cssi/SciSciGPT-SciSciNet huggingface dataset:
The γ subunit in the Escherichia coli ATP synthase complex (ECF1F0) extends through the stalk and contacts the c subunits of the F0 part

A mutant, in which a cysteine has been site-directed into the polar loop region of the c subunit at residue 44, has been studied. Cross-linking of the c subunit to both the γ and ϵ subunits was observed with cupric 1,10-phenanthrolinate treatment. The linkage between the c and γ subunits was localized to that part of the γ subunit between residues 202–286, based on peptide analysis. Reference to the high resolution structure of F1 [Abrahams et al. (1994) Nature 370, 621–628] appears to limit this contact site to the region including residues 202–230. This segment contains 4 tyrosines and 1 tryptophan as possible reactive residues for cross-linking with the c subunit cysteine.
'Catatonia' produced by alfentanil is reversed by methylnaloxonium microinjections into the brain.

Alfentanil, a short-acting and powerful analgesic, when injected peripherally to rats (0.5 mg/kg) produced a catatonic state characterized by a rigid akinesia. The present study was designed to explore the neuroanatomical location of the opiate receptors mediating the alfentanil induced catatonia. The catatonic effect of alfentanil was measured using a bar test and depression of locomotor activity in rats tested in photocell cages during an active nocturnal phase of their cycle. Methylnaloxonium HCl (MN), a quaternary derivative of naloxone which does not readily cross the blood-brain barrier, injected into the lateral ventricle significantly reduced the catatonia at doses of 0.125-2.0 micrograms as measured in both the locomotor and bar test. MN perfusion of similar doses directly into the nucleus raphe pontis, but not in the caudate nucleus significantly antagonized the catatonia. These data complement results on alfentanil-induced muscular rigidity (Blasco et al., see companion paper) where EMG indices of rigidity in rats were reversed by microinjections of low doses of MN (0.125 and 0.5 microgram) in the nucleus raphe pontis, but not the caudate nucleus even at a high dose (4.0 micrograms). Together these results suggest that the region of the nucleus raphe pontis is an important neural substrate for opiate-induced muscular rigidity, and that the catatonic state produced by opiates depends on more diffuse opiate receptor activation of which one important component may be the nucleus raphe pontis.
Dissimilar associations of two secretory peptides with a neurosecretory granule-enriched fraction from the bag cells

The bag cell neurons of Aplysia californica synthesize and secrete several neuropeptides. To gain more detailed information about their posttranslational routing and transport, we have undertaken isolation of the neurosecretory granules (NSG). Extracts of radiolabeled cells were subjected to discontinuous, isosmotic density-gradient centrifugation. Radiolabeled peptides likely to be contained in NSG were found to relocate from the starting zone and to be associated with particulate structures. Assay of enzyme markers for lysosomes and endoplasmic reticulum disclosed gradient distributions that differed from that shown by the peptides. Hence, it is probable that the position of peak concentrations of particulate peptides represents the location of NSG. Of particular interest is the further observation that the known secretory peptides ELH and AP do not evidence strict covariance across the gradient. This deviation from covariance is consistent with hypotheses that the peptides are in different associations with the NSG cores or that more than one type of neurosecretory granule is produced in the bag cells.
Policing the drunk driver: Measuring law enforcement involvement in reducing alcohol-impaired driving

Abstract Introduction With many thousands of deaths still annually attributable to driving under the influence (DUI), it remains imperative that we continually address the problem of producing and sustaining effective countermeasures, and that we subject these efforts to empirical scrutiny. This article presents relevant findings from state-wide datasets. Results A formula generating a potentially useful metric for assessing aspects of the DUI prosecutorial chain is presented, focusing on the rate of proactive DUI arrests. While in need of cautious interpretation due to issues of inherent inaccuracies in large databases, small numbers of crashes and/or arrests in multiple jurisdictions, and the lack of replication in other states, the analyses show no relationship between the level of DUI arrest activity and DUI-related crashes. This finding brings into question the efficacy of the many millions of dollars devoted each year to targeted DUI enforcement, as it is currently being implemented. Conclusions Results are discussed in terms of developing adequate disincentives to DUI so as to raise general deterrence via dramatic increases in proactive DUI enforcement and then engaging in pervasive and persistent social marketing of such efforts to maximize the perception that arrest and punishment for DUI is always imminent, that penalties will be swift, certain, and severe. It is echoed that accurate data need to be collected at all levels of the DUI arrest and prosecution process in every jurisdiction within a state, so as to facilitate the empirical assessment of countermeasure efficacy in reducing alcohol-related crashes. Impact on Industry Given that this work needs to be replicated, the impact on the traffic safety industry is potentially huge. The present data indicate that law enforcement efforts to further abate DUI-related crashes are apparently ineffective, though likely necessary to maintain reductions achieved in the 80s and early 90s. Thus, to attain additional systematic reductions, a dramatic increase in enforcement will be necessary as will a diversification of abatement efforts, including an increase in aggressive social marketing tactics to positively impact our traffic safety culture by making DUI universally unacceptable (for a discussion of this latter issue and on the use of positive reinforcement to change driver behavior, see Dula & Geller, 2007).
Effect of particle size distribution on segregation in vibrated systems

