cssi/SciSciGPT-SciSciNet huggingface dataset:
Multiple forms of flounder muscle glyceraldehyde 3-phosphate dehydrogenase. Subunit composition, properties, and tissue distribution of the forms.

Abstract The major forms of glyceraldehyde 3-phosphate dehydrogenase have been isolated from the muscle and liver of the marine fish winter flounder, Pseudopleuronectes americanus. The isolation procedure is a two-step process utilizing ammonium sulfate fractionation and column isoelectric focusing. The three muscle forms have isoelectric points of 8.4, 8.2, and 7.9, respectively. Electrofocusing of the crude soluble fraction yields the same pattern as the purified preparation, and refocusing of each form produces one peak at its respective isoelectric point. The 70 to 90% salt fraction lacks the 8.2 form while the 60 to 90% fraction contains it. The isolated muscle forms are homogeneous after electrophoresis on polyacrylamide gels with the 8.4 and 7.9 enzymes being completely resolved upon concurrent electrophoresis. The subunits appear to be identical as judged by electrophoresis in 8 m urea and 0.1% sodium dodecyl sulfate gels with a molecular weight of 39,000. The kinetic properties (Km values) of the muscle forms are similar as are the pH optima. The forms did display significant differences in their requirement for sulfhydryl-reducing agents in the assay mixture, number of p-chloromercuribenzoate-reactive sulfhydryl groups, heat stability (50°), and bound NAD content. Incubation of a muscle preparation in the presence of 40 mm NAD gave rise to two additional forms with pI values of 7.8 and 7.6. Flounder liver glyceraldehyde 3-phosphate dehydrogenase was prepared by a procedure similar to that used for muscle. The multiple form pattern differs markedly from that of muscle with the five major forms having pI values of 7.1, 6.8, 6.6, 6.5, and 6.3. The results indicate that the multimeric enzyme glyceraldehyde 3-phosphate dehydrogenase, consisting of apparently identical subunits, exists as a mixture of multiple forms having distinct properties. The evidence presented supports the concept of distinct conformational forms of a multimeric enzyme composed of one subunit type.
Study of floating gate nitride etch with high selectivity on flash technology

A new recipe was studied for floating gate etching of flash technology. The scheme for defining floating gate was BARC/SIN/POLY. The main etching step etched through BARC and stopped on SlN, and over etching step etched SIN completely and stopped on poly. Because the selectivity of BARC/SIN was very low with fluorine based recipe, the main step might etch through SIN and make poly loss too much. Four optimum parameters and O/sub 2/ was adopted in main etching step to increase the selectivity. Moreover, to reduce poly loss, high polymer gas CH/sub 3/F was added in over etching step. The result showed appropriate CH/sub 3/F/CF/sub 4/ ratio was positive to reduce poly loss. The modified recipe also was tested on the structure wafer and the product. The modified recipe got less poly loss than that of original recipe, and there was no difference on the shape of floating gate for both recipes. The electrical result also showed comparable performance to original CHF/sub 3/ based recipe.
Optimal placement of light splitters and wavelength converters for multicast in WDM networks

In wavelength-division multiplexing (WDM) optical networks, sparse light splitting and sparse wavelength conversion can achieve most benefit of full splitting and full wavelength conversion, provided that the light splitters and wavelength converters are properly placed. We propose an integer linear programming model for the optimal solution of the combined problem of light splitter placement and wavelength converter placement, in the sense that the total number of wavelength channels required by multicast requests is minimized. Solving the ILP model supplies the optimal placement of light splitters and wavelength converters, as well as the routing and wavelength assignment (RWA) approach under the presented sparse splitting and sparse wavelength conversion placement. The model can be applied to any optical network topology with any multicast traffic configuration, and can be used to get performance benchmarks when dealing with optical multicast under wavelength continuity constraint and multicast capability constraint.
Fructose 1,6-diphosphatase from Rhodopseudomonas palustris: I. Purification and properties

The fructose 1,6-diphosphatase (d-fructose 1,6-diphosphate I-phosphohydrolase, EC 3.1.3.11) of Rhodopseudomonas palustris has been purified 800-fold and found to have a molecular weight of approximately 130,000. Enzyme stored in the cold in the presence of Mn2+ ions for longer than 3 weeks dissociates into fully catalytically active dimers of molecular weight of about 65,000. The enzyme was shown to have optimal activity at pH 8.5 and demonstrated an absolute requirement for divalent cations which could be satisfied by Mn2+ or Mg2+. Maximal catalytic activity in the presence of Mg2+ was only 27% of the maximum activity observed with Mn2+. Univalent cations such as Li+, Na+, K+, NH4+, and Cs+ were found to inhibit the enzyme to varying degrees. Enzymatic activity was activated fourfold by sulfhydryl reagents such as reduced glutathione and dithiothreitol. p-Hydroxymercuribenzoate completely inactivated the enzyme. Only the cofactor Mn2+ offered protection against inhibition by this reagent. The enzyme was inactivated 65% after heating for 1 min at 50 °C, whereas in the presence of 0.3 mm Mn2+ only 12% of the catalytic activity was lost after 1 min. The Km values for fructose 1,6-diphosphate and Mn2+ were calculated to be 4.5 × 10−5m and 2.2 × 10−5m, respectively. Sedoheptulose 1,7-diphosphate was cleaved at 22.4% of the rate of hydrolysis of fructose 1,6-diphosphate and has a Km of 30 × 10−5m. Fructose 1,6-diphosphatase activity was competitively inhibited by sedoheptulose 1,7-diphosphate with the KI calculated to be 29 × 10−5m. The enzyme was inactive toward all other substrates tested.
Taxation of Virtual World Economies: A Review of the Current Status

