guanine 2-NH 2 group is to enhance substrate binding at the primary recognition site by ~2.6 kcal/mol. Values of ( k cat K m ) showed the order NpC > NpU (N = A, G, and I) which evidences the existence of a subsite for the leaving nucleoside group that prefers cytidine: interactions at this subsite are reflected in k cat rather than K m .
Control of corrosion in coal liquefaction plant fractionation columns

Severe corrosion has been encountered in fractionation columns at the solvent refined coal (SRC) pilot plants in Fort Lewis, Washington, and Wilsonville, Alabama, as well as at the H-Coal Pilot plant in Catlettsburg, Kentucky, and the Exxon Donor Solvent Pilot Plant in Baytown, Texas. At the SRC plants, corrosion rates as high as 25 mm per year (one inch per year) on carbon steel and 6.4 mm per year (250 mils per year) on type 18-8 stainless steels have been measured in the portions of the columns operating at 220 to 260 °C (428 to 500 °F). Less severe corrosion is generally found at temperatures outside this range. The severity of this corrosion is related to the chlorine content of the coal. Studies of this corrosion problem by Oak Ridge National Laboratory (ORNL) personnel included exposure of corrosion coupons in the pilot plant columns, analyses of liquids collected at the pilot plants, and performance of laboratory experiments. As a result of this work, we can specify alloys with adequate corrosion resistance for construction of fractionation columns, identify the chlorine-bearing compounds, and propose chlorine transport and corrosion mechanisms. Identification of the corrodent and its mechanisms enables us to suggest process changes to remove the corrodent and thereby to control the corrosion.
The effect of growth hormone treatment in idiopathic short stature with SHOX mutation • 496

The effect of growth hormone treatment in idiopathic short stature with SHOX mutation • 496
Investigation of the Relaxation of Persistent Current in Superconducting Closed Loops Made Out of YBCO Coated Conductors

Coated conductors allow the fabrication of closed superconducting loops of arbitrary size. Various mechanisms can play a role in the decay of a persistent current in one such loop and in an assembly of multiple loops magnetically coupled with each other. We report recent experimental results on the relaxation rate of the persistent current in an assembly of closed superconducting loops made out of the currently manufactured coated conductors. One of the main goals of this study is to find the effective ways to control the relaxation rate so as to make it small enough to enable such high temperature persistent magnets to be considered as potential alternatives for energy storage, MRI magnets, and magnetic levitation applications. Here we report the effect of appropriately modified current sweep reversal method on the relaxation rate.
Digital holographic data storage in a high-performance photorefractive polymer composite.

Binary information in the form of a 256 × 256 pixel array has been stored holographically within a polymeric photorefractive composite of 130-µm thickness. Devices used consisted of 55-wt. % organic chromophore 1-(2′-ethylhexyloxy)-2,5-dimethyl-4-(4″nitrophenylazo) benzene and up to 11.2-wt. % 2,4,7-trinitro-9-fluorenone (TNF) dispersed within a poly(N-vinyl carbazole) matrix. In a degenerate four-wave mixing arrangement, the refractive-index modulation and speed were 10-3 and 200 ms, respectively. The high TNF concentration leads to short digital hologram recording times of 2 s without detriment in optical quality. Although not yet optimized, a figure of merit, M#, for holographic storage in this composite has been measured to be 0.017, and this is estimated to reach 0.18 in a revised experimental geometry.
Elastically Equivalent Potentials

We define a nondenumerably infinite class of two-body potentials that give $T$ matrix elements that are identical on the energy shell but are different off shell. The existence of this class is shown to be related to a nonuniqueness in the off-shell continuation of the Schr\"odinger equation. A relation for the difference between off-shell elements of $T$ matrices that are equal on shell is given in a form that is convenient for the systematic study of off-shell effects in systems of more than two nucleons. In particular, these relations allow one to investigate subclasses of elastically equivalent interaction potentials that satisfy restrictions such as finite range. The possibility that elastically equivalent interactions have different off-shell symmetry properties is discussed, and some observations concerning the use and interpretation of elastically equivalent potentials in many-body calculations are presented.
The interaction of α2 macroglobulin with trypsin releases a soluble glycopeptide

Abstract When human α 2 macroglobulin (α 2 M) or its asialo-[ 3 H]galactose derivative reacts with trypsin, a glycopeptide of molecular weight 3500–4000 is released from the α 2 M. The glycopeptide was purified on Biogel P-4 columns and its amino acid and carbohydrate composition were determined. The oligosaccharide contains sialic acid, galactose, mannose and GlcNAc in a ratio of 1.0:0.73:3.85:2.85 and is apparently attached to protein in a GlcNAc→asparagine linkage.
Simulation hierarchical manufacturing control

