cssi/SciSciGPT-SciSciNet huggingface dataset:
Muon g-2 Constraints to SUSY Dark Matter over the Next Decade

The anomalous magnetic moment of the muon has been measured to 0.5 ppm in a series of precision experiments at the Brookhaven Alternating Gradient Synchrotron. The individual results for each sign: a(mu+)= 11 659 204(7)(5) E-10 and a(mu-) = 11 659 214(8)(3) E-10 are consistent with each other, so that we can write the average anomaly as a(mu)(exp) = 11 659 208(6) E-10 (0.5 ppm). A discrepancy between the measured value and the Standard Model (Delta a(mu)) is a signal for new physics. Assuming that such a discrepancy is due to contributions from supersymmetric particles provides a framework which can be used to constrain the mass of the dark matter particles, assumed to be the lightest neutral supersymmetric particles. The deviation from the standard model has varied between 1.5 sigma and 3 sigma significance, dominated by uncertainties in the hadronic contribution to the standard model calculation. Currently the standard model prediction is calculated to 0.6 ppm precision and Delta a(mu) = 23.5 (9.0) E-10, representing a 2.6 sigma deviation. We expect that the error on a(mu)(SM) will be reduced by a factor of two within the next decade. To fully utilize this improvement, a new g-2 run is proposed for the near future. If the mean Delta a(mu) remains the same, this would result in close to a 6 sigma discrepancy. In this case, we would expect to see SUSY particles at the LHC and use the g-2 results to measure tan beta. If, instead, the Standard Model is confirmed to this precision, gauginos must have masses higher than ~ 500 GeV/c2 and simple SUSY dark matter models will be severely constrained.
Neonatal esophageal perforation: nonoperative management

Abstract Background Esophageal perforation is a rare complication of enteric instrumentation in neonates. Enteric tube placement in micro-preemies poses a particular hazard to the narrow lumen and thin wall of the developing esophagus. The complication may be difficult to recognize or misdiagnosed as esophageal atresia, and is associated with considerable mortality. Historically, management of this life-threatening iatrogenic disease was operative, but trends have shifted toward nonoperative treatment. Here, we review neonatal esophageal perforation at our own institution for management techniques, risk factors, and outcomes. Materials and methods Seven neonatal patients with esophageal perforation were identified and charts reviewed for demographics, comorbidities, etiology of perforation, diagnostic modalities, management decisions, complications, and outcomes. Results Mean gestational age was 27.2 ± 4.0 wk, and weight at diagnosis was 892 ± 674 g. All seven patients had esophageal perforation resulting from endotracheal or enterogastric intubation and were managed nonoperatively. Treatment included removal of the offending tube, nil per os , and antibiotics. Five patients required additional interventions: four tube thoracostomies for pneumothoraces and one peritoneal drain for pneumoperitoneum. Three patients died because of sequelae of prematurity (intraventricular hemorrhage, necrotizing enterocolitis, and sepsis). One patient was diagnosed as having esophageal atresia; esophagoscopy before surgical repair established the correct diagnosis. Conclusions Neonates, particularly those under 1500 g, are at substantial risk for iatrogenic esophageal perforation during enterogastric intubation. Nonoperative management may be a safe initial strategy in the neonatal setting, but more aggressive interventions may ultimately be required. Despite recent improvement in early recognition of this injury, misdiagnosis still occurs.
Beyond objects-first: a project-driven CS2 course

After we adopted an objects-first approach in CS1, we had to redesign our CS2 and data structures courses. This paper reports on our efforts to develop a project-driven CS2 course that expands on the object-oriented methodology introduced in the CS1 course. We omitted some traditional data structures material and focused on using data structures in meaningful, large-scale projects that guided the course content. This helped students understand why these structures are important before concentrating on implementation in the subsequent data structures and algorithms course. This paper focuses on the pedagogical aspects of our CS2 course; a companion paper [4] discusses object-oriented methodology in more detail.
Stability properties of human reaching movements

Through an experimental study of the stability properties of the human neuromuscular system while it performs simple point-to-point arm movements, this paper evaluates the concepts of equilibrium and virtual trajectories as a means of executing movement of the arm. Human subjects grasped the instrumented handle of a two-link robot manipulandum and performed specified point-to-point planar arm trajectories. Computer-controlled brakes were used to subtly change the movements by constraining the trajectory along an arc of radius equal to the length of one link of the manipulandum. Target points were arranged to lie along the arc so that the subject could complete the movement even when constrained. Three situations were tested: (1) unconstrained throughout the movement, (2) constrained through the entire movement, and (3) initially constrained and then released during movement. Experimental results showed that the constraint evoked significant forces strongly oriented so as to restore the hand to the unconstrained hand path. In addition, when released from the constraint, these forces caused a strong tendency to return the hand to the unconstrained path before the end of the movement was reached. Such strong positional stability properties of the arm reinforce the notion that a moving attractor point dominates the dynamics of the arm during movement. Additionally, bounds on the shape of the virtual trajectory were found which indicate that the equilibrium point remains close to the actual movement produced. These results, showing that a controlled equilibrium point may be used for planning and coordinating multijoint movements, are consistent with an equilibrium point hypothesis.
Direct Evidence That Involucrin Is a Major Early Isopeptide Cross-linked Component of the Keratinocyte Cornified Cell Envelope