0 0 1 153 1005 Colorado State University 17 2 1156 14.0 Normal 0 false false false EN-US JA X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:Times;} The taxation of virtual world economies is uncharted terrain, one that both researchers and government officials are just beginning to scrutinize. Taxes are inevitable in any economy, but what about the increasingly lucrative virtual world economies? The market for virtual goods and services is estimated to be in the millions of dollars, so it is no wonder that governments are beginning to take notice. Experts are divided as to the feasibility of taxation of virtual economies. Most experts agree however that there is significant ambiguity in the current U.S. Internal Revenue Code with respect to virtual worlds. It is unclear if transactions occurring in a virtual world are taxable in the U.S., and the Internal Revenue Service has to date not offered any strong guidance regarding the issue. In this article, we argue that virtual transactions are already subject to taxation under current U.S. law, at any point in time that the U.S. Internal Revenue Service should decide to enforce the current law, whether taking place in game worlds or unscripted worlds. This would include virtual-to-virtual transactions as well as virtual-to-real transactions, as the issue at hand is whether or not virtual activity is taxable, regardless of realization, because all goods and services have a fair market value.
On the Foundations of Combinatorial Theory IV Finite Vector Spaces and Eulerian Generating Functions

Abstract : The paper studies combinatorial aspects of the lattice of subspaces of a vector space over a finite field and its use in deriving classical and new q-identities. Set theoretic interpretations of these identities are given in terms of the enumeration of vector spaces and linear transformations. The incidence algebra of a partially ordered set is shown to be a true generalization of the notion of a generating function and Eulerian generating functions are applied to count a variety of vector space objects. Combinatorial interpretations are provided for general q-difference equations. (Author)
Neural Systems Activated during Visual Mental Imagery: A Review and Meta-Analyses

Publisher Summary This chapter demonstrates how neuroimaging has advanced the understanding of the nature of visual mental imagery. Visual mental imagery occurs when a visual short-term memory representation is present but the object is no longer being viewed. The different aspects of imagery tasks activate different regions of the brain. Medial occipital cortex (MOC) is activated when high resolution is needed and when images need to be actively suppressed; and posterior parietal lobe (PP) is activated when image transformation or suppression occurs, higher spatial resolution is required, and activation is best detected by more powerful techniques. The use of a resting baseline is associated with greater likelihood of detecting PP although the correlation is in the opposite direction for detection of MOC activation. The analysis of the PP activations is in agreement with the hypothesis—When image transformation is required, the likelihood of PP activation increases. The effects of image suppression may be due to the need to inhibit the spatial relations function of the previous image. All multipart images have some representation of the spatial relations among the parts, which need to be suppressed when a new image is to be formed.
Seeing the Fields and Forests: Application of Surface-Layer Theory and Flux-Tower Data to Calculating Vegetation Canopy Height

Canopy height is an important and dynamic site variable that affects the mass and energy exchanges between vegetation and the atmosphere. We develop a method to estimate canopy height routinely, using surface-layer theory and turbulence measurements made from a collection of flux towers. This tool is based on connecting the logarithmic wind profile generally expected in a neutral surface layer with direct measurements of friction velocity and assumptions about canopy height’s relationships with zero-plane displacement and aerodynamic roughness length. Tests over a broad range of canopy types and heights find that calculated values are in good agreement with direct measurements of canopy height, including in a heterogeneous landscape. Based on the various uncertainties associated with our starting assumptions about canopy micrometeorology, we present a blueprint for future work that is necessary for expanding and improving these initial calculations.
Multi Gbit/s, high-sensitivity all silicon 3.3 V optical receiver using PIN lateral trench photodetector

We report a 3.3 V silicon optical receiver consisting of a CMOS-compatible lateral trench PIN photodiode and a transimpedance amplifier that achieved a sensitivity of -17. 1 dBm at 2.5 Gb/s and demonstrated error-free (BER<10/sup -10/) operation up to 6.5 Gb/s at 845 nm. This is the highest reported sensitivity at data rates above 2.0 Gb/s and the fastest operation of any Si-based optical receiver.
Chinchilla "big" and "little" gastrins.