Abstract Segregation, or demixing, of granular mixtures in vertically vibrated systems is a common occurrence that has been an active area of research. In many industrial processes, such demixing often occurs during transportation and handling of granular mixtures and can lead to inferior product quality and undesired product variations. Thus, understanding granular segregation can help resolve potential problems relating to low product yield and thus offer time and cost savings to many industries which use such materials. Our work looks into size segregation in vertically vibrated cylinders with binary, ternary as well as polydisperse mixtures. Experimental results were compared to those obtained from numerical analysis in an effort to better characterize the system segregation. We first introduced a slight particle size distribution to each species in binary and ternary mixtures and then varied the amount of intermediate species in ternary mixtures. Our results suggest that adding a slight size distribution to each species in the binary and ternary mixtures reduces segregation and enhances mixing. We also notice that for a ternary mixture, the amount of segregation is reduced as the mass fraction of intermediate species present in the system is increased.
Reciprocity: you have to think different.

There has been a proliferation of models seeking to explain the evolution of altruism over the past few years, and Lehmann and Keller should be commended for this very well-reasoned and clearly written attempt to bring order out of chaos. There is much good sense in this paper, especially the emphasis on the importance of assortment for the evolution of altruism, the excellent discussion of green beard models and the important role of constraints, particularly in punishment models. I fear, however, that the elegance and simplicity of their results may mislead some readers about the implications of this work for the evolution of reciprocity. Lehmann and Keller consider the evolution of reciprocity in between pairs of individuals. Unlike most authors, they assume that helping is a continuous variable. The incremental cost of helping is C and the benefit B, so a focal individual who helps an amount z suffers a cost Cz and his partner receives a benefit Bz. The strategy set is limited to linear reactive strategies. If a focal’s partner helped an amount z on the previous turn, then the focal helps mbz on this turn. Then, Lehman and Keller show that altruism among unrelated individuals can be favoured by selection when:
Fiberoptic Bronchial Blockade in a Small Bronchopleural Fistula

A patient with bronchopleural fistula was successfully treated by selective intrabronchial injection of doxycycline and blood under fiberoptic bronchoscopic guidance. This simple and relatively noninvasive therapeutic approach is an effective and safe alternative in treating selective patients with a bronchopleural fistula.
Joint processing of Hartmann sensor and conventional image measurements to estimate large aberrations: theory and experimental results

We report experimental results for what we believe to be a new technique for estimating aberrations that extends the strength of an aberration that may be sensed with Hartmann sensor technology by means of an algorithm that processes both a Hartmann sensor image and a conventional image formed with the same aberration. We find that the theory and the experiment match well within the experimental error and that strong defocus aberrations can be accurately sensed with this technique.
Specificity of Na+ binding to phosphatidylserine vesicles from A 23Na NMR relaxation rate study

23Na NMR relaxation rate measurements show that Na+ binds specifically to phosphatidylserine vesicles and is displaced partially from the binding site by K+ and Ca2+ but to a considerably less extent by tetraethylammonium ion. The data indicate that tetraethylammonium ion affects the binding of Na+ only slightly, by affecting the surface potential through its presence in the double layer, without competing for a phosphatidylserine binding site. Values for the intrinsic binding constant for the Na+-phosphatidylserine complex that would be consistent with the competition experiments (and the dependence of the relaxation rate on concentration of free Na+) fall in the range 0.4--1.2 M-1 with a better fit towards the higher values. We conclude that in the absence of competing cations in solution an appreciable fraction of the phosphatidylserine sites could be associated with bound Na+ at 0.1 M Na+ concentration.
Microparticulates: Isolation from Water and Identification of Associated Chlorinated Pesticides

