cssi/SciSciGPT-SciSciNet huggingface dataset:
A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression.

Cancer subtype information is critically important for understanding tumor heterogeneity. Existing methods to identify cancer subtypes have primarily focused on utilizing generic clustering algorithms (such as hierarchical clustering) to identify subtypes based on gene expression data. The network-level interaction among genes, which is key to understanding the molecular perturbations in cancer, has been rarely considered during the clustering process. The motivation of our work is to develop a method that effectively incorporates molecular interaction networks into the clustering process to improve cancer subtype identification. We have developed a new clustering algorithm for cancer subtype identification, called “network-assisted co-clustering for the identification of cancer subtypes” (NCIS). NCIS combines gene network information to simultaneously group samples and genes into biologically meaningful clusters. Prior to clustering, we assign weights to genes based on their impact in the network. Then a new weighted co-clustering algorithm based on a semi-nonnegative matrix tri-factorization is applied. We evaluated the effectiveness of NCIS on simulated datasets as well as large-scale Breast Cancer and Glioblastoma Multiforme patient samples from The Cancer Genome Atlas (TCGA) project. NCIS was shown to better separate the patient samples into clinically distinct subtypes and achieve higher accuracy on the simulated datasets to tolerate noise, as compared to consensus hierarchical clustering. The weighted co-clustering approach in NCIS provides a unique solution to incorporate gene network information into the clustering process. Our tool will be useful to comprehensively identify cancer subtypes that would otherwise be obscured by cancer heterogeneity, using high-throughput and high-dimensional gene expression data.
Non-linear dynamics of viscoelastic flows in axisymmetric conduits with abrupt changes

Abstract Viscoelastic flows of a PIB/PB/C14 polymer solution in axisymmetric cavity geometries have been studied. Multiple elastic flow transitions of spatial and temporal types are observed. The critical conditions for the onset of instabilities and the spatial and temporal structures of the flow are examined using instantaneous differential pressure measurements and flow visualization by streakline photography. Cavity dominated flow features are observed in short cavities while the entry flow dominates in longer cavities. The pressure fluctuations generated by elastic flow instabilities are as much as 30% of the nominal value and the dynamics of the flow become strongly non-linear and very complicated especially at high flow rates.
Measurement of attogram quantities of 231Pa in dissolved and particulate fractions of seawater by isotope dilution thermal ionization mass spectroscopy.

A technique has been developed to quantify ultratrace 231Pa (50−2000 ag; 1 ag = 10-18 g) concentrations in seawater using isotope-dilution thermal ionization mass spectrometry (TIMS). The method is a modification of a process developed by Pickett et al. (Pickett, D. A.; Murrell, M. T.; Williams, R. W. Anal. Chem. 1994, 66, 1044−1049) and extends the technique to very low levels of protactinium. The procedural blank is 16 ± 15 ag (2σ), and the ionization efficiency (ions generated/atom loaded) approaches 0.5%. Measurement time is <1 h. The amount of 231Pa needed to produce 231Pa data with an uncertainty of ±4−12% is 100−1000 ag (∼3 × 105 to 3 × 106 atoms). Replicate measurements made on known standards and seawater samples demonstrate that the analytical precision approximates that expected from counting statistics and that, based on detection limits of 38 and 49 ag, protactinium can be detected in a minimum sample size of surface seawater of ∼2 L for suspended particulate matter and <0.1 L for filtered (<...
Postmodernism in Special Education

As a basis for policy, constructivism has an ideological character that draws from but is not identical to Piagetian or Vygotskian notions of constructed knowledge. Special educators should be wary of borrowing fashionable rhetoric of postmodernism to justify development or reform of instruction and curriculum unless accompanying constructs and values can first be disentangled. In reflecting on the articles in this special issue, I indicate that there are higher stakes for special education, particularly in national curriculum and testing reform, that accompany constructivism as a rationale or framework for development of instructional curricular strategies for students with disabilities.
Principal component analysis and interpolation of stochastic processes: methods and simulation

This work proposes a theoretical and experimental study of the Principal Component Analysis of a stochastic Process (PCAP). It aims to clarify the theoretical framework and provides a simulation experimental basis for evaluating potential errors when using the PCAP as a mapping technique.
Atypical Experience: A Case Series of Pediatric Aripiprazole Exposures

Background: Aripiprazole is a new psychotropic agent that possesses a unique pharmacologic profile. The drug demonstrates mixed dopamine and serotonin agonist-antagonist activity and has been labeled a third-generation antipsychotic and dopamine-serotonin system stabilizer. Overdose experience is limited, especially in pediatrics. Case Series: Of five pediatric cases identified, toxicity was mainly evident in younger patients. A 2-year-old who ingested 40 mg experienced vomiting and significant lethargy lasting approximately 30 h. A 6-year-old who received two doses of aripiprazole therapeutically experienced lethargy, drooling, and flaccid facial muscles which improved with diphenhydramine. Two adolescents remained asymptomatic despite doses of 120 mg and 300 mg while a third adolescent with an unknown dose experienced transient lethargy. Conclusion: Aripiprazole is capable of producing marked lethargy and gastrointestinal upset in pediatric patients. Adolescents in this series experienced only minor, if...
Thrombophilia and Stroke