Gastrin heptadecapeptides (gastrins I and II which differ in the presence of sulfate on the tyrosine of the latter) have been purified and sequenced from several mammalian species including pig, dog, cat, sheep, cow, human and rat. A 34 amino acid precursor (“big” gastrin), generally accounting for only 5% of total gastrin immunoreactivity, has been purified and sequenced only from the pig, human, dog and goat. Recently we have demonstrated that guinea pig (GP) “little” gastrin is a hexadecapeptide due to a deletion of a glutamic acid in the region 6–9 from its NH2-terminus and that GP “big” gastrin is a 33 amino acid peptide. The chinchilla, like the GP, is a New World hystricomorph. This report describes the extraction and purification of “little” and “big” gastrins from 31 chinchilla antra. Chinchilla “little” gastrin is a hexadecapeptide with a sequence identical to that of the GP and its “big” gastrin is a 33 amino acid peptide with the following sequence: 〈ELEPQGPPHLGTDLSKKQGPWAEEEAAYGWMDF#
Inégalités sociales de santé et santé publique : des recherches aux politiques

This paper analyses the main results and prospects concerning research and studies about social inequalities in health in France. Research orientations, which may contribute usefully to defining health and social policies in this field and favour their development are then proposed. Health policy content and implementation placing high priority on the problem of social inequalities in health are discussed.
Addition of borohydride ion to coordinated isocyanides: the structure of π-C5H5Fe(CO)[(CHNCH3)2BH2]

Abstract The structure of π-C5H5Fe(CO)[(CHNCH3)2BH2] has been determined from three dimensional X-ray diffractometer data collected by counter methods. The compound crystallizes in the space group P21/a with four molecules in a cell of dimensions a = 12.33(3), b = 6.14(2) and c = 16.21(7)A with β = 105.0(2)°. The observed and calculated densities are 1.37(2) and 1.379(6) g/cm3 respectively. Full-matrix least-squares refinement has resulted in R = 0.113 for the 1238 data with F2o ⩾ σ (F2o). The structure results from a BH−4 anion adding across two coordinated isocyanide ligands to form a six-membered heterocyclic ring containing BN bonds.
Campus wide information system development at three UK universities

Campus wide information systems (CWIS) are the newest development in the electronic campus, providing information on many aspects of campus life. This article gives a brief overview of CWIS development in the United Kingdom as at summer 1993. As yet there is no definitive CWIS, so a range of third generation systems were looked at in detail at the Universities of Birmingham, Bradford and Stirling. Within each, attention is given to differences in organisational policy, functionality, software and information provision. An appraisal of the specific case studies was undertaken both onsite and remotely via a national gateway. A comparison of the systems draws out features that should be available on an ideal CWIS. Future developments, including the advent of standards such as X.500 and Z39.50 and the adoption of common software, will lead to greater interaction between institutions. All of this coupled with the development of hypermedia and multimedia will ensure CWISs will become a powerful tool in the provision of information.
EFFECTS OF SODIUM NITRITE ON Clostridium botulinum TOXIN PRODUCTION IN FRANKFURTER EMULSIONS FORMULATED WITH MEAT AND SOY PROTEINS

Botulinal toxin production, residual nitrite depletion, and total microbial growth were measured in meat and/or soy-containing frankfurter formulations during 27° C temperature abuse. Botulinal toxin production in formulations containing soy proteins was equal to or less rapid than in all-meat samples, both in the absence and presence of nitrite. Of the nine soy proteins examined, nitrite did not delay C. botulinurn toxin production in products made from the isolate form, whereas it was an effective control in textured, flours and concentrates. In all-meat formulations the effectiveness of nitrite decreased with increasing spore load. Residual nitrite depletion in meat wasmore rapid than in soy-containing treatments. Among the soy proteins, nitrite depletion was more rapid in the isolate than in the textured form tested. Total microbial growth was similar in both meat and soy-containing samples. Gas production was an inadequate index of toxin development.
Incidence and Risk Factors for Cholestasis in Neonates Receiving Total Parenteral Nutrition: 1995-98

Incidence and Risk Factors for Cholestasis in Neonates Receiving Total Parenteral Nutrition: 1995-98
Freezing Points and Enthalpies of Dilution of Aqueous Formic, Acetic, Propionic, and Butyric Acids. Free Energies and Enthalpies of Solute-Solute Interactions

Freezing-point depressions and enthalpies of dilution for aqueous solutions of the straight chain, aliphatic carboxylic acids, C1 through C4, have been measured. These data, together with the corresponding apparent molal heat capacities, have been used to calculate the pairwise free energy and enthalpy of interaction of undissociated acid molecules at 298.150K. As expected, the effect of dimer and triplet interaction increases with chain length, reflecting the hydrophobic nature of the hydrocarbon portion of the molecules. The group-interaction additivity principle of Savage and Wood applied to these results gives an excellent correlation and yields values of the group interaction parameters,Gi,j andHi,j for the CH2 and COOH groups. These parameters confirm previous results for the interaction of polar and hydrophobic groups in water. The primary data have been fitted to the activity expansion equations of Wood, Lilley, and Thompson to yield values of dimer and trimer “sociation” constants and their temperature derivatives. This procedure allows for the simultaneous treatment of the dissociation effects of these acids as weak electrolytes together with their tendency to form associated clusters.
Generic features of vacuum phase transitions in the early universe

Abstract A simple Higgs model is utilized to show the occurrence of a four-phase pattern of vacuum symmetry. As temperature changes, an interplay of spontaneous symmetry breaking and spontaneous symmetry restoration ensues, and resonant field interchange occurs. The generality of models which may contain a sequence of vacuum phase transitions is emphasized. The laboratory for these multi-phase transitions is the early Universe.
Single-step switching at a nonlinear interface

Theoretical predictions of the behavior of a light beam crossing a plane interface between a linear and nonlinear dielectric medium indicate staircased multiple threshold switching in nondiffusive media when an incident Gaussian beam instead of a plane wave is assumed. We report experimental findings showing unexpected high-contrast single-threshold switching, which may have important implications for optical signal processing. No evidence was found for the existence of bistable behavior indicated by previous experiments.
Regulation of gene expression of hepatic drug metabolizing enzymes and transporters by the Toll-like receptor 2 ligand, lipoteichoic acid.