This paper addresses a new unified framework for simulation that includes both physical and decision making processes of manufacturing systems. The developed methodology uses a state-space representation based simulation-modeling formalism along with object oriented software design. The modularity of user's conceptual model in terms of physical and decision making entities with their programmed and non-programmed decisions and the capability of modeling these entities and processes at different hierarchical levels can vastly improves simulation's role as a decision making tool.
NICU Treatment Team Function and Its Effect on Parental Stress

Through a literature review this paper explores the operation of the NICU treatment team. It examines how the team's smooth functioning and family focus can effectively help the family cope with the stresses encountered in the birth of an infant with a critical medical condition. The paper progresses through a discussion of the following areas: (a) parental reactions to the birth of an infant with a chronic condition, and the causes of stress on the family unit, (b) the NICU environment and its part in parental stress, (c) stress factors for NICU treatment team members, (d) hospital culture and reducing stress through teamwork, (e) the role of the occupational therapist as a collaborator in the neonatal intensive care unit, and (f) reducing parental stress through the teamwork of family-centered care. The author concludes that a smoothly functioning treatment team, incorporating the principles of family-centered care, is essential to reducing parental stress and empowering the parent to take an active par...
Correlated noise propagation in wavefront reconstruction from phase differences

The propagation of noise in wavefront reconstructors has been investigated for the case of spatially uncorrelated noise. In some situations, the detection noise may be spatially correlated. Here we investigate the noise propagation for the case of spatially correlated noise. We compute the error in wavefront reconstruction as a function of correlation length and noise strength. Results are presented describing noise propagation in a non-iterative complex wavefront reconstructor.© (1994) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Transfer of inflammatory cytokines across the placenta.

Objective The purpose of this study was to determine whether the placental transfer of interleukin (IL)-1alpha, IL-6, and tumor necrosis factor-alpha (TNF-alpha) occurs. Methods Four normal-term placentas were perfused for maternal-fetal transfer of the cytokines, 2 placentas for fetal-maternal transfer, and 4 additional placentas were used for an endogenous control. The ex vivo isolated cotyledon human placental perfusion model was used. The reference compound antipyrine was used to determine the transport fraction and clearance index of the cytokines. The cytokines were added to either the maternal or fetal circulations, and samples were collected for 1 hour in a constant-flow open circulation. Cytokine levels were compared between the study and control placentas. Concentrations of the cytokines were measured by sandwich enzyme immunoassay. Results The clearance index for the maternal-fetal transfer of IL-1alpha and TNF-alpha was 0.001, suggesting minimal transfer to the fetal circulation. The clearance index for IL-6 was 0.30, indicating transfer to the fetal circulation. When the cytokines were added to the fetal circulation, the clearance index for IL-1alpha was 0.001, again indicating minimal transfer. The clearance index for TNF-alpha in the fetal-maternal study was not determined. IL-6 had a clearance index of 0.23, which was similar to that observed with maternal-fetal transfer. IL-6 concentrations in the study placentas were higher than the concentrations found in the controls. Conclusion There appears to be bidirectional transfer of IL-6 in the healthy-term human placental perfusion model. Level of evidence II-2
Extended quantitative structure–activity relationships for 80 aromatic and heterocyclic amines: Structural, electronic, and hydropathic factors affecting mutagenic potency

The mutagenic/carcinogenic heterocyclic amines formed during the cooking of protein foods have been determined to be probable or possible human carcinogens. As part of a comprehensive study of the food mutagens, our laboratory has produced a series of quantitative structure–activity relationships (QSARs) of aromatic and heterocyclic amines, to attempt to elucidate the mechanisms of mutagenesis/carcinogenesis. Amines are genotoxically active only after activation by a series of reactions converting the parent compound to an electrophilic derivative, which is postulated to be a nitrenium ion that covalently binds to and damages DNA. An important agent in this conversion is cytochrome P450. In this report we develop a QSAR for 80 amines of diverse structure and a range of 10 orders of magnitude in mutagenic potency. New structural factors and quantum chemical ab initio and Huckel calculations are included. The results are interpreted to show that a main determinant of mutagenic potency is the extent of the aromatic π-electron system. Small contributions are made by both the dipole moment and the calculated stability of the nitrenium ion. Multiple linear regression models account for nearly two-thirds of the variance in potency, leaving room for additional unknown factors. The role of cytochrome P450 1A in amine toxification is supported, and further theoretical and experimental research on its reaction mechanisms and modeling of its active site are proposed. Environ. Mol. Mutagen. 38:268–291, 2001. Published 2001 Wiley-Liss, Inc.
CdZnTe and CdTe detector arrays for hard X-ray and gamma-ray astronomy

Abstract A variety of CdZnTe and CdTe detector arrays were fabricated at NASA/GSFC for use in hard X-ray and gamma-ray astronomy. Mosaic, pixel, and 3-D position-sensitive detector arrays were built to demonstrate the capabilities for high-resolution imaging and spectroscopy for 10 to 2 MeV. This paper will summarize the different arrays and their applications for instruments being developed at NASA/GSFC. Specific topics to be addressed include materials characterization, fabrication of detectors, ASIC readout electronics, and imaging and spectroscopy tests.
Shape factors for airborne particles.