Microparticulates suspended in lake water were collected by continuous centrifugation and either examined directly or placed on a linear sucrose gradient. Total residue as well as fractions of the centrifuged gradient were extracted with hexane and examined by gas chromatography for the presence of chlorinated hydrocarbon pesticides. Hexane extracts of total residues were also examined by thin-layer chromatography. Lindane and endrin were shown, by gas-liquid chromatography and thin-layer chromatography, to be associated with microparticles. These and other pesticides appeared to be selectively associated with microparticles of different densities, when gas-liquid chromatography was used, although concentrations were below the detection limits required for confirmation by thin-layer chromatography. Samples taken at different times from different locations in Lake Erie revealed different associations with hexane-soluble electron-capturing compounds.
Chance‐constrained data envelopment analysis

Data envelopment analysis (DEA) is extended to the case of stochastic inputs and outputs through the use of chance-constrained programming. The chance-constrained frontier envelops a given set of observations ‘most of the time’. As an empirical illustration, we re-examine the pioneering 1981 study of Program Follow Through by Charnes, Cooper and Rhodes.
The later stages of spinodal decomposition and the beginnings of particle coarsening

Abstract Several features of the later stages of spinodal decomposition leading to two phases and particle coarsening can be obtained by considering terms in the diffusion equation that originate from a composition dependent diffusion coefficient. These give rise to harmonic distortions of the composition waves typical of spinodal decomposition. Two classes of distortions are identified and related to the free energy curve through the composition dependence of the thermodynamic factor in diffusion. Asymmetric free energy curves give even harmonics that are consistent with the lever rule, i.e. a minor phase far from the average composition and a major matrix phase. Odd higher harmonics, originating from higher even derivatives of the free energy function flatten the extremes in composition and sharpen the interfaces leading to the composition distribution expected for a two-phase alloy. The initial stages of particle coarsening can also be described and two types of effects are distinguished. One mechanism occurs only in unsymmetric alloys and it is suggested that such alloys should coarsen much more rapidly than the symmetric ones.
W O Microemulsion Studies with Mono- and Dialkyl Amic Acid Surfactants

Abstract A series of new surfactants was prepared by reacting aromatic anhydrides and dianhydrides with long-chain amines to give mono- and bis-(N-alkylamic acids), which was then converted to water-soluble potassium salts. As an example, the reaction product of dodecyl amine and benzophenone tetracarboxylic dianhydride was neutralized with potassium hydroxide to form a surfactant. Two types of surfactants were synthesized and their structures are: The ability of the new surfactants to stabilize water-in-oil ( W O ) microemulsions was examined by determining the pseudoternary component phase behavior of each material in combination with water, pentanol (cosurfactant), and benzene (oil). In general, the monofunctional surfactants could support higher water content microemulsions than those of the corresponding difunctional (bis) surfactants. Microemulsions prepared from the latter materials, however, were more stable to the addition of hydrocarbon. The structure of the parent three-component systems and the four-component microemulsions was probed by measuring the self-diffusion coefficients of water, cosurfactant, and oil at various levels of water and hydrocarbon. The diffusion coefficient measurements were consistent with an inverted to normal micelle transition occurring at high water levels. From inverted micellar solutions, the addition of benzene (up to 50%) formed closed W O structures.
Visible absorption and resonance Raman spectra of alkaline earth metal ozonides in argon and nitrogen matrices at 10 K

Abstract Optical and resonance Raman spectra of the reaction products of Mg, Ca, Sr, and Ba with ozone were observed in argon and nitrogen matrices. The visible spectra were characterized by strong, vibronically structured absorptions between 540 and 350 nm, and are assigned to the alkaline earth metal ozonides, A + O 3 − . Vibrational analysis yielded ω1′ and ω1x1 values of about 900 and 6 cm−1, respectively, with only slight variation from metal to metal. Resonance Raman spectra consisted of a strong fundamental near 1020 cm−1 and two overtones with decreasing intensity. Oxygen-18 substitution confirmed the vibrational assignments, which agree very well with the alkali metal ozonide spectra. These results suggest that the +1 oxidation state plays an important role in the chemistry of the alkaline earth metals under conditions where aggregation does not occur to favor the +2 state. A thorough search was made for absorptions due to the alkaline earth oxide species, but no bands were observed.
History, Memory and Iranian-Armenian Memoirs of the Iranian Constitutional Revolution