Abstract Expression of hepatic drug metabolizing enzymes (DMEs) is altered in infection and inflammation. However, the role of Gram+ve bacterial components and their receptor, Toll-like receptor (TLR) 2 in regulation of hepatic DMEs is unknown. Gene expression of DMEs is regulated by members of the nuclear receptor superfamily (PXR, CAR and RXRα). The TLR2 ligand, lipoteichoic acid (LTA) reduced RNA levels of CAR and its target genes, Cyp2b10, Cyp2a4 and Sultn in mouse liver (∼60–80% reduction). Hepatic genes regulated by PXR and CAR, Cyp3a11 and Mrp2 were moderately reduced by LTA, along with ∼50% reduction of PXR RNA and nuclear protein levels of RXRα. The effects of LTA were significantly attenuated by pre-treatment with the Kupffer cell inhibitor, gadolinium chloride, indicating that Kupffer cells contribute to LTA-mediated down-regulation of hepatic genes. These results indicate that treatment with Gram+ve bacterial components preferentially down-regulate CAR and its target genes in the liver.
Photonic crystal waveguide based sensors

Waveguide based sensors allow independent control over sensitivity and dynamic range, which is not possible in resonance based sensors. In this paper, we present a refractive index sensor based on using photonic crystal waveguides (PCWs) in an unbalanced Mach-Zehnder interferometer configuration. In this configuration the dynamic range of the sensor is determined by the path difference between the two arms and the sensitivity is controlled by the length of the PCW. We show that by using PCWs we can get a factor of 8 improvement in sensitivity over a ridge-waveguide based sensor. This enhanced sensitivity is achieved due to reduced group velocity in a PCW. By reducing the loss at low group velocities the sensitivity can be further improved.
GATA-6 is a novel transcriptional repressor of the human Tenascin-C gene expression in fibroblasts.

In this study we show that GATA-6 is a novel repressor of TN-C gene expression. We demonstrated that overexpression of GATA-6 in fibroblasts inhibited basal levels, as well as markedly decreased IL-4- and TGF-β-induced TN-C mRNA and protein levels. A GATA-6 response element was mapped to position −467~ −460 of the TN-C promoter. In addition, we showed that GATA-6 binds this site both in vitro and in vivo.
External beam radiation with 'curative intent' in advanced ovarian cancer: an uncommon but rational management approach based on the natural history of cancer in an individual patient.

based on the observations noted above. It is most uncommon for recurrent ovarian cancer to be anatomically localized to the pelvic region, with radiographic imaging studies or surgical exploration providing confirmation for macroor micro-metastatic cancer within the upper abdomen (or even more extensive spread). Therefore, when the cancer of an individual patient with ovarian cancer is documented to be present within the pelvis and there is no evidence of disease outside the confines of this anatomic location, it is reasonable to suggest that this particular cancer in this specific patient behaves, biologically, in a manner quite different from what is expected. Moreover, under such circumstances, it is rational to argue that by achieving local disease control in the pelvis (following external beam radiation delivered with the intent of attaining this goal) it is possible the patient may experience a prolonged period of disease-free survival (measured in ‘years’). The concept of carefully observing the natural history of a cancer in an individual patient and the increasingly common use of performing molecular profiling of a patient’s malignancy to help define relevant driver mutations are both critically relevant components of a therapeutic focus on delivering ‘personalized cancer care’ that is designed to maximize the opportunity of a favorable clinical outcome. On the surface, it is difficult to think of a setting where the concept of the delivery of external beam radiation with ‘curative intent’ would be more inappropriate. Advanced ovarian cancer is recognized to be widespread throughout the peritoneal cavity in the large majority of patients at diagnosis. In fact, the rationale for considering ‘stage 2’ ovarian cancer as an objectively valid clinical entity has been questioned, suggesting that, in the large majority of cases, one is really dealing with ‘stage 3’ disease even though it is not possible to confirm (during surgery) the presence of micro-metastatic disease in the upper abdomen. Furthermore, the statistically more favorable outcome for such patients (stage 2), compared to women who present with documented metastatic disease outside the pelvis, is likely the result of the presence of a substantially reduced tumor bulk rather than being due to the specific anatomic localization of the cancer. Yet, Machida et al. [1] in this issue of Oncology and other investigators have reported that a small subset of patients with recurrent ovarian cancer treated with external beam radiation following the failure of cytotoxic chemotherapy may experience very long-term survival (and possibly a ‘cure’ of the malignant process) [1–3] . Of interest, the fundamental justification for this strategy in a highly selected patient population is actually Published online: May 13, 2014
Actinic degeneration and pigmentary change in association with psoralen and UVA treatment: A 20-year prospective study