Involucrin was the first protein to be identified as a likely constituent of the insoluble cornified cell envelope (CE) of stratified squamous epithelia. However, to date, direct isolation from CEs of involucrin cross-linked by way of the transglutaminase-induced isopeptide bond has not been reported. We have treated human foreskin CEs with methanol/KOH (saponification) to hydrolyze off much of the lipids. By immunogold electron microscopy, this exposed large amounts of involucrin epitopes as well as of desmoplakin, a desmosomal structural protein. About 20% of the total CE protein could be solubilized by proteolytic digestion after saponification, of which involucrin was the most abundant. Subsequent amino acid sequencing revealed many peptides involving involucrin cross-linked either to itself or to a variety of other known CE protein components, including cystatin α, desmoplakin, elafin, keratins, members of the small proline-rich superfamily, loricrin, and unknown proteins related to the desmoplakin family. Specific glutamines or lysines of involucrin were used to cross-link the different proteins, such as glutamines 495 and 496 to desmoplakin, glutamine 288 to keratins, and lysines 468, 485, and 508 and glutamines 465 and 489 for interchain involucrin cross-links. Many identical peptides were obtained from immature CEs isolated from the inner living cell layers of foreskin epidermis. The multiple cross-linked partners of involucrin provide experimental confirmation that involucrin is an important early scaffold protein in the CE. Further, these data suggest that there is significant redundancy in the structural organization of the CE.
The PCAOB Meets the Constitution: The Supreme Court to Decide on the PCAOB’s Conformity with the Separation of Powers Doctrine and Appointments Clause

SYNOPSIS: This commentary provides an overview of the case currently before the U.S. Supreme Court that alleges constitutional problems with the Public Company Accounting Oversight Board (PCAOB). The PCAOB, a Board designed to oversee auditing for publicly traded firms, was created by Congress when it passed the Sarbanes-Oxley Act of 2002 (hereafter, SOX). To enhance PCAOB’s independence from political pressures, Congress established it as a private-sector, non-profit organization, and gave oversight powers to the Securities and Exchange Commission (hereafter, SEC), an independent agency. The plaintiffs in this case allege that Congress empowered the PCAOB with broad executive powers, yet limited the President’s ability to appoint Board members (thus violating the appointments clause of the Constitution) and to control and/or remove Board members (thus violating the separation of powers doctrine of the Constitution). The Supreme Court’s decision about the constitutionality of the PCAOB is important becaus...
Recall Communications: Discourse Genres, Symbolic Charging, and Message Design

Recall messages embody organizations' strategic choices to temper audience impressions and satisfy audiences' concerns about the existence of product defects, the rectifying of the defects, and the organizations' continuing focus on quality. This article presents a grounded approach to understanding and managing the rhetorical nature of recall announcements as a discourse genre for strategic communication. After brief discussion of genre theory applied to strategic communication, the essay places recall messages in the context of the relevant research literature. An analysis of product recall messages reveals the genre to be comprised of fear-appeal elements, stylistic choices related to language intensity, and pragmatic concerns for projecting an organizational image focused on quality. The essay concludes with implications for theory, practice, and future research.
Fool Me Once, Shame on You; Fool Me Twice, Shame on Oxytocin

In this issue of Neuron , a study by Baumgartner et al. investigates the influence of oxytocin on trust behavior and its neural mechanisms. The authors report that, following breaches of trust, oxytocin facilitates prosocial behavior while modulating neural signals in the amygdala and caudate nucleus. The findings have implications for an array of mental disorders where social behavior is compromised.
Abstract 2857: Induced expression of DUSP4 and PPM1A in ER-negative breast cancer cells suppresses proliferation and invasion