Shape factors for dry aerosol particles generated from 1% solutions by weight of sodium chloride, uranine, or combinations of these two compounds were measured. A factor was obtained for each aerosol, relating particle projected area diameter to aerodynamic diameter, mass, and resistance to viscous flow. The density of dry uranine aerosol particles was calculated to be 1.51 ± 0.12 gm/cm3, or essentially the same as the material's bulk density.
Centrifugal and Centripetal Forces in Radical New Product Development Under Time Pressure

Organizations must be ambidextrous to successfully develop new products—they must act creatively as well as collectively. However, how to do this is not clear. The author analyzes this problem and reviews the literature in terms of two opposing forces: the first increases the quantity and quality of ideas, information, and knowledge available for creative action while the second integrates these things into collective action. The author then models these forces to explain how the coexistence of contradictory structural elements and processes increases the probability of successful development.
The Herschel mission

Abstract The Herschel space observatory, a cornerstone mission of the European Space Agency, with a Principal-Investigator-provided science payload, and contributions from the US National Aeronautics and Space Administration, is designed to explore the far-infrared and submillimeter spectral range with a powerful set of astronomical instruments built by multinational consortia of scientists and engineers. Herschel is expected to be launched in the spring of 2007. It will house a 3.5-m passively cooled telescope and three instruments operating in the wavelength range from 60 to 650 μm. The photodetector array camera and spectrometer will be capable of imaging photometry and imaging-line-spectroscopy in the 60–210 μm regime with a spectral resolution of ∼175 km s−1, corresponding to a spectral resolving power R∼1500. The spectral and photometric imaging receiver will operate in the 200–650 μm range, to map large areas of the sky. It will also carry out low resolution Fourier transform spectroscopy, whose resolution can be varied at least over the range of 1–0.4 cm−1, corresponding to R∼19 to 48 at 520 μm, but with a goal of increasing this range from 2 to 0.04 cm−1. The heterodyne instrument for the far-infrared will provide very high spectral resolving power up to R∼3×106 in the spectral frequency band from ∼480 to 1910 GHz (625–158 μm). This article describes these instruments and the astronomical problems they are expected to address.
IUE Observations of Circumstellar Emission from the Late Type Variable R Aquarii (M7 + pec)

The IUE observations of R Aqr (M7 + pec) obtained in low dispersion are discussed with particular reference to circumstellar emission. Strong permitted, semiforbidden, and forbidden emission lines are seen, superimposed on a bright ultraviolet continuum. It is deduced that the strong emission line spectrum that involves C III, C IV, Si III, (0 II) and (0 III) probably arises from a dense compact nebula the size of which is comparable to the orbital radius of the binary system of which R Aqr is the primary star. The low excitation emission lines of Fe II, Mg II, 0 I, and Si II probably a white dwarf, comparable to or somewhat brighter than the Sun, since such a star can produce enough ionizing photons to excite the continuum and emission line spectrum and yet be sufficiently faint as to escape detection by direct observation. The UV continuum is attributed to Balmer recombination from the dense nebula and not to blackbody emission from the hot companion.
A new niche for Notch on Deltex

The structure of the Deltex tandem WWE repeats reported by Barrick and colleagues in this issue of Structure reveals an intimate interface between the repeats, which together combine to create a binding site for the ankyrin repeat domain of Notch.
Mask roughness induced LER control and mitigation: aberrations sensitivity study and alternate illumination scheme