Abstract Background: Changes in the appearance of the skin including actinic degeneration and pigmentary changes have been noted in patients treated with psoralen and UVA (PUVA). Objective: Our purpose was to quantify risk factors for increased extent and progression of actinic degeneration and pigmentary changes in the skin of patients treated with PUVA. Methods: On the basis of standardized dermatologic examination conducted in 1977 and 1998 of patients enrolled in the PUVA Follow Up Study, we assessed the prevalence of and changes in the extent of actinic degeneration and pigmentary abnormalities on the hands and buttocks. Results: From 1977 to 1998, the prevalence of moderate or severe actinic degeneration increased from 15.6% to 60.5% on the hands and from 2.2% to 21.3% on the buttocks. During this same period, the prevelance of pigmentary changes of this degree increased from 15.6% to 58.6% on the hands and 12.6% to 24.7% on the buttocks. Extent of exposure to PUVA was the strongest predictor of an increased extent of clinical actinic degeneration or pigmentary change. Conclusion: Long-term exposure to PUVA is associated with persistent increases in actinic degeneration and pigmentary abnormalities of the skin on both usually sun-exposed and sun-protected sites. (J Am Acad Dermatol 2003;48:61-7.)
A note on approximations and convergence in distribution for spearman's rank correlation coefficient

The convergence of the exact distribution of Spearman's Correlation Coefficient to normality is examined for n-9 to 18. Seven recommended approximations are examined for accuracy to the exact distribution and some recommendations are made.
Ligand-binding domains in vitellogenin receptors and other LDL-receptor family members share a common ancestral ordering of cysteine-rich repeats

Insect vitellogenin and yolk protein receptors (VgR/YPR) are newly discovered members of the low-density lipoprotein receptor (LDLR) family, which is characterized by a highly conserved arrangement of repetitive modular elements homologous to functionally unrelated proteins. The insect VgR/YPRs are unique in having two clusters of complement-type cysteine-rich (class A) repeats or modules, with five modules in the first cluster and seven in the second cluster, unlike classical LDLRs which have a single seven-module cluster, vertebrate VgRs and very low density lipoprotein receptors (VLDLR) which have a single eight-module cluster, and LDLR-related proteins (LRPs) and megalins which have four clusters of 2–7, 8, 10, and 11 modules. Alignment of clusters across subfamilies by conventional alignment programs is problematic because of the repetitive nature of the component modules which may have undergone rearrangements, duplications, and deletions during evolution. To circumvent this problem, we “fingerprinted” each class A module in the different clusters by identifying those amino acids that are both relatively conserved and relatively unique within the cluster. Inter-cluster reciprocal comparisons of fingerprints and aligned sequences allowed us to distinguish four cohorts of modules reflecting shared recent ancestry. All but two of the 57 modules examined could be assigned to one of these four cohorts designated A, B, C, and D. Alignment of clusters based on modular cohorts revealed that all clusters are derived from a single primordial cluster of at least seven modules with a consensus arrangement of CDCADBC. All extant clusters examined are consistent with this consensus, though none matches it perfectly. This analysis also revealed that the eight-module clusters in vertebrate VgRs, insect VgR/YPRs, and LRP/ megalins are not directly homologous with one another. Assignment of modules to cohorts permitted us to properly align 32 class A clusters from all four LDLR subfamilies for phylogenetic analysis. The results revealed that smaller one-cluster and two-cluster members of the family did not originate from the breakup of a large two-cluster or four-cluster receptor. Similarly, the LRP/ megalins did not arise from the duplication of a two-cluster insect VgR/YPR-like progenitor. Rather, it appears that the multicluster receptors were independently constructed from the same single-cluster ancestor.
Entropy generation in a ten-dimensional cosmological model admitting decompressive forces

By allowing the equation of state for matter to be of a decompressive nature we study the effect on entropy generation in a ten-dimensional cosmological model. We study the three cases when bulk viscosity is constant, depends on the energy density, and lastly, on the square of the curvature.
Cost Savings Due to Variance Reduction in a Canning Process

Abstract We investigate a canning problem (Golhar and Pollock [2]) to study the effect of a reduction in process variance on the production cost. Exact and approximate relationships are developed for cost reduction as a function of economic parameters when the fill is a normally distributed random variable and process settings are optimized.
Decomposition in data mining: a medical case study

Decomposition is a tool for managing complexity in data mining and enhancing the quality of knowledge extracted form large databases. A typology of decomposition approaches applicable to data mining is presented. One of the decomposition approaches, the structured rule-feature matrix, is used as the backbone of a system for informed decision-making. Such a system can be implemented as a decision table, a decision map, or a decision atlas. The ideas presented in the paper are illustrated with examples and a medical case study.
Hollywood log-homotopy: movies of particle flow for nonlinear filters