…the present generation may rewrite history but it does not write it on a blank page.1 1 Maurice Halbwachs, On Collective Memory, ed. and trans. with an introduction by Lewis A. Coser (Cambridge:...
Submillimetre wave response of superconducting YBa/sub 2/Cu/sub 3/O/sub 7-x/ using coherent time-domain spectroscopy

A coherent time-domain technique using freely propagating radiation bursts is used to study the submillimetre-wave response (extending to 1.4 THz) of a YBa2Cu3O7−x thin film above and below the critical temperature. From these measurements the complex dielectric response, and hence the complex conductivity, were directly obtained.
A Nonlinear Optimization Model of Time and Resource Allocation Decisions in Projects With Uncertainty

Abstract:We formulate a nonlinear optimization model for managing project efforts where there is significant uncertainty in the duration, resource requirements, and outcomes of individual tasks. This formulation represents a significantly different view of project planning than the one implied by traditional project scheduling and focuses attention on important resource allocation decisions faced by project managers. The model can be used to optimize any of several possible performance measures for the project as a whole. We include a small computational example that focuses on maximizing the probability of successful completion of a project whose tasks have uncertain outcomes. The resource allocation problem formulated here has importance and direct application to the management of information system projects, which often contain significant uncertainty.
Achieving Target Refraction after Cataract Surgery

Purpose To evaluate the difference between target and actual refraction after phacoemulsification and intraocular lens implantation at an academic teaching institution's Comprehensive Ophthalmology Service. Design Retrospective study. Participants We examined 1275 eye surgeries for this study. Methods All consecutive cataract surgeries were included if they were performed by an attending or resident surgeon from January through December 2010. Postoperative refractions were compared with preoperative target refractions. Patients were excluded if they did not have a preoperative target refraction documented or if they did not have a recorded postoperative manifest refraction within 90 days. Main Outcome Measures The main outcome measure was percentage of cases achieving a postoperative spherical equivalent ±1.0 diopter (D) of target spherical equivalent. Results We performed 1368 cataract surgeries from January through December of 2010. Of these, 1275 (93%) had sufficient information for analysis. Of the included cases, 94% (1196 of 1275) achieved ±1.0 D of target refraction by 90 days after cataract surgery. Conclusions This paper establishes a new benchmark for a teaching hospital, where 94% of patients achieved within 1.0 D of target refraction after cataract surgery. The refractive outcomes after cataract surgery at this academic teaching institution were higher than average international benchmarks.
Etiology and outcomes of veterans with spinal cord injury and disorders hospitalized with community-acquired pneumonia

Abstract Chang HT, Evans CT, Weaver FM, Burns SP, Parada JP. Etiology and outcomes of veterans with spinal cord injury and disorders hospitalized with community-acquired pneumonia. Objective To determine whether documentation of a causative organism for community-acquired pneumonia (CAP) is associated with outcomes, including mortality and length of stay (LOS), in hospitalized veterans with spinal cord injuries and disorders (SCID confidence interval, .12–.99). Pathogen-based CAP diagnosis was significantly associated with longer LOS (adjusted r 2 =.023, P =.024). Conclusions There was no association between etiologic diagnosis of CAP and 30-day mortality among people with SCI&D. Documentation of CAP etiology was associated with the variance in LOS. Pneumococcal vaccination and antibiotic therapy with antipseudomonal activity may be particularly prudent in these patients given the high frequency of these pathogens among SCI&D patients with CAP.
Intensive studies of Sierra Nevada cloudwater chemistry and its relationship to precursor aerosol and gas concentrations