Here we conduct a mask-roughness-induced line-edge-roughness (LER) aberrations sensitivity study both as a random distribution amongst the first 16 Fringe Zernikes (for overall aberration levels of 0.25, 0.50, and 0.75nm rms) as well as an individual aberrations sensitivity matrix over the first 37 Fringe Zernikes. Full 2D aerial image modeling for an imaging system with NA = 0.32 was done for both the 22-nm and 16-nm half-pitch nodes on a rough mask with a replicated surface roughness (RSR) of 100 pm and a correlation length of 32 nm at the nominal extreme-ultraviolet lithography (EUVL) wavelength of 13.5nm. As the ideal RSR value for commercialization of EUVL is 50 pm and under, and furthermore as has been shown elsewhere, a correlation length of 32 nm of roughness on the mask sits on the peak LER value for an NA = 0.32 imaging optic, these mask roughness values and consequently the aberration sensitivity study presented here, represent a worst-case scenario. The illumination conditions were chosen based on the possible candidates for the 22-nm and 16-nm half-pitch nodes, respectively. In the 22-nm case, a disk illumination setting of σ = 0.50 was used, and for the 16-nm case, crosspole illumination with σ = 0.10 at an optimum offset of dx = 0 and dy = .67 in sigma space. In examining how to mitigate mask roughness induced LER, we considered an alternate illumination scheme whereby a traditional dipole's angular spectrum is extended in the direction parallel to the line-and-space mask absorber pattern to represent a "strip". While this illumination surprisingly provides minimal improvement to the LER as compared to several alternate illumination schemes, the overall imaging quality in terms of image-log-slope (ILS) and contrast is improved.
Dynamic motion of paxillin on actin filaments in living endothelial cells

Our three-dimensional (3-D) images showed that paxillin co-localized on actin filaments as fibrous structures, as well as clusters, in endothelial cells (ECs). In living ECs under flow condition, we monitored concurrently the intracellular dynamics of DsRed2-paxillin and GFP-actin by time-lapse video recording and dual-color fluorescence imaging. The results showed that the dynamic motion of paxillin as fibrous structures was associated with actin filaments, but not with microtubules. Our findings suggest that the actin network plays an important role not only in the assembly/disassembly of paxillin at focal adhesions, but also as a track for the intracellular transport of paxillin, which is involved in signaling pathway.
The role of class II molecules in Mls 1a recognition by CD4+ T cells is independent of the CD4 molecule.

Abstract The interpretation of previous antibody inhibition and cell depletion experiments was that major histocompatibility complex (MHC) class II molecules are involved in presentation of Mls molecules to T cell receptors. However, a possible conclusion of several subsequent studies was that T cell receptors may in fact recognize Mls molecules in a class II-unassociated manner. We considered that if this interpretation of the relevant data was correct, the earlier demonstrated role of MHC class II molecules on Mls 1 a antigen presenting cells in the response of CD4 + T cells might be only to serve as a ligand for the CD4 molecule on the responder cells. To test the possibility that the inhibition of the anti-Mls 1 a response by anti-class II antibodies solely reflected such a CD4 class II molecular interaction we derived CD4 - variants of two independent T cell receptor Vβ6-expressing, Mls 1 a -responsive T hybrid clones. Since preliminary experiments to screen for responsiveness revealed that the CD4 - variants of both T hybrid clones retained responsiveness to Mls 1 a and the variants of one that was also responsive to staphylococcal enterotoxin B retained that responsiveness we concluded that there is no qualitative dependency of the responses of Vβ6 T cells to these two superantigens on a CD4-mediated activity. More importantly, the responses of the CD4 - variants of the two T hybrid clones to MIs 1 a retain the same susceptibility to inhibition by antibodies to MHC class II molecules exhibited by the parental T hybrids. These results indicate that the blocking of responses of CD4 + T cells to Mls 1 a by both anti-H-2A and anti-H-2E antibodies is not due only to disruption of interactions between CD4 and H-2A or H2E molecules. The data are thus consistent with the class II molecule-dependent models of Mls 1 a presentation to the T cell receptor which are discussed in the light of recent findings on the biochemical nature of the Mls 1 a molecule.
Influence of a New Monofilament Polyester Mesh on Inflammation and Matrix Remodeling

ABSTRACTSynthetic mesh is widely used for hernia repairs, but mesh-induced chronic inflammatory responses may lead to postoperative complications. We previously showed an elevated response to multifilament polyester (PE) versus monofilament polypropylene (PP) and polytetrafluoroethylene (PTFE) meshes, but it is unclear whether this discrepancy is due to the differences in chemical composition or filament structure. This study compares the influence of a newly available monofilament PE mesh to that of multifilament PE, monofilament PP, and monofilament PTFE on the expression of genes important in inflammation and extracellular matrix remodeling in a rat model. Full thickness abdominal wall defects were corrected with onlay repair or suture repair with no mesh. Explants were harvested 7 or 90 days after repair and divided for histology and mRNA analyses using real-time quantitative polymerase chain reaction arrays to profile expression at the tissue-mesh interface. Monofilament PE elicited a reduced foreign...
The Impact of Time‐Served and Regime on Prisoners' Anticipation of Crime: Female Prisonisation Effects