In this paper we show five movies of particle flow to provide insight and intuition about this new algorithm. The particles flow solves the well known and important problem of particle degeneracy. Bayes' rule is implemented by particle flow rather than as a pointwise multiplication. This theory is roughly seven orders of magnitude faster than standard particle filters, and it often beats the extended Kalman filter by two orders of magnitude in accuracy for difficult nonlinear problems.
Lactational Response to Dried Whey in Concentrate Mixture Fed to Dairy Cows

Abstract Previous short (6 to 13 wk) experiments indicated that including small amounts (5% or less)of dried whey in the concentrate mixture fed to lactating cows increased milk fat percentage but decreased milk production slightly. Five percent dried whey product was included in the concentrate mixture fed to 10 Holstein cows from 3 wk postpartum to the end of lactation to determine if previous responses were positive increases in milk fat percentages caused by feeding dried whey or a normal response to drying cows off prematurely. The dried whey product replaced a portion of the corn, soybean meal, and dicalcium phosphate in the 10 controls’ concentrate mixture. Cows were fed concentrate at 1 kg/3 kg milk produced, 7 kg alfalfa hay daily, and corn silage ad libitum. Actual milk production was similar from cows fed the control and dried whey product diets (22.4 and 22.3 kg/day), while fat percent was higher from cows fed dried whey product (3.49 and 3.62%). Persists ency with which production was maintained throughout lactation was similar with both diets, but persistency of 4% fat-corrected milk was greater for cows fed dried whey product. Percentages of protein and solids-not-fat in milk were not affected by treatment. Feeding small amounts of dried whey to lactating cows will not affect milk production adversely.
Production of interleukin-1β by periodic acid-oxidized human peripheral blood mononuclear cells

Interleukin-1 (IL-1) production by periodic acid (H5IO6)-oxidized human peripheral blood mononuclear (PBMN) cells was assessed by the thymocyte co-mitogenesis assay. Maximum IL-1 levels (∼ 1.2 U/ml) in the conditioned media of PBMN cells were registered within the first 24 hrs post-oxidation, whereas no IL-1 was detected in the media from 24 hrs control cultures. Thymocyte proliferation, driven by periodic acid-induced IL-1, was abolished by an antibody to IL-1alpha and IL-1β. Quantitative analysis of IL-1-containing medium by radioimmunoassay (RIA) indicated that IL-1β comprised about 80% of total IL-1. Partial characterization of H5IO6-induced IL-1β indicated that it was identical to IL-1 produced by lipopolysaccharide-stimulated macrophages. It is concluded that oxidation of human PBMN cells by H5IO6 triggers synthesis and release of IL-1, most of which was in its IL-1β form.
The crystal structure of human S-adenosylmethionine decarboxylase at 2.25 A resolution reveals a novel fold.

Abstract Background: S-Adenosylmethionine decarboxylase (AdoMetDC) is a critical regulatory enzyme of the polyamine synthetic pathway, and a well-studied drug target. The AdoMetDC decarboxylation reaction depends upon a pyruvoyl cofactor generated via an intramolecular proenzyme self-cleavage reaction. Both the proenzyme-processing and substrate-decarboxylation reactions are allosterically enhanced by putrescine. Structural elucidation of this enzyme is necessary to fully interpret the existing mutational and inhibitor-binding data, and to suggest further experimental studies. Results: The structure of human AdoMetDC has been determined to 2.25 A resolution using multiwavelength anomalous diffraction (MAD) phasing methods based on 22 selenium-atom positions. The quaternary structure of the mature AdoMetDC is an ( α β ) 2 dimer, where α and β represent the products of the proenzyme self-cleavage reaction. The architecture of each ( α β ) monomer is a novel four-layer α / β -sandwich fold, comprised of two antiparallel eight-stranded β sheets flanked by several α and 3 10 helices. Conclusions: The structure and topology of AdoMetDC display internal symmetry, suggesting that this protein may be the product of an ancient gene duplication. The positions of conserved, functionally important residues suggest the location of the active site and a possible binding site for the effector molecule putrescine.
Protein folding bottlenecks: A lattice Monte Carlo simulation.

Results of Monte Carlo simulations of folding of a model ``protein,'' which is a freely joined 27-monomer chain on a simple cubic lattice with nearest-neighbor interactions, are reported. All compact self-avoiding conformations on this chain have been enumerated, and the conformation (``native'') corresponding to the global minimum of energy is known for each sequence. Only one out of thirty sequences folds and finds the global minimum. For this sequence, the folding process has a two-stage character, with a rapid noncooperative compactization followed by a slower transition over a free-energy barrier to the global minimum. The evolutionary implications of the results are discussed.
A phase I study of gemcitabine plus palliative radiation therapy for advanced lung cancer.