Thrombophilia is defined as an enhanced tendency to form intravascular thrombi, which may be arterial or venous. Of the inherited thrombophilias, factor V Leiden and the prothrombin 20210 mutation have been associated with stroke, but this association is statistically significant only in children and adults under age 40. The risk of stroke in persons with these mutations is substantially increased by concomitant exposure to oral contraceptives. Hyperhomocystinemia is a major risk factor for stroke as well as Alzheimer’s disease; persons with deficiencies of vitamin B12 or folic acid are especially vulnerable to these complications. Of the acquired thrombophilias, the antiphospholipid antibody syndrome is strongly associated with transient ischemic attacks, cerebral infarction, Sneddon syndrome, and dementia. The diagnosis of thrombophilia should be considered in stroke patients who are young, have a family history of thrombosis, suffer venous dural sinus thrombosis, or have recurrent strokes.
4-Oxocyclohexanecarboxylic acid: Hydrogen bonding in the monohydrate of a δ-keto acid

The title monohydrate, C(7)H(10)O(3).H(2)O, aggregates as a complex hydrogen-bonding network, in which the water molecule accepts a hydrogen bond from the carboxyl group of one molecule and donates hydrogen bonds to ketone and carboxyl C=O functions in two additional molecules, yielding a sheet-like structure of parallel ribbons. The keto acid adopts a chiral conformation through rotation of the carboxyl group by 62.50 (15) degrees relative to the plane defined by its point of attachment and the ketone C and O atoms. Two C-H.O close contacts exist in the structure.
Scanning Electrochemical Microscopy Assessment of Rates of Molecular Transport through Mesoporous Thin-Films of Porphyrinic “Molecular Squares”†

Scanning electrochemical microscopy (SECM), in combination with electrode platform micropatterning, has been used for qualitative characterization of molecular sieving and exceptionally precise quantitative measurement of molecular permeation through thin films of meso- and microporous materials composed of porphyrinic “molecular squares”. SECM measurements reveal that modification of the squares, to reduce cavity sizes and alter the size cutoff for permeation, has only a modest effect upon the permeabilities of those probe molecules small enough to pass through the modified films. Additional experiments as a function of electrolyte composition show that the ability to observe sieving behavior electrochemically is determined not only by the relative sizes of redox-active permeant molecules and film-based cavity openings, but also by the steric properties of ions needed for charge compensation − even when the permeant molecule is initially neutral. As expected, when the size of the opening is altered the s...
Gabapentin suppresses cortical spreading depression susceptibility

Cortical spreading depression (CSD) is an intense depolarization wave implicated in the pathophysiology of brain injury states and migraine aura. As Ca(v)2.1 channels modulate CSD susceptibility, we tested gabapentin, which inhibits Ca(v)2.1 through high-affinity binding to its alpha(2)delta subunit, on CSD susceptibility in anesthetized rats. Gabapentin, 100 or 200 mg/kg, elevated the electrical threshold for CSD and diminished recurrent CSDs evoked by topical KCl, when administered 1 hour before testing. With its favorable safety and tolerability profile, gabapentin may have a role in suppression of injury depolarizations in stroke, intracranial hemorrhage, and traumatic brain injury.
Hemorrhagic Shock-Induced Alterations in Circulating and Bronchoalveolar Macrophage Nitric Oxide Production

Abstract Local and systemic host immune functions are markedly altered after trauma. Activated macrophages (Mφ) are the major effector cells of protective immunity, mediated in part by nitric oxide (NO). This study was undertaken to determine the effects of hemorrhage (HEM) on Mφ cytotoxic function as measured by NO production. Male Sprague-Dawley 350- to 400-g rats were studied. Sham animals only had their carotid artery exposed and ligated. Hemorrhaged animals had carotid artery cannulation followed by HEM to SBP of 40 mmHg, sustained for 4.5 min, followed by resuscitation with shed blood and crystalloid. Recovered animals were sacrificed ( n = 5 each) at 6, 12, 24, and 72 hr after HEM; blood and alveolar Mφ were then isolated and examined. A monolayer of adherent Mφ was examined for NO production in resting state and after in vitro LPS stimulation. (1) HEM resulted in significantly reduced alveolar Mφ yield at 12 and 24 hr. (2) HEM increased NO production by circulating Mφ at 24 hr ( P P
Chemokine 'grooming' by cLECs directs DC migration

Migrating dendritic cells follow precise navigational chemokine gradients established by lymph node stromal cells through their asymmetric expression of the atypical chemokine receptor CCRL1.
Bioaccumulation factors of chlorinated hydrocarbons between mussels and seawater

Abstract The bioaccumulation of PCB and DDT compounds by mussels, Mytilus spp., from ambient seawater was determined by measuring concentrations of these chlorinated hydrocarbons in both mussels and seawater at four sites on the Mediterranean coast of France and two sites in California. Bioaccumulation factors were found to vary over an order of magnitude. Ratios of the concentrations of PCB in mussels, consisting predominantly of pentachloro-and hexachlorobiphenyls, to concentrations in ambient seawater ranged between 69 000 and 690 000; the corresponding ratios of concentrations of p , p ′-DDE or p , p ′-DDT ranged from 40 000 to 690 000. Although mussels appear to be appropriate and convenient indicator organisms of local chlorinated hydrocarbon contamination levels, the factors contributing to this variance must be determined before mussels are widely used in global monitoring programmes.
Recruitment mechanisms in speed and fine-direction discrimination tasks