To examine the extent of time-served and regime on incarcerated females, 304 inmates were surveyed about prior lifestyles, violent orientations, and future anticipations of future crime. Results show that women who led a non-violent lifestyle prior to incarceration might, once released, commit crimes of violence largely due to prison experiences through a prisonisation process. A conclusion arising from this finding is that short prison sentences can be as effective a punishment as long prison sentences with less future options toward acts of criminality. Some implications of this finding are that organisational membership changes attitudes and that female prisonisation is as salient among female inmates as it is among male inmates. A longitudinal study should be conducted on released female offenders and recidivism.
Polygonal Surface Advection applied to Strange Attractors

Strange attractors of 3D vector field flows sometimes have a fractal geometric structure in one dimension, and smooth surface behavior in the other two. General flow visualization methods show the flow dynamics well, but not the fractal structure. Here we approximate the attractor by polygonal surfaces, which reveal the fractal geometry. We start with a polygonal approximation which neglects the fractal dimension, and then deform it by the flow to create multiple sheets of the fractal structure. We use adaptive subdivision, mesh decimation, and retiling methods to preserve the quality of the polygonal surface in the face of extreme stretching, bending, and creasing caused by the flow. A GPU implementation provides efficient visualization, which we also apply to other turbulent flows.
Reference measurements of hydrogen's dielectric permittivity

We used a quasi-spherical cavity resonator to measure the relative dielectric permittivity e r of H2 at frequencies from 2.4 to 7.3 GHz, at pressures up to 6.5 MPa, and at the temperatures 273 K and 293 K. The resonator was calibrated using auxiliary measurements of e r(p, T) for helium together with the accurate ab initio values of helium's dielectric permittivity. The measurements determine accurate values of hydrogen's molecular electric polarizability and its temperature dependence. At 273 K, we obtained = (8.9568 ± 0.0008) × 10−41 F m2 (all uncertainties reported here are one standard uncertainty), which agrees with the value (8.9566 ± 0.0026) × 10−41 F m2 that was obtained by combining Rychlewski's ab initio calculations with estimates of rotational level populations. Our results yield the temperature dependence = × (1.1 ± 0.3) × 10−5 K−1, which agrees with the calculated value × 1.0 × 10−5 K−1. Our data also determine hydrogen's second dielectric virial coefficient, = (0.03 ± 0.05) cm3 mol−1, a pro...
Lisp extensions for multiprocessing

Extensions to Common Lisp for concurrent computation on multiprocessors are discussed. Functions for process creation, communication, and synchronization are described. Process objects create multiple threads of control. Processes are lightweight so that programmers can use them to take advantage of fine-grained parallelism. Communication and synchronization are managed with mailboxes. Signals allow processes to communicate using asynchronous interrupts. These constructs are used to implement several higher-level multiprocessing abstractions. These include structured processes, a parallel tree search, and dataflow computation. >
OrthoParaMap: Distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies

In eukaryotic genomes, most genes are members of gene families. When comparing genes from two species, therefore, most genes in one species will be homologous to multiple genes in the second. This often makes it difficult to distinguish orthologs (separated through speciation) from paralogs (separated by other types of gene duplication). Combining phylogenetic relationships and genomic position in both genomes helps to distinguish between these scenarios. This kind of comparison can also help to describe how gene families have evolved within a single genome that has undergone polyploidy or other large-scale duplications, as in the case of Arabidopsis thaliana – and probably most plant genomes. We describe a suite of programs called OrthoParaMap (OPM) that makes genomic comparisons, identifies syntenic regions, determines whether sets of genes in a gene family are related through speciation or internal chromosomal duplications, maps this information onto phylogenetic trees, and infers internal nodes within the phylogenetic tree that may represent local – as opposed to speciation or segmental – duplication. We describe the application of the software using three examples: the melanoma-associated antigen (MAGE) gene family on the X chromosomes of mouse and human; the 20S proteasome subunit gene family in Arabidopsis, and the major latex protein gene family in Arabidopsis. OPM combines comparative genomic positional information and phylogenetic reconstructions to identify which gene duplications are likely to have arisen through internal genomic duplications (such as polyploidy), through speciation, or through local duplications (such as unequal crossing-over). The software is freely available at http://www.tc.umn.edu/~cann0010/ .
Homogeneous charge compression ignition engine operating on synthesis gas