To determine the maximum-tolerated dose (MTD) and antitumor activity of twice-weekly gemcitabine when combined with palliative-dose thoracic radiation therapy (RT) in patients with recurrent or progressive lung cancer. Patients were enrolled in a dose-escalating study of gemcitabine with a starting dose level of 40 mg/m2 given as 30-minute infusions twice weekly concurrent with RT. The RT dose was 30 Gy in 10 fractions, 5 fractions per week. A total of 18 patients were enrolled on three dose levels: 40, 50, and 65 mg/m2. Four patients came off study early due to rapid progression of disease and therefore were not evaluated. The MTD of gemcitabine was found to be 50 mg/m2. Dose-limiting toxicities were grade-4 esophagitis in one patient and grade-4 neutropenia in another patient. Overall response included 1 partial response (PR). Local response included six PR, four minor response (MR), three stable disease (SD), and one progressive disease (PD). The MTD of gemcitabine with concominant palliative thoracic radiation therapy is 50 mg/m2 twice weekly. The DLTs observed were grade-4 esophagitis and grade-4 myelotoxicity at 65 mg/m2.
Spontaneous self-assembly of metal-organic cationic nanocages to form monodisperse hollow vesicles in dilute solutions.

In this communication we report the unprecedented spontaneous self-assembly of cationic nanoporous metal−organic coordination cages (nanocages) into giant hollow vesicle-like structures in polar solvents. Such highly soluble nanocages (macrocations) have separated hydrophobic regions. However, their assembly is not due to hydrophobic interactions but the counterion-mediated attractions, very similar to the unique self-assembly of polyoxometalate macroanions into single-layer, spherical blackberry structures, as characterized by laser light scattering and TEM studies. This is the first study on the solution behavior of metal−organic nanocages and also the first report on the self-assembly of soluble macrocations. Therefore, the blackberry structure is likely to be a universal type of self-assembly for soluble macroions. In addition, the self-assembled nanocages can provide blackberry structures a wide range of organic functionalities that are impossible to reach with purely inorganic systems, which may ope...
Measurement Error in Nonlinear Models: A Modern Perspective

(2008). Measurement Error in Nonlinear Models: A Modern Perspective. Journal of the American Statistical Association: Vol. 103, No. 481, pp. 427-427.
Angelopoulos receives Scarf Award

AGU's third annual F.L. Scarf Award has been awarded to Vassilis Angelopoulos for his Ph.D. thesis, “Transport Phenomena in the Earth's Plasma Sheet,” which he completed at the University of California, Los Angeles, under the supervision of Charles Kennel. As part of the award, Angelopoulos will give an invited talk on a related topic at the upcoming AGU Fall Meeting in San Francisco. The award was established to honor Fred L. Scarf, a pioneer and leader in solar-planetary research. The award is given by the Space Physics and Aeronomy (SPA) section for outstanding dissertation research that contributes directly to solar-planetary science. The major criterion for the award is the impact or potential impact of the research on the field of solar-planetary studies. The awardee receives $1000 and is invited to deliver a paper at one of the following year's AGU meetings.
The challenges of recording phenotype in a generalizable and computable form.

Pharmacogenomics research attempts to ‘correlate genotype with phenotype’ in the context of pharmacotherapy. Public databases of interest to pharmacogenomics researchers will therefore need to store phenotypic data. One goal of electronic storage will be to make it amenable to programs that perform ‘data mining’, a form of automated hypothesis discovery.1 Genotype is reasonably straightforward to represent computationally, as variations from a consensus sequence. Most of these variations are simple substitutions in the form of single nucleotide polymorphisms (SNPs), although one must also consider insertions, deletions and substitutions of greater length, such as variable numbers of tandem repeats (VNTRs). Much research today, rather than focusing on individual variants in isolation, considers the set of several such variants that are inherited as a unit (the haplotype). Existing public databases such as dbSNP,2 which in turn point to databases containing consensus sequence such as Genbank, address the representation of both genotype as well as haplotype.3 By contrast, representing phenotype— ‘the outward, physical manifestation of internally coded, inheritable information’4— in a generic, computable way is much more problematic. Below, we first consider the extreme variability of phenotypic parameters, which are the source of the challenge. We describe how phenotype is represented in individual data sets. We then discuss how individual phenotypic parameters in a data set must be adequately described in order to be comprehensible and minimize the possibility of misinterpretation, and how even the nature of these descriptors depends on the broad category of phenotype that one is describing. We finally consider the requirements of software tools to assist submission of phenotypic data to an electronic repository, and the means by which such standardization of such software could be facilitated.
The Effect of Small Changes in Web Page Navigation Links on the Performance of Users Who Revisit Sites

This paper examines the results of a study conducted to determine if small changes to a site's primary navigation structure would significantly impact user performance. Between a user's first visit...
Mixing cell method for solving the solute transport equation with spatially variable coefficients

The advection-dispersion equation with spatially variable coefficients does not have an exact analytical solution and is therefore solved numerically. However, solutions obtained with several of the traditional finite difference or finite element techniques typically exhibit spurious oscillation or numerical dispersion when advection is dominant. The mixing cell and semi-analytical solution methods proposed in this study avoid such oscillation or numerical dispersion when advection dominates. Both the mixing cell and semi-analytical solution methods calculate the spatial step size by equating numerical dispersion to physical dispersion. Because of the spatial variability of the coefficients the spatial step size varies in space. When the time step size Δt → 0, the mixing cell method reduces to the semi-analytical solution method. The results of application to two cases show that the mixing cell and semi-analytical solution methods are better than a finite difference method used in the study.
777-3 Establishment of a Dose-Response Relationship for High Power Chilled-Tip Radiofrequency Current Ablation in Sheep