The minimum information necessary to specify motion requires a change in position across time. Previous studies have shown that human motion measurements improve with more than two frames of motion. This study clarifies how motion information is integrated to produce the best speed and direction discrimination. Using random-dot kinematograms, fine-direction discrimination thresholds and speed discrimination thresholds are assessed as a function of dot lifetime. Specifically, we ask if performance on both tasks depends on dot lifetime in the same manner. If both speed and direction discrimination performance improve the same way with increasing dot lifetime, this would indicate that both tasks have the same integration limit and both tasks may depend on the same underlying mechanisms. Experiment 1 shows that for both tasks a four-frame dot lifetime is necessary for observers to reach asymptotic threshold levels. The absolute level of performance improves with increasing stimulus duration or signal-to-noise ratio, but the integration limit itself does not vary. Experiment 2 examines whether this integration limit is constrained by the number of frames or by the temporal duration of the dot lifetime. The data in Experiment 2 suggest that both a minimum number of samples and a minimal temporal integration period determine the integration limit for recruitment mechanisms. The results suggest that speed and fine-direction discrimination depend upon the same underlying motion mechanisms. These results are discussed in relation to possible underlying physiological substrates and computational models of motion measurement.
Quality of life after bilateral prophylactic mastectomy.

Bilateral prophylactic mastectomy in women with increased breast cancer risk dramatically reduces breast cancer occurrence but little is known about psychosocial outcomes. To examine long-term quality of life after bilateral prophylactic mastectomy, we mailed surveys to 195 women who had the procedure from 1979 to 1999 and to a random sample of 117 women at increased breast cancer risk who did not have the procedure. Measures were modeled on or drawn directly from validated instruments designed to assess quality of life, body image, sexuality, breast cancer concerns, depression, health perception, and demographic characteristics. We used logistic regression to examine associations between quality of life and other domains. The response rate was 58%, with 106 women with and 62 women without prophylactic mastectomy returning complete surveys. Among women who underwent bilateral prophylactic mastectomy, 84% were satisfied with their decision to have the procedure; 61% reported high contentment with quality of life compared with an identical 61% of women who did not have the procedure (P = 1.0). Among all subjects, diminished contentment with quality of life was not associated with bilateral prophylactic mastectomy but with dissatisfaction with sex life (adjusted ratio [OR] = 2.5, 95% confidence interval [CI] = 1.0–6.2), possible depression (CES-D > 16, OR = 4.9, CI = 2.0–11.8), and poor or fair general health perception (OR = 8.3, 95% CI = 2.4–29.0). The majority of women reported satisfaction with bilateral prophylactic mastectomy and experienced psychosocial outcomes similar to women with similarly elevated breast cancer risk who did not undergo prophylactic mastectomy. Bilateral prophylactic mastectomy appears to neither positively nor negatively impact long-term psychosocial outcomes.
Permeability of the 17-day fetal rat pancreas to glycerol and dimethylsulfoxide.

Abstract Experimentally induced diabetes in rats can be reversed by the transplantation of several fresh or frozen-thawed fetal pancreases. An important question to both the mechanistic and practical aspects of cryobiology is the role played by the permeation of protective additives during freezing, thawing, and subsequent dilution. Answers require knowledge of the kinetics of permeation of the specific additive into the cell or tissue. In this paper, we report isotopic measurements of the rate of permeation of 2 M glycerol and 1 and 2 M dimethylsulfoxide (Me2SO) into 17-day fetal pancreases at 0 and 22 °C. In Me2SO, equilibrium was achieved in about 10–15 min at 0 °C and in less than 10 min at 22 °C. In glycerol, equilibrium was attained in about 60 min at 22 °C; but at 0 °C permeation was only 65% complete after 180 min. In general, Me2SO permeated 10–30 times more rapidly than glycerol at 0 °C, and glycerol permeated about 10 times more rapidly at 22 than at 0 °C. The kinetics of permeation were more characteristic of a two-compartment than a single-compartment system. In all probability, the two compartments are the intercellular space and the intracellular space. The permeability data suggest that each compartment occupies about half the total volume.
Status of the J-series 30-cm mercury ion thruster

This paper describes the status of the 30-cm J-series mercury ion thruster. This thruster was baselined for the Solar Electric Propulsion System (SEPS) vehicle. This thruster is described and several modifications plus suggested modifications are presented. Some of the modifications resulted from tests performed with the thruster. The operational characteristics of eight J-series thrusters are presented. Isolator contamination and flake formation are also discussed.
Wrap-around services: an analysis of community-based mental health services for children.