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Background: ER-negative breast cancers are poor prognosis tumors that occur more commonly in young women. Current treatments for ER-negative tumors include cytotoxic chemotherapy, or for those ER-negative breast cancers that overexpress HER2, the anti-HER2 antibody herceptin. Targeted therapy for ER-negative tumors, particularly those that do not express HER2 (“triple-negative breast cancer”) is urgently needed. We previously identified kinases that are critical for the growth of “triple-negative” breast cancer. In this project, we investigated whether phosphatases are differentially expressed in ER-negative as compared to ER-positive breast cancers. We hypothesized that: (1) the specific phosphatases that govern the growth of ER-negative cancers are different from those of ER-positive cancers, (2) Induced expression of those phosphatases that are lowly expressed in ER-negative breast cancers will suppress the growth and invasion of ER-negative breast cancers. Methods: Using 277 human breast tumors (56 ER-positive and 221 ER-negative) from the Baylor Breast Center tumor bank, we isolated RNA and performed Affymetrix microarray studies. cDNA was synthesized and Biotin-labeled and was then hybridized onto an Affymetrix HGU133A GeneChipTM, comprised of 22,000 genes. Statistical analysis of phosphatases was done with dChip software, and phosphatases more highly (>1.5 fold; FDR=0.05) or lowly ( 1.5 fold; FDR=0.05), and 29 lowly-expressed (<0.66-fold; FDR=0.05) phosphatases in ER-negative human breast cancers. We selected two lowly expressed phosphatases (DUSP4 and PPM1A) for further study. Induced expression of DUSP4 and PPM1A in ER-negative MDA-MB-468 cells inhibited anchorage-dependent and -independent growth. Induced expression of DUSP4 and PPM1A also suppressed the invasion of MDA-MB-468 cells. We are currently investigating the cellular and molecular consequences of induced DUSP4 and PPM1A expression in other ER-negative and ER-positive breast cancer cell lines. Conclusion: We identified a set of highly expressed and lowly expressed phosphatases in ER-negative breast cancers as compared to ER-positive cancers. Two phosphatases (DUSP4 and PPM1A) when expressed in an ER-negative breast cancer cells inhibit growth and invasion of these cells. By identifying the molecules that regulate breast cancer cell growth we will identify potential new targets for the treatment of these aggressive ER-negative breast cancers. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2857. doi:1538-7445.AM2012-2857
Numerical Modeling of the Flow in Cerebral Aneurysms Can Predict Thrombus Deposition Regions Following Vascular Interventions

Giant intracranial aneurysms present a grave danger of hemorrhage, cerebral compression, and thromboembolism. Fusiform aneurysms present a particular challenge for interventional treatment since these lesions cannot be completely removed from the circulation by clipping or coiling without sacrificing flow to the distal vasculature. In some cases, these lesions can be treated by interventions eliminating pathological hemodynamics, such as indirect aneurysm occlusion or deployment of a flow diverter stent (FDS). The first approach consists of proximal occlusion, distal occlusion, or trapping, sometimes performed with a bypass supplying flow from collateral circulation. In the second approach, a flow diverter device is used to reconstruct the parent vessel geometry and redirect the flow away from the aneurysmal sac. This is achieved due to the denser struts of an FDS relative to a standard stent, which provide resistance to the flow across its walls. Both interventional approaches often result in thrombus deposition (TD) in the aneurysm sac that is considered protective. Despite their advantages, these treatments introduce complications related to thrombotic occlusion of vital perforators or branch arteries. A virtual model, that could predict TD regions that result from flow alteration could help evaluate various treatment options. In addition to biochemical factors, an important role in the TD process may be played by hemodynamics. Previous studies demonstrated that flow regions with elevated TD potential are characterized by low velocities and near-wall shear stresses as well as increased flow residence time [1, 2]. The current study extends this patient-specific CFD methodology to predict TD regions following vascular interventions, such as proximal vessel occlusion and FDS deployment.Copyright © 2013 by ASME
An RNA interference model of RPS19 deficiency in Diamond-Blackfan anemia recapitulates defective hematopoiesis and rescue by dexamethasone: identification of dexamethasone-responsive genes by microarray.

Diamond-Blackfan anemia (DBA), a congenital erythroblastopenia, is a model disease for the study of erythroid differentiation but is poorly understood. RPS19 is the only gene yet to have been associated with DBA, but its relevance to erythroid differentiation is unclear. The molecular basis for the stimulation of erythropoiesis by glucocorticoids in patients with DBA has not been identified. We demonstrate that targeted degradation of the RPS19 transcript, through retroviral expression of short hairpin RNAs (shRNAs), blocks the proliferation and differentiation of erythroid progenitor cells in cultured human CD34+ cells. Treatment of RPS19-deficient cells with dexamethasone restores erythroid differentiation to normal levels. We investigated the molecular basis of pharmacologic therapies for DBA using oligonucleotide microarrays to survey gene expression in CD34+ cells treated with combinations of dexamethasone, erythropoietin, stem cell factor, and interleukin-3. Dexamethasone did not alter expression of RPS19 but activated a genetic program that includes a set of key hematopoietic regulatory genes. Genes specific to erythroid progenitor cells were up-regulated by dexamethasone, while genes specific to nonerythroid lineages were down-regulated. Deficiency of RPS19 therefore blocks proliferation of immature erythroid progenitor cells, and dexamethasone activates proliferation of the same cell population through mechanisms independent of RPS19. (Blood. 2005;105:4620-4626)
Using advanced dispersion models and mobile monitoring to characterize spatial patterns of ultrafine particles in an urban area