Measurements of inorganic aerosol and gas phase species are presented for three sites in central California during a 4 day period in April 1988. The measurement sites were located along an east-west transect at Visalia, Ash Mountain, and Lower Kaweah, with elevations of 90, 550 and 1900 m, respectively. Aerosol compositions were nearly neutral at all locations, however large concentrations of NH_3 at Visalia contributed significant excess alkalinity to the air mass sampled there. Concentrations of all major species were observed to decrease with elevation during most of the sampling periods. Concentrations at the upper two sites exhibited diurnal fluctuations, with peaks in the late afternoon, consistent with the transport of pollutants from San Joaquin Valley sources by daytime upslope winds. Concentrations of most of these species reached a maximum at the elevated sites on 28 April, as a weak cold front approached, reducing the atmospheric stability over the valley floor. Concentrations at Visalia on this day were somewhat lower than those observed earlier in the week. Clouds intercepting the mountain slopes on 28 April were sampled at two locations. The coudwater pH at both sites was observed to fall throughout the event, dropping as low as 4.34. Precursor concentrations of aerosol NO_3^−, SO_4^(2-) and NH_4^+, and gas phase HNO_3 and NH_3, were sufficient to account for the observed cloudwater loadings of NO_3^−, SO_4^(2-) and NH_4^+. In-cloud measurements made near the cloud base indicated a considerable S(IV) oxidation potential in the form of H_2O_2, but only low S(IV) concentrations. Cloudwater concentrations of formic acid were approximately three times acetic acid concentrations. Carbonyl concentrations were dominated by formaldehyde and glyoxal.
The Identification of Giftedness: A Comparison of White, Hispanic and Black Families.

A survey was sent to White, Hispanic and Black parents of children in the gifted and talented program of a large urban school district. The results indicated that there were few differences among the three parent groups in either the characteristics that had indicated to them that their child might be gifted, or in the attributes which they believed were current descriptors of their gifted child. Large group differences were present, however, between the White sample and the two minority group samples in the percentage of families who requested an evaluation of their child for possible placement in the gifted and talented program. Fewer of the minority parents made such a request. This factor could contribute to the underrepresentation of minority students in gifted programs.
Comparing the Gradual Deformation with the Probability Perturbation Method for Solving Inverse Problems

Inverse problems are ubiquitous in the Earth Sciences. Many such problems are ill-posed in the sense that multiple solutions can be found that match the data to be inverted. To impose restrictions on these solutions, a prior distribution of the model parameters is required. In a spatial context this prior model can be as simple as a Multi-Gaussian law with prior covariance matrix, or could come in the form of a complex training image describing the prior statistics of the model parameters. In this paper, two methods for generating inverse solutions constrained to such prior model are compared. The gradual deformation method treats the problem of finding inverse solution as an optimization problem. Using a perturbation mechanism, the gradual deformation method searches (optimizes) in the prior model space for those solutions that match the data to be inverted. The perturbation mechanism guarantees that the prior model statistics are honored. However, it is shown with a simple example that this perturbation method does not necessarily draw accurately samples from a given posterior distribution when the inverse problem is framed within a Bayesian context. On the other hand, the probability perturbation method approaches the inverse problem as a data integration problem. This method explicitly deals with the problem of combining prior probabilities with pre-posterior probabilities derived from the data. It is shown that the sampling properties of the probability perturbation method approach the accuracy of well-known Markov chain Monte Carlo samplers such as the rejection sampler. The paper uses simple examples to illustrate the clear differences between these two methods
A physicochemical mechanism for the ignition of the Seveso accident

The so-called Seveso ‘explosion’ of 10 July 1976 was completely unexpected, and various speculations about its initiation have been entertained, including the possibility of sabotage1. Seveso has remained the focus of undiminished interest and publicity1,2 and the puzzle concerning the occurrence of its accident persists. The explanation proposed here is based on our recent investigations of the relevent chemical kinetics and heat transfer phenomena. This physicochemical mechanism involves the combination of (1) exothermic reactions starting (personal communication from the Givaudan Company) below the previously known 230 °C threshold and (2) a thermal conduction–convection–radiation process responsible for channelling the normally negligible (in global sense) upper reactor wall heat into a small portion (10%) of the reactor contents, thus yielding the temperature range conducive to these exothermic reactions.
Evaluation of insect-mediated seed set among soybean lines segregating for male sterility at the ms6 locus☆