Topic Wrap-around services-individualized, community-based mental health services for children in their homes and schools-for children with severe emotional and behavioral disorders. Purpose To conduct an analysis of the social policy antecedents that culminated in wrap-around services in one state and consider the development of one state's implementation and relevant value issues. Sources Policy and historical literature; the first author's experience as a director of a large wrap-around program. Conclusions While the advent of wrap-around services and the expansion of Medicaid represent significant steps forward in the treatment of children with mental health problems, outcome studies of these services are sorely needed.
Diffraction by a circular aperture as a model for three-dimensional optical microscopy

Existing formulations of the three-dimensional (3-D) diffraction pattern of spherical waves that is produced by a circular aperture are reviewed in the context of 3-D serial-sectioning microscopy. A new formulation for off-axis focal points is introduced that has the desirable properties of increased accuracy for larger field angles, invariance to shifts of the focal point about spheres of constant radius when the detection point is on the sphere for both intensity and amplitude fields, and invariance to shifts in three transformed coordinates for intensity fields. Finally, calculated intensity fields for both on-axis and off-axis focal points are included to illustrate the proposal that the classical 3-D diffraction patterns that have been used as analytical models in 3-D serial-sectioning fluorescence microscopy may not be accurate enough for this application.
Wake IQ: Using a smartphone to reduce sleep inertia

This paper presents Wake IQ, a smartphone program to reduce sleep inertia. Wake IQ aims at waking its user with proper timing so as to reduce or eliminate sleep inertia and increase overall alertness, while maintaining a convenience conducive to everyday use. It is constructed based on machine learning techniques, phone accelerometer data sampled during slumber, and user alertness test scores. Tests of the system have demonstrated a gradually increasing average response speed to reaction time tests over a period of a number of weeks, indicative of a trend towards reduced sleep inertia arising from use of the smartphone application.
Studies on the Condensation Pathway to and Properties of Diiron Azadithiolate Carbonyls.

Reaction of Fe2(SH)2(CO)6 and HCHO, which gives Fe2[(SCH2)2NH](CO)6 in the presence of NH3, affords the possible intermediate Fe2(SCH2OH)2(CO)6, which has been characterized crystallographically as its axial−equatorial isomer. Fe2(SCH2OH)2(CO)6 was shown to react with ammonia and amines to give Fe2[(SCH2)2NR](CO)6 (R = H, alkyl). Related hemithioacetal intermediates were generated by treatment of Fe2(SH)2(CO)6 with RC(O)C(O)R (R = H, Ph, 4-F-C6H4) to give cycloadducts. The benzil derivative Fe2[S2C2(OH)2Ph2](CO)6, a C2-symmetric species, was also characterized crystallographically. The acylated azadithiolate Fe2[(SCH2)2NAc](CO)6 was prepared by reaction of Li2Fe2S2(CO)6 with (ClCH2)2NC(O)Me. DNMR experiments show that the free energies of activation for rotation of the amide bond are the same for Fe2[(SCH2)2NAc](CO)6 and Fe2[(SCH2)2NAc](CO)4(PMe3)2, which implies that the ligands on the iron centers do not strongly affect the basicity of the nitrogen. As a control, we showed that the thioamide Fe2[(SCH2)2...
A Comparison of Strontium Sorption to Hydrous Aluminum, Iron, and Manganese Oxides.

Abstract Strontium sorption to hydrous aluminum (HAO) and manganese (HMO) oxides was studied using macroscopic studies on short- and long-term bases. These studies were compared with previous results for strontium sorption to hydrous ferric oxide (HFO). Sorption to these microporous oxides can be described as a two-step process: a rapid and reversible adsorption reaction to the external surface including the macropores is followed by a slow surface diffusion along the micropore walls of the oxides. Strontium adsorption is a physical type of reaction, where the sorbate retains its hydration sheath. Because the relationship between the amount sorbed and the bulk aqueous concentration was linear (over six orders of magnitude), the range of surface sites can be described with one average type of site. Thermodynamically, this adsorption is an entropy-driven endothermic reaction. Transient studies revealed surface diffusion coefficients ranged from 10−12 to 10−11 cm2/s; these diffusivities were compared to theoretical diffusivities using site activation theory. Results observed in these studies are consistent with those of HFO where for all the oxides, the energy barrier between sites is approximately equivalent. The long-term studies revealed as much as 90% of the total sites were located on the internal surfaces of the hydrous oxides. Therefore, current transport models must include the contribution from intraparticle diffusion to accurately describe the migration of Sr in the aquatic environments.
Effect of hard-sphere structure on pure-component equation of state calculations

Abstract Hard-sphere fluid structure is shown to be important in describing the thermodynamic properties of the square-well fluid. A simple local composition model using the exponential approximation (EXP) of Anderson and Chandler (1972) for the pair correlation function is developed. The hard-sphere pair correlation function is determined using the analytic solution to the Percus-Yevick theory (Wertheim, 1964). The model is shown to predict the properties of the square-well fluid that are in good agreement with molecular dynamics data. The equation is used to predict the properties of argon and methane. The equation is also incorporated into the Simplified-Perturbed-Hard-Chain Theory (SPHCT), and the new equation improves calculations of vapor pressures and saturated densities for non-polar and polar fluids.
Utility of MR arthrography in the diagnosis of adhesive capsulitis.