Abstract In urban settings with elevated bridges, buildings, and other complex terrain, the relationship between traffic and air pollution can be highly variable and difficult to accurately characterize. Atmospheric dispersion models are often used in this context, but incorporating background concentrations and characterizing emissions at high spatiotemporal resolution is challenging, especially for ultrafine particles (UFPs). Ambient pollutant monitoring can characterize this relationship, especially when using continuous real-time monitoring. However, it is challenging to quantify local source contributions over background or to characterize spatial patterns across a neighborhood. The goal of this study is to evaluate contributions of traffic to neighborhood-scale air pollution using a combination of regression models derived from mobile UFP monitoring observations collected in Brooklyn, NY and outputs from the Quick Urban & Industrial Complex (QUIC) model. QUIC is a dispersion model that can explicitly take into account the three-dimensional shapes of buildings. The monitoring-based regression model characterized concentration gradients from a major elevated roadway, controlling for real-time traffic volume, meteorological variables, and other local sources. QUIC was applied to simulate dispersion from this same major roadway. The relative concentration decreases with distance from the roadway estimated by the monitoring-based regression model after removal of background and by QUIC were similar. Horizontal contour plots with both models demonstrated non-uniform patterns related to building configuration and source heights. We used the best-fit relationship between the monitoring-based regression model after removal of background and the QUIC outputs ( R 2 = 0.80) to estimate a UFP emissions factor of 5.7 × 10 14 particles/vehicle-km, which was relatively consistent across key model assumptions. Our joint applications of novel techniques for analyzing mobile monitoring data and the advanced dispersion model QUIC provide insight about source contributions above background levels and spatiotemporal air pollution patterns in urban areas.
Stereoisomers of perhydrophenanthrene. The synthesis and crystal structure of a derivative of the trans-syn-trans isomer

Abstract The trans-syn-trans isomer of perhydrohenanthrene has the central ring in a boat conformation. A crystalline derivative (the dibenzoate of the cis 9,10-diol) was prepared, and the crystal structure was determined. The boat conformation is slightly twisted, as predicted by molecular mechanics.
Adaptive Coherent Aperture Combining for small disadvantaged SatCom terminals

Satellite earth terminals with small, sub-meter antenna apertures provide an attractive method for beyond line of sight communications to mobile platforms. Satellite operators frequently classify small terminals as “disadvantaged” because the relatively small, low gain antennas consume a disproportionate share of valuable satellite downlink resources. Small terminal uplinks also typically suffer from limited power and subsequent capacity limitations. Adaptive Coherent Aperture Combining (ACAC) provides an effective solution to the challenges of using small terminals. ACAC combines the energy from two or more antennas, thereby increasing overall signal gain, thus improving the Signal to Noise Ratio (SNR) and Effective Isotopic Radiated Power (EIRP). ACAC differs from a traditional phased array because combining is performed on widely spaced, irregular placed antenna elements. The ACAC employs a unique Blind Source Separation (BSS) algorithm. ACAC performs equally well for both the uplink and downlink. The adaptability of the ACAC combining technique can also be used to mitigate interference from jamming. Since the energy from the antenna elements is optimally combined and not switched, ACAC offers the additional benefits of mitigating blockage and graceful degradation. This paper describes an ACAC application to the small disadvantaged terminal problem, along with tangential technology benefits.
Power delay profile in a cluttered environment

A stochastic-ray model of wave propagation based on the theory of random walks that accounts for only two parameters: the amount of clutter and the amount of absorption in the environment is considered. This model applies to indoor and outdoor environments, characterized by a large number of (small) scattering objects. Examples are microcells for personal communication and networks of multihop wireless sensors or laptop computers. We extend our previous results on narrowband signals to impulse waveforms, deriving a closed form solution for the power delay profile of the received signal.
Analysis of seismic surface waves using PDP-15 interactive graphics

Abstract Using an interactive seismic processing system (ISPS) developed by Texas Instruments Incorporated, a large volume of seismic signals can be more efficiently and more realistically processed for various purposes, such as the evaluation of seismic recording stations, the discrimination study, the seismic source mechanism study and so on. The ISPS has been implemented on the PDP-15 Computer located at the Seismic Data Analysis Center in Alexandria, Virginia. Its principal components are: 1. (1) interactive seismic processing modules employing advanced signal analysis software for event detection, parameter extraction and discrimination while retaining visual control over the procedures: 2. (2) a graphics console device to serve as the communication interface between computer system and analyst; and 3. (3) a seismic command language to control processing module execution within the console environment. Using the ISPS, the long-period seismic surface waves of around sixty events in the 1974 Sinkiang, China, earthquake swarm were processed to obtain the observed surface wave dispersions and to extract the demultipathed surface wave spectra, which in turn were used to estimate the source mechanism solutions of these events by employing the multi-site, multi-period least-squares spectral fitting procedure. The solutions indicated two kinds of source mechanisms in this earthquake swarm: 1. (1) vertical strike-slip fault, and 2. (2) dip-slip fault with a dip angle of forty degrees. The results suggested that these events occurred at shallow depths with the estimated source depth varying between 4 km and 14 km.
Chemotherapy-Induced Changes in Cardiac Capillary Permeability Measured by Fluorescent Multiple Indicator Dilution