Currently, there is no economical way to produce large quantities of F1 hybrid soybean seed in the USA. One of the fundamental requirements for hybrid seed production is the availability of a stable male-sterile, female-fertile system. However, the more challenging barrier is the efficient transfer of pollen from the male parent to the female parent. This could potentially be achieved through pollinator insects. Our observations suggested that seed set on male-sterile, female-fertile plants is a good indicator of insect attraction. The objective of this study was to evaluate seed set among male-sterile, female-fertile lines segregating for male-sterile, female-fertile ms6 allele by using Megachilerotundataaspollinatorvector.Thirty-fourpairs ofnear-isogeniclines,thems6w1w1donorparent,and itstwoisogeniclinesW1w1 and w1w1 segregating for male-sterile (ms6) allele were used. The W1 locus controls flower color and hypocotyle pigmentation. Seed set was evaluated on field-grown plants in 2001‐2003 near Ames, IA. Although the observed seed set was not commercially acceptable, our results indicated significantdifferences in seedsetamong lines.This suggeststhat preferential attraction ofpollinators occurred,and selection among male-sterile, female-fertile linescouldbeused toobtain femaleparentssuitable toproducelargeramounts ofhybridsoybeanseed. Inaddition, the effect of flower color on seed set was statistically significant. White-flowered lines (w1w1) produced more seed set compared to purpleflowered lines (W1W1). Lastly, the important effect of year suggested that the effect of environmental conditions on seed set among lines segregating for male sterility was of paramount importance to plant‐pollinator interactions. This needs to be assessed in order to establish an efficient hybrid soybean program. Published by Elsevier B.V.
Evidence for superoxide formation during hepatic metabolism of tamoxifen.

Abstract Spin trapping of free radicals during the hepatic metabolism of tamoxifen was investigated; the spin trap employed in this study was 5,5-dimethyl-1-pyrroline-1-oxide (DMPO). The spin adduct 2-hydroxy-5,5-dimethyl-1-pyrrolidinyloxyl (DMPO-OH) was detected in an in vitro incubation mixture of phenobarbital-treated rat hepatocytes containing tamoxifen, dimethyl sulfoxide, and DMPO. However, since the spin adduct 2,5,5-trimethyl-1-pyrrolidinyloxyl (DMPO-CH3) was not observed, the DMPO-OH resulted from the cellular bioreduction of 2-hydroperoxy-5,5-dimethyl-1-pyrrolidinyloxyl (DMPO-OOH) by glutathione peroxidase. Addition of Superoxide dismutase (SOD) to the in vitro system indicated that Superoxide production was intracellular. When noninduced hepatocytes were utilized, free radical production was not evident. Thus, the cytochrome P450 monooxygenase system was responsible, in part, for the intermediacy of Superoxide anion during hepatic metabolism.
Saturn's central flash from the 3 July 1989 occultation of 28 Sgr

We present observations of Saturn's central flash obtained from Palomar and McDonald Observatories during the 3 July 1989 occultation of 28 Sgr. As the star passed close to the geometric center of Saturn's shadow, the focusing of the incident starlight by the planet's atmosphere formed multiple stellar images along the limb which were detected in infrared images obtained at wavelengths of 3.9 (Palomar) and 2.1 microns (McDonald). These are the first reported observations of a central flash due to Saturn, and the first of any planet in which the signal flash from each stellar image could be determined separately, permitting a comparison of both intensity and position for each image with model predictions. Four separate flashes were observed from each observatory, corresponding to points on the limb where the starlight passed through the Cassini Division and the relatively transparent C Ring, with maximum brightness reaching 1-2% of the unocculted stellar intensity. The timing of the flashes is quite sensitive to the shape of Saturn's limb, which depends in turn on the planet's zonal gravity harmonics and on the zonal wind profile in the lower stratosphere, near the 2.5-mbar pressure level. The locations of the images along the limb, as well as the timing, shapes, and amplitudes of the individual flash light curves, are well matched by a smoothed model based on a tropospheric zonal wind profile obtained from tracking cloud features in Voyager images and the Saturn ring optical depth profile obtained from the Voyager Photopolarimeter experiment. The smoothing required to give the best match to the data exceeds that attributable to the finite angular extent of the occulted star and may be due to refractive scattering by turbulence or wave structure in Saturn's atmosphere. There is no evidence of significant atmospheric absorption at the observed wavelengths, which correspond to spectral regions of weak methane absorption.
ASAP: an environment for automated preprocessing of sequencing data.