Objective. Arthrographically, adhesive capsulitis is characterized by decreased joint volume; histologically, the capsule and synovium are thickened. We therefore compared using MR arthrography the joint volumes and capsule/synovial thickness of patients with and without adhesive capsulitis in order to assess the utility of MR arthrography in diagnosing adhesive capsulitis.
Coase on entrepreneurship

Following a short biography of Nobel Laureate economist Ronald H. Coase, this two part interview explores (1) Coase’s life history and thoughts on academic scholarship and (2) Coase’s perspective on the field of entrepreneurship. Coase describes his experiences during his visiting scholarship to America in 1932, early career at the London School of Economics, and government work during World War II. He discusses the virtues of scholarship and the role of technology. In the second part of the interview, Coase views entrepreneurship as a vital source of endogenous change in the economy and outlines the importance of investigating the structure of production, and other important research and policy questions. Coase elaborates on how entrepreneurship has changed over time, and describes his most recent work on entrepreneurship in China. The interview concludes with Coase’s thoughts on the evolution of scholarship and his efforts to advance the field.
Linear free energy relationships reveal structural changes in hydrogen-bonded host-guest interactions.

Hydrogen bond strength in host–guest systems is modulated by many factors including preorganization, steric effects, and electronic effects. To investigate how electronic effects impact barbiturate binding in bifurcated Hamilton receptors, a library of receptors with differing electronic substituents was synthesized and 1H NMR titrations were performed with diethyl barbital. The Hammett plot revealed a clear break between the different electronic substituents suggesting a change in binding conformation. The titration data were complimented with computational studies confirming the change in structure.
Introgression of Novel Traits from a Wild Wheat Relative Improves Drought Adaptation in Wheat

Root architecture traits are an important component for improving water stress adaptation. However, selection for aboveground traits under favorable environments in modern cultivars may have led to an inadvertent loss of genes and novel alleles beneficial for adapting to environments with limited water. In this study, we elucidate the physiological and molecular consequences of introgressing an alien chromosome segment (7DL) from a wild wheat relative species (Agropyron elongatum) into cultivated wheat (Triticum aestivum). The wheat translocation line had improved water stress adaptation and higher root and shoot biomass compared with the control genotypes, which showed significant drops in root and shoot biomass during stress. Enhanced access to water due to higher root biomass enabled the translocation line to maintain more favorable gas-exchange and carbon assimilation levels relative to the wild-type wheat genotypes during water stress. Transcriptome analysis identified candidate genes associated with root development. Two of these candidate genes mapped to the site of translocation on chromosome 7DL based on single-feature polymorphism analysis. A brassinosteroid signaling pathway was predicted to be involved in the novel root responses observed in the A. elongatum translocation line, based on the coexpression-based gene network generated by seeding the network with the candidate genes. We present an effective and highly integrated approach that combines root phenotyping, whole-plant physiology, and functional genomics to discover novel root traits and the underlying genes from a wild related species to improve drought adaptation in cultivated wheat.
Charge transfer between rigid spheres separated in an electric field

Measurements have been made of the maximum separation X at which charge is transferred by means of a discharge process between two rigid spheres of radii r and R located in a uniform external electric field E. The experimental relationships between X, E, r and R are in good agreement with the calculations of Davis (1964). It was observed that for small separations charge transfer occurs even in the presence of weak external fields because the local field between the near surfaces of the spheres is greater than the external field strength by an amount that increases rapidly as their separation decreases.
CD109 represents a novel branch of the α2-macroglobulin/complement gene family

We report here the genomic organization and phylogenic relationships of CD109, a member of the the alpha2-macroglobulin/complement (AMCOM) gene family. CD109 is a GPI-linked glycoprotein expressed on endothelial cells, platelets, activated T-cells, and a wide variety of tumors. We cloned full-length CD109 cDNA from the mammalian U373 cell line by RT-PCR and performed analysis of its corresponding genomic sequence. The CD109 cDNA spans 128 kb of chromosome 6q with its 33 exons constituting approximately 3.3% of the total CD109 genomic sequence. Sequence analysis revealed that CD109 contains specific motifs in its N-terminus, that are highly conserved in all AMCOM members. CD109 also shares motifs with certain other AMCOM members including: (1) a thioester 'GCGEQ" motif, (2) a furin site of four positively charged amino acids, and (3) a double tyrosine near the C-terminus. Based on a phylogenic analysis of human CD109 with other human homologs as well as orthologs from other mammalian species, C. elegans (ZK337.1) and E. coli homologs, we propose CD109 represents a novel and independent branch of the alpha2-macroglobulin/complement gene family (AMCOM) and may be its oldest member.
THERAPY OF HEPATITIS C. OTHER OPTIONS