Abstract Mixtures of hydrogen and carbon monoxide were used to simulate the fuel component of synthesis gas and operate a single cylinder engine in homogeneous charge compression ignition (HCCI) mode. The engine was originally an air-cooled direct injection (DI) compression ignition (CI) engine. The original diesel fuel injection system was removed and a port fuel injection (PFI) system with intake air heating was added. The engine speed was maintained at a constant 1800 RPM. Three synthesis gas fuel compositions were tested, which comprised of 100% H 2 , 75/25 H 2 /CO ratio, and 50/50 H 2 / CO ratio, by volume. These compositions were investigated at an equivalence ratio (EQR) of 0.26 and 0.30. In-cylinder pressure and H 2 /CO emissions measurements were made at all conditions. To achieve peak indicated mean effective pressure (IMEP) at a given equivalence ratio, the intake air temperature had to be increased with increasing CO fraction in the synthesis gas mixture. For the EQR = 0.26 conditions, the intake air temperature required for best IMEP was 78 °C, 84 °C, and 98 °C, for 100% H 2 , 75/25 H 2 /CO ratio, and 50/50 H 2 /CO ratio, respectively. For the EQR = 0.30 conditions, the intake air temperature requirements were 62 °C, 71 °C, and 81 °C, for the same respective H 2 /CO proportions. The peak in-cylinder temperatures for all conditions tested ranged from roughly 1200 K–1500 K depending on intake air temperature, mixture concentration, and fuel composition. The combustion event was short, with the rapid burn angle ranging from 9.5 CAD to 11.5 CAD for all conditions tested, and the synthesis gas mixture composition did not change this significantly. The combustion efficiency was between 83% and 88% for the peak IMEP conditions tested.
Ultrastructural effects of estrogen replacement on postmenopausal endometrium

Endometrial adenocarcinoma occurs almost exclusively in postmenopausal women, and excessive or unopposed estrogen stimulation is suspect as a causative factor in its pathogenesis. Furthermore, the incidence of endometrial adenocarcinoma has increased in women undergoing estrogen replacement therapy. In the present study, the cellular response of premenopausal and postmenopausal endometrium to estrogenic stimulation was compared with endometrial adenocarcinoma by the electron microscope. Tissues were obtained at hysterectomy, endometrial biopsy, or endometrial curettage and were processed routinely for light and electron microscopy. Ultrastructurally the endometrium from postmenopausal patients undergoing estrogen replacement therapy was similar to normal cyclic endometrium in the late proliferative phase. At least three features of the estrogen-treated postmenopausal tissue resembled those observed in adenocarcinoma of the endometrium: accumulation of lipid droplets, irregular nuclei, and perinuclear whorls of microfibrils.
The renin-angiotensin system and insulin resistance

Insulin resistance upregulates the renin-angiotensin system (RAS), which contributes to the pathogenesis of hypertension, heart failure, and atherosclerosis. RAS inhibition decreases cardiovascular and renal morbidity and mortality and the incidence of new-onset type 2 diabetes. To the same degree, angiotensin II impairs insulin signaling, induces inflammation via the nuclear factor-kappaB pathway, and reduces nitric oxide availability and facilitates vasoconstriction, leading to insulin resistance and endothelial dysfunction. Thus, the RAS, insulin resistance, and inflammation perpetuate each other and coordinately contribute to endothelial dysfunction, vascular injury, and atherosclerosis.
No-fault insurance for vaccine related injuries: Jeffrey O'Connell proposes an alternative insurance scheme for vaccine-injury victims

Under tort law in effect throughout most of the western world, a party injured by adverse effects from a vaccine can be paid under a legal claim only by proving the manufacturer or its product faulty. If successful, the claimant would be paid not only for his medical expense and wage loss but for his pain and suffering. But proving (a) the defendant's conduct or product faulty and (b) the monetary value of nonmonetary loss (pain and suffering) is usually so complex that many injury victims are paid not at all, or only a fraction of their losses in settlement, only after long delay, and only after lawyers on both sides are paid large amounts of insurance dollars in litigation costs.
Response to Treatment and Survival of Patients with Non-Small Cell Lung Cancer Undergoing Somatic EGFR Mutation Testing

Somatic mutations in the epidermal growth factor receptor (EGFR) gene are associated with clinical response and prolonged survival in patients with non-small cell lung cancer (NSCLC) treated with EGFR tyrosine kinase inhibitors (TKIs). We began screening patients for somatic EGFR mutations by DNA sequencing as part of clinical care in 2004. We performed a retrospective cohort study of 278 patients with NSCLC referred for EGFR testing over a 10-month period. Tumor samples underwent direct DNA sequence analyses of EGFR exons 18 through 24. We determined the clinical characteristics and EGFR mutation status of the patients and analyzed their response to therapy and survival. EGFR somatic mutations were identified in 68 (24%) of patients. A minimal smoking history was the strongest clinical predictor of harboring a mutation. In multivariable analyses, each pack-year of smoking corresponded to a 5% decreased likelihood of having an EGFR mutation. Among 92 patients with unresectable disease undergoing subsequent systemic therapy, EGFR mutations were associated with an increased response rate to EGFR TKIs (p < .0001) but not chemotherapy. Overall survival was significantly prolonged in EGFR mutation-positive patients (p = .001), with a median survival of 3.1 years compared with 1.6 years in mutation-negative patients, after adjusting for age, gender, and stage at diagnosis. Integrating molecular profiling into clinical care is feasible in NSCLC patients and provides useful clinical information.
Substantive and Statistical Considerations in the Interpretation of Multiple Measures of SES