Anthracyclines cause severe irreversible cardiac toxicity. The study of changes in cardiac permeability with chemotherapy could enhance the understanding of mechanisms behind cardiac damage, and provide useful information to evaluate anthracycline cardiotoxicity. Thirty-six rats (12 Sprague–Dawley, 12 Wistar, 12 Fischer-344) were randomly assigned to control (n = 21) or doxorubicin (n = 15), and injected i.p. with a cumulative dose of 18 mg/kg doxorubicin in saline (vehicle) or vehicle alone over 12 days. Echocardiography was performed at baseline and on day 11. An isolated heart experiment was done on day 12 to obtain perfused heart pressure values, and to measure cardiac capillary permeability using a Texas Red/sodium fluorescein multiple indicator dilution method. Control animals had significantly lower average permeability-surface-area-products (0.035 ± 0.013 cm3/s) than doxorubicin animals (0.066 ± 0.023 cm3/s), PSP ± SD, p < 0.001. These permeability changes correlated with significant functional changes. There was a significant decline in cardiac function with a deleterious effect of chemotherapy on fractional shortening (p < 0.001), left ventricular developed pressure (p < 0.001), contractility (p < 0.001), and relaxation (p = 0.02). Based on our results, cardiac capillary permeability changes can be detected after in vivo chemotherapy treatment using our fluorescent multiple indicator dilution technique, and may provide valuable information in evaluating cardiotoxicity of novel drugs.
Proximity networks and epidemics

Abstract Disease spread in most biological populations requires the proximity of agents. In populations where the individuals have spatial mobility, the contact graph is generated by the “collision dynamics” of the agents, and thus the evolution of epidemics couples directly to the spatial dynamics of the population. We first briefly review the properties and the methodology of an agent-based simulation (EPISIMS) to model disease spread in realistic urban dynamic contact networks. Using the data generated by this simulation, we introduce the notion of dynamic proximity networks which takes into account the relevant time-scales for disease spread: contact duration, infectivity period, and rate of contact creation. This approach promises to be a good candidate for a unified treatment of epidemic types that are driven by agent collision dynamics. In particular, using a simple model, we show that it can account for the observed qualitative differences between the degree distributions of contact graphs of diseases with short infectivity period (such as air-transmitted diseases) or long infectivity periods (such as HIV).
Cytochrome b oxidation and reduction reactions in the ubiquinone-cytochrome b/c2 oxidoreductase from Rhodopseudomonas sphaeroides

1. The kinetics of cytochrome b reduction and oxidation in the ubiquinone-cytochrome b/c2 oxidoreductase of chromatophores from Rhodopseudomonas sphaeroides Ga have been measured both in the presence and absence of antimycin, after subtraction of contributions due to absorption changes from cytochrome c2, the oxidized bacteriochlorophyll dimer of the reaction center, and a red shift of the antenna bacteriochlorophyll. 2. A small red shift of the antenna bacteriochlorophyll band centered at 589 nm has been identified and found to be kinetically similar to the carotenoid bandshift. 3. Antimycin inhibits the oxidation of ferrocytochrome b under all conditions; it also stimulates the amount of single flash activated cytochrome b reductions 3- to 4-fold under certain if not all conditions. 4. A maximum of approximately 0.6 cytochrome b-560 (Em(7) = 50 mV, n = 1, previously cytochrome b50) hemes per reaction center are reduced following activating flashes. This ratio suggests that there is one cytochrome b-560 heme functional per ubiquinone-cytochrome b/c2 oxidoreductase. 5. Under the experimental conditions used here, only cytochrome b-560 is observed functional in cyclic electron transfer. 6. We describe the existence of three distinct states of reduction of the ubiquinone-cytochrome b/c2 oxidoreductase which can be established before activation, and result in markedly different reaction sequences involving cytochrome b after the flash activation. Poising such that the special ubiquinone (Qz) is reduced and cytochrome b-560 is oxidized yields the conditions for optimal flash activated electron transfer rates through the ubiquinone-cytochrome b/c2 oxidoreductase. However when the ambient redox state is lowered to reduce cytochrome b-560 or raised to oxidize Qz, single turnover flash induced electron transfer through the ubiquinone-cytochrome b/c2 oxidoreductase appears impeded; the points of the impediment are tentatively identified with the electron transfer step from the reduced secondary quinone (QII) of the reaction center to ferricytochrome b-560 and from the ferrocytochrome b-560 to oxidized Qz, respectively.
Drainage of liquid from surfaces of different rugosities

Abstract Two hydrocarbon oils were allowed to drain from stainless steel plates of 9 different roughnesses. The theory of the drainage was derived; its predictions were approximately fulfilled by the smoothest plates. On the rough plates an apparently stagnant liquid layer existed whose thickness was nearly equal to the average height of hills on the solid surface, as determined with two stylus instruments. This result (a) refutes one of the proofs for the existence of long-range molecular forces, (b) confirms the hypothesis that the magnitude of electro-kinetic phenomena is reduced by rugosity, (c) shows the necessity of considering roughness in adhesion measurements, and (d) renders possible a new method of measuring surface roughness.
An efficient dynamic programming algorithm for phosphorylation site assignment of large-scale mass spectrometry data