Because current standard therapy of chronic hepatitis C with alpha interferon is less than ideal, numerous other approaches have been studied. Iron in the liver, particularly that found in vascular endothelial cells of portal tracts, has been associated with decreased responsiveness to alpha interferon therapy. Iron reduction alone, generally achieved by therapeutic phlebotomy, regularly has been associated with biochemical improvement (decrease in serum alanine aminotransferase), but not with virological improvement. Iron reduction has been reported to increase the therapeutic response to alpha interferon. Most studies of this combination have been conducted in patients who had not responded to interferon alone; in these patients, improved responsiveness has been observed in some, but not all studies. In patients not previously treated, iron reduction was found in a recent trial to improve the sustained biochemical and virological response rate from 5% to 29%. Hepatic iron and chronic hepatitis C increase oxidative stress in the liver and are associated with decreases in hepatic glutathione levels. In one report, administration of N-acetyl cysteine, a sulfhydryl donor, led to improved response to interferon in chronic hepatitis C. Several cytokines and immunomodulators have undergone limited study; perhaps the most promising of these is thymosin alpha-1. In one small study, amantadine was found to produce some response in patients who previously had failed to respond to interferon. Ursodiol improves serum aminotransferase levels in chronic hepatitis C but has no antiviral effect, nor has it been found to improve histologic abnormalities. The future of therapy of chronic hepatitis C will likely include measures to decrease oxidative stress and injury and multidrug combinations, including inhibitors of the hepatitis C viral protease and RNA polymerase.
Electron Spin Resonance Evidence for a Trapped Electron and its Reversible Reaction in Gamma-irradiated Acetonitrile- d 3

ALTHOUGH the effect of ionizing radiation is known to produce solvated and trapped electrons in a variety of liquid and glassy systems, we are not aware of any reports on the radiation-induced formation of localized electrons in molecular crystals. Bennett, Mile and Thomas1 have observed electron spin resonance (ESR) and optical absorption spectra of trapped electrons in polycrystalline ice, but the method of preparation in this case was to deposit water vapour and alkali metals together on the rotating drum of a cryostat at 77° K. A very interesting feature of this work1 was the observation of hyperfine splitting in the ESR spectrum of the trapped electron as the temperature of a potassium–water sample was raised to 173° K. The seven hyperfine lines have been attributed to the interaction of the trapped electron writh six equivalent protons in an octahedral arrangement.
Biodegradation of plant cell walls, wall carbohydrates, and wall aromatics in wheat grown in ambient or enriched CO2 concentrations

Mature internodes from wheat (Triticum aestivum L) grown in control (ambient at c 370 μnol mol−1) or enriched (to 550 μmol mol−1) concentrations of atmospheric CO2 in the free-air CO2 enrichment (FACE) system were analyzed for potential changes in biodegradation of constituents due to predicted increases in atmospheric levels of CO2. The first internodes below the grain were incubated with the lignocellulose-degrading white rot fungus, Phanerochaete chrysosporium K-3, or incubated without microorganisms. Plant samples were then analyzed for dry weight loss, disposition of specific cell types to biodegradation using electron microscopy, carbohydrates and lignin using solid state NMR spectroscopy, and ester-and ether-linked aromatics using gas chromatography. Phanerochaete chrysosporium extensively degraded stems cells (c 75%) and both carbohydrate and aromatic portions of the wheat stems; proportionately more carbohydrates were removed by the fungus from the stems. Enriched CO2 did not affect the chemical composition of wheat stems or the biodegradation by P chrysosporium of plant cell walls or wall components for the most part. Data from various methods all indicated that enriched CO2 did not substantially alter the biodegradation of wheat cell wall internodes or wall components. Evidence was not found for an influence on C cycling due to CO2 concentrations in this study.
Isolation and fluorescence studies on a lipophorin from the weevil diaprepes abbreviatus

Lipophorin was isolated from larvae of a root weevil, Diaprepes abbreviatus (Coleoptera: Curculionidae), using density gradient ultracentrifugation. D. abbreviatus lipophorin contained two apoproteins, apolipophorin-I (Mr = 226,000) and apolipophorin-II (Mr = 72,100) and had a density of 1.08. Relative to other larval lipophorins, D. abbreviatus lipophorin contained little cysteine (determined as cysteic acid) and methionine. Fluorescence spectroscopy of intrinsic tyrosine and tryptophan residues excited at 290 nm revealed a single broad emission peak at 330 nm. Upon denaturing and delipidating lipophorin in guanidine HCl, this peak resolved into two peaks with maxima at 305 and 350 nm. Excitation spectra suggested that the two peaks were due to tyrosine and tryptophan, respectively. Fluorescence quenching agents, iodide and acrylamide, were used to determine accessibility of tyrosine and tryptophan residues to the aqueous environment. Iodide, a polar quenching agent, did not quench fluorescent emission from native lipophorin; quenching by iodide increased to moderate levels when lipophorin was denatured in guanidine HCl. Acrylamide quenched the fluorescence of native lipophorin moderately and very efficiently quenched fluorescence of denatured lipophorin. No difference was observed between fluorescence quenching of denatured vs. denatured and delipidated lipophorin by either iodide or acrylamide.
The Arginine Decarboxylase Pathways of Host and Pathogen Interact to Impact Inflammatory Pathways in the Lung