Tissue heating and lesion formation during high power radiofrequency (RF) current ablation are limited by abrupt impedance rise when electrode tip temperatures exceed 100°C. Electrode tip chilling by continuous intra-electrode saline infusion has allowed use of higher power while delaying or preventing impedance limitation, thus creating larger lesions. Neither a dose-response relationship nor size limit for lesions produced in this manner have been established. Twelve sheep (mean wt. 65 kg) received chilled RF ablation at up to 8 separate LV sites. High power RF current of 40, 50, 60 or 70W was delivered via modified 7Fr deflectable catheter with a 4 mm tip through which saline (26°C) was continuously infused at 0.6 ml/sec. RF current duration was 60 seconds or until impedance rise occurred. Lesion dimensions were determined by stereomorphometric analysis. Results A total of 77 lesions were analyzed. Lesion volume increased with higher power from 40 to 60W (0.61 ± 0.08 cm3 vs. 1.01 ± 0.10 cm3, P = 0.006) (Figure). Beyond 50W, power duration was progressively limited by earlier impedance rise (Figure) and was associated with diminished lesion volume at 70W (0.71 ± 0.44 cm3; P = 0.04, 60 vs 70W). Download : Download high-res image (85KB) Download : Download full-size image Conclusion A dose-response relationship for chilled-tip RF ablation can be demonstrated in vivo, and lesion volume is maximized with RF power of 60W, a value substantially higher than that found with standard RF ablation.
Error and error mitigation in low-coverage genome assemblies

The recent release of twenty-two new genome sequences has dramatically increased the data available for mammalian comparative genomics, but twenty of these new sequences are currently limited to ∼2× coverage. Here we examine the extent of sequencing error in these 2× assemblies, and its potential impact in downstream analyses. By comparing 2× assemblies with high-quality sequences from the ENCODE regions, we estimate the rate of sequencing error to be 1–4 errors per kilobase. While this error rate is fairly modest, sequencing error can still have surprising effects. For example, an apparent lineage-specific insertion in a coding region is more likely to reflect sequencing error than a true biological event, and the length distribution of coding indels is strongly distorted by error. We find that most errors are contributed by a small fraction of bases with low quality scores, in particular, by the ends of reads in regions of single-read coverage in the assembly. We explore several approaches for automatic sequencing error mitigation (SEM), making use of the localized nature of sequencing error, the fact that it is well predicted by quality scores, and information about errors that comes from comparisons across species. Our automatic methods for error mitigation cannot replace the need for additional sequencing, but they do allow substantial fractions of errors to be masked or eliminated at the cost of modest amounts of over-correction, and they can reduce the impact of error in downstream phylogenomic analyses. Our error-mitigated alignments are available for download.
Models for catalytic pore plugging: application to hydrodemetallation

Abstract A model for pore structure changes caused by solids deposition reactions in a catalyst pellet is developed. The case of catalyst deactivation by site coverage and pore plugging is considered in detail. Expressions are developed for the evolution of topological properties under two idealized modes of local deposition, uniform an discrete, and the implications of each are presented. The onset and spread of pore plugging through the particle is depicted and the effect of pore space connectivity on useful catalyst life time is demonstrated. The model based on deactivation via the growth of discrete metal deposits shows qualitative agreement with trends observed experimentally in the hydrodemetallation of petroleum.
Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands

Cytosine, 5-methylcytosine, and 5-hydroxymethylcytosine were identified during translocation of single DNA template strands through a modified Mycobacterium smegmatis porin A (M2MspA) nanopore under control of phi29 DNA polymerase. This identification was based on three consecutive ionic current states that correspond to passage of modified or unmodified CG dinucleotides and their immediate neighbors through the nanopore limiting aperture. To establish quality scores for these calls, we examined ~3,300 translocation events for 48 distinct DNA constructs. Each experiment analyzed a mixture of cytosine-, 5-methylcytosine-, and 5-hydroxymethylcytosine-bearing DNA strands that contained a marker that independently established the correct cytosine methylation status at the target CG of each molecule tested. To calculate error rates for these calls, we established decision boundaries using a variety of machine-learning methods. These error rates depended upon the identity of the bases immediately 5' and 3' of the targeted CG dinucleotide, and ranged from 1.7% to 12.2% for a single-pass read. We estimate that Q40 values (0.01% error rates) for methylation status calls could be achieved by reading single molecules 5-19 times depending upon sequence context.
Infrared color vision: separating objects from backgrounds

The concept of multi-band infrared color vision is discussed in terms of combining two or more bands of infrared imagery into a single composite color image. This work is motivated by emerging new technologies in which two or more infrared bands are simultaneously imaged for improved discrimination of objects from backgrounds. One of the current objectives of this work is to quantify the improvement obtained over single band infrared imagery to detect dim targets in clutter. Methods are discussed for mapping raw image data into an appropriate color space and then processing it to achieve an intuitively meaningful color display for a human viewer. In this regard, the final imagery should provide good color contrast between objects and backgrounds and consistent colors regardless of environmental conditions such as solar illumination and variations in surface temperature. Initial performance measures show that infrared color can improve discrimination significantly over single band imaging.