Background Next-generation sequencing (NGS) has yielded an unprecedented amount of data for genetics research. It is a daunting task to process the data from raw sequence reads to variant calls and manually processing this data can significantly delay downstream analysis and increase the possibility for human error. The research community has produced tools to properly prepare sequence data for analysis and established guidelines on how to apply those tools to achieve the best results, however, existing pipeline programs to automate the process through its entirety are either inaccessible to investigators, or web-based and require a certain amount of administrative expertise to set up.
Nonlinear liquid crystals in periodic structures

ABSTRACT We report optical and photoresponsive behavior of nonlinear liquid crystals in two-dimensional (2D) periodicstructure. 2D structure made of photoresist and titania is constructed by interference photolithography using gratingmask. Then azobenzene-doped nematic liquid crystal is infiltrated into these arrays, and photoresponsive behavior ofthe azobenzene-doped liquid crystal in the periodic structure is investigated. In particular, we show that the diffractionfrom these liquid crystal infiltrated grating structures can be optically modulated by an Ar + laser at 488 nm.Keywords: Nonlinear liquid crystals, confined structure, periodic arrays, diffraction 1. INTRODUCTION Nematic liquid crystals (NLC) possess very broadband [from 400 nm to 20 microns] birefringence andtransparency, and extraordinarily large optical nonlinearity [1,2]. By far the largest nonlinear refractive index changingmechanism is the optically induced reorientation of the nematic axis of aligned nematic films. Conventional methods ofaligning NLCs employ either surfactant- or rubbed-polymer coated cell windows, for homeotropic or planar alignment,respectively. In a previous publication [3], we have demonstrated that planar aligning action may also be engendered bya 1-D sub-wavelength grating inscribed on the glass windows. Furthermore, we showed that the surface gratings, incombination with the intensity dependent refractive index of the liquid crystal, could function as a nonlinear diffraction.In this paper, we report a novel method of fabricating 2-D grating structures, and observation of nonlinear diffractionfrom these structures impregnated with supra-nonlinear nematic liquid crystals [4].
Utility of daily image guidance with intensity-modulated radiotherapy for tumors of the base of skull

Background This study was carried out to report our experience using intensity-modulated radiotherapy (IMRT) with daily image-guided radiotherapy (IGRT) for tumors involving the base of skull. Methods In all, 100 patients were prospectively treated with IMRT to a median dose of 64 Gy (range, 45–70 Gy). Daily helical megavoltage computed tomography (MVCT) scans were obtained as part of an IGRT registration protocol for patient alignment. Results The 2-year local-regional control was 91%. A total of 3295 daily MVCT scans were obtained. The mean shift to account for interfraction motion was 1.18 ± 1.75 mm, 1.81 ± 1.34 mm, and 1.33 ± 1.19 mm for the medial–lateral (ML), superior–inferior (SI), and anterior–posterior (AP) directions, respectively. Pretreatment shifts of >3 mm occurred in 10%, 26%, and 18%, in the ML, SI, and AP directions, respectively. Conclusions The feasibility and efficacy of daily IGRT as a complement to IMRT for skull base were demonstrated. © 2011 Wiley Periodicals, Inc. Head Neck, 2011
ASYMPTOTIC EXPANSION OF THE PERCENTILES FOR A SAMPLE MEAN STANDARDIZED BY GMD IN A NORMAL CASE WITH APPLICATIONS

This paper develops an asymptotic expansion of a percentile point of the Ginibased standardized sample mean. Such approximate percentiles can be used for proposing tests of hypotheses or confidence intervals of μ when samples arrive from a normal distribution with unknown mean μ and standard deviation σ. We have asymptotically expressed the percentile point bm,α of the Gini-based pivot (1.5), that is, the Gini-based standardized sample mean. Using large-scale simulations, approximations, and data analyses, we report that the Gini-based test and confidence interval procedures for μ perform better or practically as well as the customarily employed Student’s t-based procedures when samples arrive from a normal distribution with suspect outliers. This interesting finding is especially noteworthy when we have a small random sample from a normal population with possible outliers.
Sharing Books: Examining How and Why Mothers Deviate from the Print