The arginine decarboxylase pathway, which converts arginine to agmatine, is present in both humans and most bacterial pathogens. In humans agmatine is a neurotransmitter with affinities towards α2-adrenoreceptors, serotonin receptors, and may inhibit nitric oxide synthase. In bacteria agmatine serves as a precursor to polyamine synthesis and was recently shown to enhance biofilm development in some strains of the respiratory pathogen Pseudomonas aeruginosa. We determined agmatine is at the center of a competing metabolism in the human lung during airways infections and is influenced by the metabolic phenotypes of the infecting pathogens. Ultra performance liquid chromatography with mass spectrometry detection was used to measure agmatine in human sputum samples from patients with cystic fibrosis, spent supernatant from clinical sputum isolates, and from bronchoalvelolar lavage fluid from mice infected with P. aeruginosa agmatine mutants. Agmatine in human sputum peaks during illness, decreased with treatment and is positively correlated with inflammatory cytokines. Analysis of the agmatine metabolic phenotype in clinical sputum isolates revealed most deplete agmatine when grown in its presence; however a minority appeared to generate large amounts of agmatine presumably driving sputum agmatine to high levels. Agmatine exposure to inflammatory cells and in mice demonstrated its role as a direct immune activator with effects on TNF-α production, likely through NF-κB activation. P. aeruginosa mutants for agmatine detection and metabolism were constructed and show the real-time evolution of host-derived agmatine in the airways during acute lung infection. These experiments also demonstrated pathogen agmatine production can upregulate the inflammatory response. As some clinical isolates have adapted to hypersecrete agmatine, these combined data would suggest agmatine is a novel target for immune modulation in the host-pathogen dynamic.
Empirical bayes analysis of sequencing-based transcriptional profiling without replicates

Background Recent technological advancements have made high throughput sequencing an increasingly popular approach for transcriptome analysis. Advantages of sequencing-based transcriptional profiling over microarrays have been reported, including lower technical variability. However, advances in technology do not remove biological variation between replicates and this variation is often neglected in many analyses.
Packing systematics of the silica polymorphs: The role played by O-O nonbonded interactions in the compression of quartz

terize the role of tetrahedral distortion and O-O interactions in the compression of quartz. Quartz has eight crystallographically nonequivalent tetrahedra, one occupied by silicon and seven unoccupied. These tetrahedra completely fill space, something that cannot be done using only regular tetrahedra. In ideal BCC quartz, the nonequivalent tetrahedra are identical in size and shape with a unique geometry and are referred to as Sommerville tetrahedra. In reality, the unoccupied tetrahedra of quartz are very distorted from both regular and Sommerville tetrahedra. Changes in the unoccupied tetrahedra are responsible for most of the compression in quartz with pressure, as the volume of the Si tetrahedron decreases by <1% over 10.2 GPa, but the volume of the bulk structure decreases by almost 16%. The ideal BCC quartz has been used to quantify the distortion from ideal BCC of the O arrangement in quartz at several pressures up to 10.2 GPa. Distortion decreases by over 60% across this domain. Other parameters have been derived to quantify the distortion of the unoccupied and occupied tetrahedra in quartz from Sommerville tetrahedra, the characteristic tetrahedra of BCC. By all measures, the anion packing in quartz approaches ideal BCC as pressure increases. The compression mechanisms of quartz are compared to those of cristobalite and coesite. Si-O-Si angle-bending controls compression in each of these minerals. The bulk moduli of these minerals are shown to correlate with average nearest intertetrahedral anion distances, consistent with the hypothesis that anion-anion interactions stiffen the Si-O-Si angle as inter-tetrahedral anion distances decrease. The tetrahedral distortion in quartz with pressure is attributed to anion-anion interaction, and is not considered a compression mechanism.
Computational Game Theory for Security and Sustainability

Security is a critical concern around the world that arises in protecting our ports, airports, transportation and other critical national infrastructure from adversaries, in protecting our wildlife and forests from poachers and smugglers, and in curtailing the illegal flow of weapons, drugs and money; and it arises in problems ranging from physical to cyber-physical systems. In all of these problems, we have limited security resources which prevent full security coverage at all times; instead, security resources must be deployed intelligently taking into account differences in priorities of targets requiring security coverage, the responses of the attackers to the security posture, and potential uncertainty over the types, capabilities, knowledge and priorities of attackers faced. Game theory, which studies interactions among multiple selfinterested agents, is well-suited to the adversarial reasoning required for security resource allocation and scheduling problems. Casting the problem as a Bayesian Stackelberg game, we have developed new algorithms for efficiently solving such games that provide randomized patrolling or inspection strategies. These algorithms have led to some initial successes in this challenging problem arena, leading to advances over previous approaches in security scheduling and allocation, e.g., by addressing key weaknesses of predictability of human schedulers. These algorithms are now deployed in multiple applications: ARMOR has been deployed at the Los Angeles International Airport (LAX) since 2007 to randomize checkpoints on the roadways entering the airport and canine patrol routes within the airport terminals [17]; IRIS, a game-theoretic scheduler for randomized deployment of the US Federal Air Marshals (FAMS) requiring significant scaleup in underlying algorithms, has been in use since 2009 [17]; PROTECT, which schedules the US Coast Guard’s randomized patrolling of ports using a new set of algorithms based on modeling bounded-rational human attackers, has been deployed in the
Role of Hydrogen Microstructure in Amorphous Silicon