Phosphorylation site assignment of large-scale data from high throughput tandem mass spectrometry (LC-MS/MS) data is an important aspect of phosphoproteomics. Correct assignment of phosphorylated residue(s) is important for functional interpretation of the data within a biological context. Common search algorithms (Sequest etc.) for mass spectrometry data are not designed for accurate site assignment; thus, additional algorithms are needed. In this paper, we propose a linear-time and linear-space dynamic programming strategy for phosphorylation site assignment. The algorithm, referred to as PhosSA, optimizes the objective function defined as the summation of peak intensities that are associated with theoretical phosphopeptide fragmentation ions. Quality control is achieved through the use of a post-processing criteria whose value is indicative of the signal-to-noise (S/N) properties and redundancy of the fragmentation spectra. The algorithm is tested using experimentally generated data sets of peptides with known phosphorylation sites while varying the fragmentation strategy (CID or HCD) and molar amounts of the peptides. The algorithm is also compatible with various peptide labeling strategies including SILAC and iTRAQ. PhosSA is shown to achieve > 99% accuracy with a high degree of sensitivity. The algorithm is extremely fast and scalable (able to process up to 0.5 million peptides in an hour). The implemented algorithm is freely available at http://helixweb.nih.gov/ESBL/PhosSA/ for academic purposes.
Purification and properties of two forms of ATP sulfurylase from Euglena.

Two forms of ATP sulfurylase have been purified to homogeneity from mitochondria (ATPSm) and cells (ATPSc) of Euglena gracilis Klebs var. bacillaris Cori (aplastidic mutant W 10BSmL). Both forms are monomeric, ATPSc is 52.3 kDa and ATPSm is 55 kDa. The pI is 7.9 for ATPSc and 5.8 for ATPSm. Therefore, ATPSm binds to DEAE-cellulose at pH 7.4; ATPSc does not. After cleavage by CNBr, the two forms of ATP sulfurylase show different sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) patterns, suggesting that they differ in amino acid sequence. ATPSm is mainly associated with the mitochondrial membrane and ATPSc is mainly soluble in the cells. Both enzymes require similar conditions in the molybdolysis assay, but show different pH optima when sulfate is used as substrate. ATPSc is more sensitive to adenosine 5′-phosphosulfate (APS) inhibition than ATPSm in the SO 42− incorporation reaction. In the reverse reaction, ATPSc requires much higher concentrations of PPi and MgCl 2 to saturate the reaction than ATPSm. The data indicate that the two enzymes are quite distinct and may have different roles in cell metabolism.
Abstract 3899: A coactivator role of CARM1 for the dysregulated β-catenin activity in colorectal cancer cell growth and gene expression

Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC Aberrant activation of Wnt/β-catenin signaling is recognized as a critical factor in the etiology of colorectal cancer. Evidence has suggested that dysregulated β-catenin activity is associated with the majority of colon cancers via activation of the expression of Wnt regulated oncogenes. In the nucleus, β-catenin regulates transcription by recruiting additional secondary coactivators. These secondary coactivators all have distinct and unique functions on Wnt/β-catenin target gene activation. For instance, CCAR1 (Cell Cycle and Apoptosis Regulator 1) has been shown to be important for the stable occupancy of β-catenin at the promoter of a Wnt target gene, and depletion of CCAR1 inhibits expression of several Wnt/β-catenin target genes and suppresses anchorage-independent growth of colon cancer cells (Ou CY et al. Journal of Biological Chemistry 2009;284(31);20629-20637). Here, we show that CARM1 (coactivator-associated-protein-arginine-methyltransferase 1) interacts with β-catenin and positively modulates β-catenin-mediated gene expression. In colorectal cancer cells, which have constitutively high Wnt/β-catenin activity, depletion of CARM1 inhibits the expression of Wnt/β-catenin-mediated oncogenes and suppresses anchorage-independent growth. In colorectal cancer cells that do not have constitutively high Wnt/β-catenin activity, we found that activation of Wnt/β-catenin signaling by treatment with Wnt3a increased the expression of a subset of Wnt target genes. Utilizing these cells, we demonstrated that CARM1 is specifically required for the expression of these Wnt3a-induced targets. Upon Wnt3a stimulation, CARM1-dependent dimethylation of histone H3 arginine (Arg) 17, at a Wnt-regulated promoter, is associated with the recruitment of both β-catenin and CARM1. Arg17 dimethylation by Wnt3a ligands is compromised by CARM1 knockdown, whereas Wnt3a-induced β-catenin recruitment is not affected. Finally, in a nude mouse xenograft model, compared with CARM1 knockdown cells, wild type HT29 tumor xenografts grow significantly faster. We conclude that CARM1 is an important modulator of Wnt/β-catenin transcription and may represent a novel target for therapeutic intervention in cancers involving aberrantly activated Wnt/β-catenin signaling. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3899.
Oil and Politics in Latin America: Nationalist Movements and State Companies