Sociologists disagree about the measurement of one of the core concepts in the discipline-socioeconomic status. In recent years the Duncan SEI has come to be accepted as a "standard measure," however, its interpretation, particularly when it is used in conjunction with income and education remains in dispute. Moreover, there is suspicion on the part of at least some sociologists that using the three measures together in a single regression equation results in collinearity problems. This paper first suggests an interpretation of the SEI score in terms of the contextual effects associated with occupations and then examines the statistical properties of equations containing education, SEI, and income. Using statistics derived from ridge regression, we conclude that multicollinearity is not likely to be a serious problem. Before the introduction of multiple regression and path analysis as staples of sociological research it was common to represent socioeconomic status in tabular analyses with a single composite indicator. Numerous SES scales were developed including the Hollingshead index, Warner's measure, Ellis' measure, and a variety of prestige scores beginning with the NorthHatt index and continuing through the development of Siegel's prestige score. These and other measures are described in Robinson et al. (chap. 14). By far the most commonly used single SES measure, of course, is the Duncan socioeconomic index (sEI), a measure designed to provide an optimally weighted composite of occupation-specific income and educa
Domain structure of the NRIF3 family of coregulators suggests potential dual roles in transcriptional regulation.

The identification of a novel coregulator for nuclear hormone receptors, designated NRIF3, was recently reported (D. Li et al., Mol. Cell. Biol. 19:7191–7202, 1999). Unlike most known coactivators, NRIF3 exhibits a distinct receptor specificity in interacting with and potentiating the activity of only TRs and RXRs but not other examined nuclear receptors. However, the molecular basis underlying such specificity is unclear. In this report, we extended our study of NRIF3-receptor interactions. Our results suggest a bivalent interaction model, where a single NRIF3 molecule utilizes both the C-terminal LXXIL (receptor-interacting domain 1 [RID1]) and the N-terminal LXXLL (RID2) modules to cooperatively interact with TR or RXR (presumably a receptor dimer), with the spacing between RID1 and RID2 playing an important role in influencing the affinity of the interactions. During the course of these studies, we also uncovered an NRIF3-NRIF3 interaction domain. Deletion and mutagenesis analyses mapped the dimerization domain to a region in the middle of NRIF3 (residues 84 to 112), which is predicted to form a coiled-coil structure and contains a putative leucine zipper-like motif. By using Gal4 fusion constructs, we identified an autonomous transactivation domain (AD1) at the C terminus of NRIF3. Somewhat surprisingly, full-length NRIF3 fused to the DNA-binding domain of Gal4 was found to repress transcription of a Gal4 reporter. Further analyses mapped a novel repression domain (RepD1) to a small region at the N-terminal portion of NRIF3 (residues 20 to 50). The NRIF3 gene encodes at least two additional isoforms due to alternative splicing. These two isoforms contain the same RepD1 region as NRIF3. Consistent with this, Gal4 fusions of these two isoforms were also found to repress transcription. Cotransfection of NRIF3 or its two isoforms did not relieve the transrepression function mediated by their corresponding Gal4 fusion proteins, suggesting that the repression involves a mechanism(s) other than the recruitment of a titratable corepressor. Interestingly, a single amino acid residue change of a potential phosphorylation site in RepD1 (Ser28 to Ala) abolishes its transrepression function, suggesting that the coregulatory property of NRIF3 (or its isoforms) might be subjected to regulation by cellular signaling. Taken together, our results identify NRIF3 as an interesting coregulator that possesses both transactivation and transrepression domains and/or functions. Collectively, the NRIF3 family of coregulators (which includes NRIF3 and its other isoforms) may play dual roles in mediating both positive and negative regulatory effects on gene expression.
Spectroscopic study of decontaminated corroded carbon steel surfaces