A model for correlating the observed properties of hydrogenated amorphous silicon (a-Si:H) with the underlying hydrogen microstructure is reviewed. The model provides a unified description of defect equilibration, hydrogen evolution, rehydrogenation and hydrogen diffusion measurements.
Role‐Playing and Playing Roles: The Person, Player, and Persona in Fantasy Role‐Playing

In fantasy role-playing games, participants collectively create and play fantasy personas in an imaginary universe by using a vast system of rules that function as guidelines for make-believe action and interaction. Consequently, role-playing games obligate participants to occupy a liminal role located in the boundaries of persona, player, and person. This study, based on approximately ninety hours of participant observation and forty interviews with thirty role-players, explores how role-players actively negotiate these symbolic boundaries: how role-players carve out distinct spheres of meaning between themselves, their fantasy personas, and status as players of these games. It also illustrates how these distinctions fail. Boundaries erupt and role-players prove unable to compartmentalize themselves so discretely. Through the lens of these games, we can examine simplified and exaggerated dynamics and entertain the possibility that we are all players located at the liminal margins between the people we believe ourselves to be and the personas we perform in situated social encounters. Roles may not only be played but also played at , as when children, stage actors, and other kinds of cutups mimic a role for the avowed purpose of make-believe; here, surely, doing is not being. But this is easy to deal with. A movie star who plays at being a doctor is not in the role of doctor but in the role of actor; and this latter role, we are told, he is likely to take quite seriously. The work of his role is to portray a doctor, but the work is only incidental; his actual role is no more make-believe than that of a real doctor—merely better paid. . . . These desperate performers are caught exactly between illusion and reality, and must lead one audience to accept the role portrait as real, even while assuring another audience that the actor in no way is convincing himself. —Erving Goffman, Encounters
Characterization and Solubility of SiO2-TiO2-CaO-Na2O/SrO Bioactive Glasses

This project investigates the characterization and solubility of a bioactive glass series where Strontium (Sr) and Sodium (Na) are substituted. X-ray diffraction (XRD) was employed to ensure that each starting material is amorphous. Differential Thermal Analysis (DTA) was used to determine the thermal profile of each material, in particular, the glass transition temperature (Tg), the crystallization temperature (Tc1) and the melting temperature (Tm). Magic Angle Spinning - Nuclear Magnetic Resonance (MAS-NMR) was used to probe the local 29Si environment. Simulated Body Fluid (SBF) testing revealed a CaP surface layer on each glass after 7 days.
An improved double vaseline gap voltage clamp to study electroporated skeletal muscle fibers

An improved voltage clamp with a double vaseline gap chamber was designed to study electroporated skeletal muscle fibers. The new clamp eliminated spike overshock of membrane potential when applying step stimulation occurring in the traditional configuration. It allowed greater consistency in membrane potential distribution. After the intracellular resistances of the fiber segment at the vaseline gap area were compensated, it was possible to change membrane potential more quickly. Using this technique, strong electrical pulses used to mimic the situation of electrical shock can be delivered to the cell membrane by voltage clamp. Transmembrane currents of skeletal muscle cell were simultaneously measured during a high pulsed shock and resolved into different components. Distinct transient changes of the transmembrane current, involving the time courses of the formation of electroporation and their recovery time constants, can be recorded. Because of more even membrane potential distribution and faster response to pulsed membrane potential change, this technique is also suitable for membrane study under physiological conditions.
Image driven GPS trace analysis for road map inference

The trace data generated from GPS enabled vehicles is highly valuable for applications such as map inference and traffic analysis. However, the data tends to be noisy due to signal interference. In this paper, we introduce aerial images in GPS trace analysis. Computer vision techniques are developed that effectively integrate image information with GPS data to generate road networks. An image is first segmented by an efficient factorization-based algorithm. A structure tensor approach is proposed to measure the orientation difference between a trace segment and the corresponding image patch. The segmentation result and orientation measures lead to significantly reducing the traces not aligning with roads. The traces are further processed to produce high-quality road networks. We show that our method produces promising results for very noisy GPS data with a low sampling rate and also outperforms the leading method of map inference from GPS traces.
General energy bounds for systems of bosons with soft cores

We study a bound system of N identical bosons interacting by model pair potentials of the form $V(r)=\ensuremath{\lambda}\mathrm{sgn}{(p)r}^{p}+\ensuremath{\mu}{/r}^{2},$ $\ensuremath{\lambda}g0,$ $\ensuremath{\mu}g~0.$ By using a variational trial function and the ``equivalent two-body method,'' we find explicit upper and lower bound formulas for the N-particle ground-state energy in arbitrary spatial dimensions $dg~3$ for the two cases $p=2$ and $p=\ensuremath{-}1.$ It is demonstrated that the upper bound can be systematically improved with the aid of a special large-N limit in collective field theory.
Comparing Genomic Profiles of Women With and Without Fibromyalgia.

Background:Fibromyalgia syndrome (FMS), a chronic musculoskeletal condition characterized by diffuse pain, fatigue, sleep impairment, and cognitive dysfunction, is associated with significant funct...