List of tables Preface Glossary Abbreviations Note on currencies and other units of measurement Maps Introduction Part I. The World Oil Environment: 1. The corporate ascendancy 1890-1927 2. Retrenchment and concentration 1928-41 3. The making of the post-war oil world 1942-55 4. The major companies in retreat 1955-70 5. The oil market revolution and its consequences for Latin America 1971-9 6. Latin America in the twentieth-century oil system Part II. The Major Expropriations: 7. Politics and the concession contract 8. Argentina: YPF, Yrigoyen and the 1935 oil law 9. Some nationalisations of the 1930s: Chile, Uruguay, Bolivia 10. Cardenas and the Mexican oil nationalisation 11. The formation of Petrobras 12. The nationalisation of the IPC in Peru 13. The nationalisation of Gulf Oil in Bolivia 1969 14. Oil politics in Ecuador 1972-6 15. The nationalisation of oil in Venezuela 16. Oil companies and governments in twentieth-century Latin America Part I of Gulf Oil in Bolivia 1969 14. Oil politics in Ecuador 1972-6 15. The nationalisation of oil in Venezuela 16. Oil companies and governments in twentieth-century Latin America Part III. The State Oil Companies: 17. Pemex in Mexican politics 1938-79 18. The development of Petrobras: oil company to conglomerate? 19. YPF 1932-79: public enterprise or bureaucracy? 20. Petroperu 1968-80: achievements and hard lessons 21. YPFB and the development of oil in Bolivia 22. Petroven: the birth of a giant 23. State oil companies in Latin America 24. Concluding reflections Notes Bibliography Index.
What the new US FDA guidance in assessing suicidal ideation and behavior in clinical trials means for trial design

While antidepressants have been associated with an overall reduction in the rates of suicide in patients with depression [1], case reports of increased suicidal ideation and behavior (SIB) in patients taking antidepressant medications are in long standing [2–6]. However, it is not clear whether the increased SIB seen in patients taking antidepressants is part of the natural disease course of major depressive disorder, or whether antidepressants themselves, independent of the primary disease process, are responsible for the presence of SIB. Regardless of the causal relationship, the general consensus is that patients, especially those experiencing depression, should be carefully monitored for increased SIB when changes in psychotropic medication are made (i.e., stop, start or dosage titration). The US FDA Guidance for Industry: Suicidal Ideation and Behavior: Prospective Assessment of Occurrence in Clinical Trials, expands the monitoring of SIB to be included in “all clinical trials involving any drug being developed for any psychiatric indication, as well as for all antiepileptic drugs and other neurologic drugs with central nervous system (CNS) activity, both inpatient and outpatient, including multiple-dose Phase 1 trials involving healthy volunteers” [101].
Reducing greenhouse gas emissions through strategic management of highway pavement roughness

On-road vehicle use is responsible for about a quarter of US annual greenhouse gas (GHG) emissions. Changes in vehicles, travel behavior and fuel are likely required to meet long-term climate change mitigation goals, but may require a long time horizon to deploy. This research examines a near-term opportunity: management of pavement network roughness. Maintenance and rehabilitation treatments can make pavements smoother and reduce vehicle rolling resistance. However, these treatments require material production and equipment operation, thus requiring a life cycle perspective for benefits analysis. They must also be considered in terms of their cost-effectiveness in comparison with other alternatives for affecting climate change. This letter describes a life cycle approach to assess changes in total GHG (measured in CO2-e) emissions from strategic management of highway pavement roughness. Roughness values for triggering treatments are developed to minimize GHG considering both treatment and use phase vehicle emission. With optimal triggering for GHG minimization, annualized reductions on the California state highway network over a 10-year analysis period are calculated to be 0.82, 0.57 and 1.38 million metric tons compared with historical trigger values, recently implemented values and no strategic intervention (reactive maintenance), respectively. Abatement costs calculated using $/metric-ton CO2-e are higher than those reported for other transportation sector abatement measures, however, without considering all benefits associated with pavement smoothness, such as vehicle life and maintenance, or the time needed for deployment.
Developmental Effects of Dioxins

Abstract The potent developmental toxicity of dioxin in multiple species has been known for a number of years. However, recent studies have indicated that dioxin also induces functional developmental defects, many of which are delayed. Subtle structural deficits, not detectable at birth, have also been described in multiple species and in both sexes. Certain defects have been reported not only in animals but also in children prenatally exposed to complex mixtures containing dioxinlike compounds. None of the effects can be attributed to modulation of any one endocrine system. For example, dioxin does not bind to the estrogen receptor, but it can cause effects that are both estrogenic and antiestrogenic. However, viewing dioxin and related compounds as endocrine disruptors that may alter multiple pathways sheds some light on the complexities of this potent class of growth dysregulators.
Winding of the DNA helix by divalent metal ions

When supercoiled pBR322 DNA was relaxed at 0 or 22 degrees C by topoisomerase I in the presence of the divalent cations Ca2+, Mn2+ or Co2+, the resulting distributions of topoisomers observed at 22 degrees C had positive supercoils, up to an average delta Lk value of +8.6 (for Ca2+at 0 degrees C), corresponding to an overwinding of the helix by 0.7 degrees/bp. An increase of the divalent cation concentration in the reaction mixture above 50 mM completely reversed the effect. When such ions were present in agarose electrophoresis gels, they caused a relaxation of positively supercoiled DNA molecules, and thus allowed a separation of strongly positively supercoiled topoisomers. The effect of divalent cations on DNA adds a useful tool for the study of DNA topoisomers, for the generation as well as separation of positively supercoiled DNA molecules.
Case Studies of Selected High School Environmental Education Classes

Abstract Integration of environmental education throughout the curriculum provides the range of perspectives and knowledge necessary for environmental understanding but creates other problems. One suggestion for alleviating these difficulties at the secondary level is to create distinct environmental education courses, possibly as part of the science curriculum. Although such courses may reduce the difficulties inherent in an integrated approach, other complications may arise. The author conducted case studies of selected environmental courses, taught by seven teachers in six Illinois secondary schools. The findings indicate some similarities and differences in environmental education programs at the secondary school level and suggest some directions for similar courses.
Recent development of psychiatric epidemiology in China

The authors review recently published psychiatric epidemiological data from the People's Republic of China, and compare these findings with data from Taiwan and worldwide.
Computational modeling and design of a new open clip surgical instrument.