Removal of uranium from contaminated carbon steel surfaces by chelation with hydroxycarboxylic acid has been tested as a cleaning process for decommissioning and decontaminating contaminated surfaces. Comparison of contaminated surfaces prior to decontamination with subsequently cleaned surfaces was done in order to study the effectiveness of this cleaning technique. This was accomplished using various spectroscopic techniques, including x-ray photoelectron spectroscopy, synchrotron infrared microspectroscopy, Rutherford backscattering spectroscopy and scanning electron microscopy/energy-dispersive spectroscopy. Mild carbon steel (1010) coupons were exposed to uranyl nitrate solution, which led to the formation of a lightly corroded surface. Some contaminated samples underwent further cyclic humidity treatment, during which additional corrosion took place. In this study, it was found that a citric acid–hydrogen peroxide–citric acid cleaning method successfully removed uranium in lightly corroded areas. However, the method but incompletely decontaminated some heavily corroded areas where more highly crystallized corrosion products are found or where complex surface structure can occlude contaminants. Use of complementary analytical techniques is essential to provide an accurate model of surface chemistry before and after decontamination. Copyright © 2004 John Wiley & Sons, Ltd.
Rapid Identification of Bacteria from Positive Blood Cultures by Terminal Restriction Fragment Length Polymorphism Profile Analysis of the 16S rRNA Gene

Bacteremia results in significant morbidity and mortality, especially among patient populations that are immunocompromised. Broad-spectrum antibiotics are administered to patients suspected to have bloodstream infections that are awaiting diagnosis that depends on blood culture analysis. Significant delays in identification of pathogens can result, primarily due to the dependence on growth-based identification systems. To address these limitations, we took advantage of terminal restriction fragment (TRF) length polymorphisms (T-RFLP) due to 16S ribosomal DNA (rDNA) sequence diversity to rapidly identify bacterial pathogens directly from positive blood culture. TRF profiles for each organism were determined by sizing fragments from restriction digests of PCR products derived from two sets of 16S rDNA-specific fluorescent dye-labeled primers. In addition, we created a TRF profile database (TRFPD) with 5,899 predicted TRF profiles from sequence information representing 2,860 different bacterial species. TRF profiles were experimentally determined for 69 reference organisms and 32 clinical isolates and then compared against the predicted profiles in the TRFPD. The predictive value of the profiles was found to be accurate to the species level with most organisms tested. In addition, identification of 10 different genera was possible with profiles comprising two or three TRFs. Although it was possible to identify Enterobacteriaceae by using a profile of three TRFs, the similarity of the TRF profiles of these organisms makes differentiation of species less reliable with the current method. The ability to rapidly (i.e., within ∼8 h) identify bacteria from blood cultures has potential for reducing unnecessary use of broad-spectrum antibiotics and promoting more timely prescription of appropriate antibiotics.
Fibroblast Growth Factor Receptor Two (FGFR2) Regulates Uterine Epithelial Integrity and Fertility in Mice

Fibroblast growth factors (FGFs) and their receptors (FGFRs) regulate luminal epithelial (LE) cell proliferation in the adult mouse uterus. This study tested the hypothesis that FGFR2 has a biological role in postnatal development and function of the uterus by conditionally deleting Fgfr2 after birth using progesterone receptor (Pgr)-Cre mice. Adult Fgfr2 mutant female mice were initially subfertile and became infertile with increasing parity. No defects in uterine gland development were observed in conditional Fgfr2 mutant mice. In the adult, Fgfr2 mutant mice possessed a histologically normal reproductive tract with the exception of the uterus. The LE of the Fgfr2 mutant uterus was stratified, but no obvious histological differences were observed in the glandular epithelium, stroma, or myometrium. Within the stratified LE, cuboidal basal cells were present and positive for basal cell markers (KRT14 and TRP63). Nulliparous bred Fgfr2 mutants contained normal numbers of blastocysts on Day 3.5 postmating, but the number of embryo implantation sites was substantially reduced on Day 5.5 postmating. These results support the idea that loss of FGFR2 in the uterus after birth alters its development, resulting in LE stratification and peri-implantation pregnancy loss.
Outer membrane barrier as a mechanism of antimicrobial resistance.

La barriere de permeabilite, la membrane exterieure qui entoure les bacteries gram-negatives peut etre traversee par des solutes hydrophiles a travers les canaux porine. Ces canaux peuvent etre etroits et entraver la penetration de medicaments hydrophobes et creer differents degres de resistance intrinseque aux antibacteriens
Examining the individual within marriage: Personal strengths and relationship satisfaction

The present investigation aims to identify individual strengths that may benefit efforts toward marital enhancement. Ninety-two married couples from the Southeastern United States completed questionnaires measuring positive affectivity, optimism, coping skills, personal expansion, and marital satisfaction. Results indicate that perceptions of a spouse's positive affectivity, as well as one's own positive affectivity, are related to relationship satisfaction. In addition, positive affectivity contributed to satisfaction above and beyond negative affectivity. Finally, optimism, coping skills, and personal expansion appear to be important resources for marriage via their association with each partner's affectivity. The discussion considers these results in the context of marital enhancement and relationship flourishing.