Abstract This research introduces a new surgical clip instrument with improved mechanism to apply the metal clips to patient's vessel/tissues in the surgical operations. The improved clip delivery system has been designed and developed in the instrument to improve the clip distal move from clip channel into jaw guide track and resolve the problems of clip accidental shooting out when clip is being loaded into jaw pair by compression spring that has been normally used in some current surgical clip instruments. With this improvement, this new surgical open clip instrument can prevent patient's vessels and tissues from being damaging because the distal move of clips is well controlled without clip drop-off incident. Plus the operational force to form the clip is lower than regular surgical instruments due to new mechanism design. In addition to the above, the manufacturing and product cost can be decreased because the dimensional tolerance of components, such as clip channel and jaw guide track, can be wider due to this new instrument design. The prototype of this new instrument is analyzed and optimized through computer aided modeling and simulation, in order to prove its feasible function, reliable performance, and mechanical advantage. All these improved features have also been tested and verified through the prototype. With some further improvement to this new instrument design and valuable evaluations from surgeon and clinical fields in next several months, the commercial availability of this surgical clip instrument will be anticipate in 1–2 years.
Biologic variability of human foreskin fibroblasts in 2D and 3D culture: implications for a wound healing model

The fibroblast-populated 3D collagen matrix is a model of tissue and healing which has been used since the 1980's. It was hypothesized that anchorage disruption of the collagen matrix would produce p53-dependent apoptosis in the embedded fibroblasts, but results of hypothesis testing were variant. The response of p53 to anchorage disruption in 3D culture or to UV irradiation in 2D culture was influenced both by fibroblast strain and culture conditions. It also was determined that data scatter in a collagen matrix contraction assay was related to fibroblast strain and possibly to technical factors, such as cell culture technician and/or number of matrices utilized. Subsequent analysis suggested that phenotypic drift and/or inter-strain genetic variability may have been responsible for the data scatter. In addition, several technical factors were identified that may have contributed to the scatter. Experimentation with human foreskin fibroblasts in both 2D and 3D culture can produce variant data. The underlying cause of the data scatter appears to be partially due to the biologic variability of the fibroblast.
Callose: Lateral Movement of Assimilates from Phloem

Brief heating of cotton petioles increased phloem callose and decreased lateral movement of assimilates containing carbon-14. The heat-induced phloem callose appears to have been responsible for part of this decrease; we conclude, therefore, that lateral movement from sieve tubes was along proto plasmic connections.
Visual rearrangement affects auditory localization.

Abstract The midline localizations of dichotically presented clicks are directly influenced by visual rearrangement produced by prism spectacles. There is evidence that for certain exposure conditions the visual adaptation process can be monitored by the dichotic method without recourse to pointing movements of the hand.
Mitochondrial distribution and inheritance

Mechanisms mediating the inheritance of mitochondria are poorly understood, but recent studies with the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have begun to identify components that facilitate this essential process. These components have been identified through the analysis of conditional yeast mutants that display aberrant mitochondrial distribution at restrictive conditions. The analysis of these mutants has uncovered several novel proteins that are localized either to cytoskeletal structures or to the mitochondria themselves. Many mitochondrial inheritance mutants also show altered mitochondrial morphology and defects in maintenance of the mitochondrial genome. Although some inheritance components and mechanisms appear to function specifically in certain types of cells, other conserved proteins are likely to mediate mitochondrial behavior in all eukaryotic cells.
Circulating estradiol, estrone and gonadotropin levels following the administration of orally active 17beta-estradiol in postmenopausal women.

Ingestion of a single tablet containing 2 mg micronized 17β-estradiol (E2) produced marked increases in the serum concentrations of E2 and estrone (E1) in 9 postmenopausal women. The rise in circulating E2 became significant within 2 h, reached a maximum (110 pg/ml; 437% increase) at 5 h, and remained significantly elevated at 8 h posttreatment. By 24 h, the serum E2 concentration was not significantly different than baseline. In contrast, a more rapid (within 1 h) and pronounced (4-fold) increase in the serum concentration of E1 was observed. This rise continued until a peak (467 pg/ml; 2000%) was reached 6 h posttreatment. Thereafter, the serum E1 concentration declined progressively but was still significantly elevated (140 pg/ml; P < 0.01) 24 h after treatment. Serum concentrations of FSH and LH were significantly decreased within 6 and 3 h, respectively and both gonadotropins remained significantly suppressed 24 h following the ingestion of E2. The ratios of circulating E1:E2 reported herein (ca. 3–6...