Abstract The purposes of this study are threefold: (a) to examine mothers’ deviations from the printed text, (b) to examine mothers’ reasons for deviating from the print while sharing books with children, and (c) to examine both the text deviations and reasons mothers held for those deviations across a four‐year span of age groups. Grouped according to their children's ages (6‐months, 12‐months, 18‐months, 24‐months and 4‐years) 25 mothers read two preselected children's books during two scheduled reading times. Analyses showed that mothers in this study offered three major reasons for deviating from the printed text while reading with their children: (a) simplification: to make difficult text easier, (b) elaboration: to extend their children's knowledge, and (c) engagement: to maintain their children's attention during the book reading event. Mothers of the 24‐month and 4‐year‐olds asked more questions to engage their children, and they spent more time explaining text concepts. Mothers of the 6‐month, 12...
Collaborating with Public Librarians to Promote Emergency Preparedness and Safety Awareness

The Louis Calder Memorial Library received an Express Community Day Award from the National Network of Libraries of Medicine (NN/LM) to partner with the Miami-Dade County Public Library librarians to promote emergency preparedness and safety awareness. Named Safety Fair: Keep Your Family Safe – Emergency Preparedness at Home and Away, the events improved the public librarians' knowledge of NN/LM resources, such as TOXNET, MedlinePlus®, ToxTown®, ToxMystery®, and WISER®, as well as university-created resources. A train-the-trainer program was also implemented for the public librarians.
Substantial Goodness and Nascent Human Life.

Many believe that moral value is—at least to some extent—dependent on the developmental states necessary for supporting rational activity. My paper rejects this view, but does not aim simply to register objections to it. Rather, my essay aims to answer the following question: if a human being’s developmental state and occurrent capacities do not bequeath moral standing, what does? The question is intended to prompt careful consideration of what makes human beings objects of moral value, dignity, or (to employ my preferred term) goodness. Not only do I think we can answer this question, I think we can show that nascent human life possesses goodness of precisely this sort. I appeal to Aquinas’s metaethics to establish the conclusion that the goodness of a human being—even if that being is an embryo or fetus—resides at the substratum of her existence. If she possesses goodness, it is because human existence is good.
Structure and reactivity of a pyridine-1-imido-2-thiolato complex of iridium(III), Cp*Ir(1-N-2-Spy), generated by photolysis of the (azido)(pyridine-2-thiolato) complex, Cp*Ir(2-Spy)(N3)

Photolysis of the (azido)(pyridine-2-thiolato)iridium(lll) complex Cp*Ir(2-Spy)(N 3 ) (1) gave a pyridine-1-imido-2-thiolato complex, Cp*Ir(1-N-2-Spy) (2), in which one of the nitrogen atoms of the azide ligand has been inserted into the Ir-N(py) bond (Cp* = η 5 -C 5 Me 5 ). Complex 2 reacted quantitatively with methyl iodide to give the N-methylated product, [Cp*lr(1-NMe-2-Spy)]l (3). X-ray crystallography revealed that both 2 and 3 have similar two-legged piano stool structures with planar 1-N-2-Spy 2 - or 1-NMe-2-Spy - ligands, which form iridacyclopentadienyl-like rings by moderate S(pπ)/N(pπ) to Ir(dπ) π donation.
High-n recombination lines in the solar atmosphere

The investigation of radio recombination lines if HI and heavier elements is one of the principal methods of studying the structure within the lower solar atmosphere. Spectral lines at millimeter wavelength may be formed in the solar chromosphere when Rydberg transitions between highly excited levels occur. Theoretical and observational antecedents to radio-frequency lines in the solar spectrum are summarized. Physical mechanisms that affect excited atoms immersed in a plasma are discussed and preliminary calculations of the relative line intensity for hydrogen recombination lines from H5(alpha) (7.46 micrometers ) to H42(alpha) (3.38 mm) are presented.© (1994) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Structural and Functional Bases for the Regulation of IRSp53 by Cdc42

Cell migration is a key step in tumor invasion and metastasis, involving dynamic reorganization of the actin cytoskeleton and membranes. BAR domain containing proteins have emerged as important regulators of the cytoskeleton that aid in coupling membrane and cytoskeleton dynamics to signaling pathways. IRSp53 is a BAR domain containing protein that is a potent inducer of lamellipodia- and filopodia-based cell motility under the control of Rho-family GTPases, making it a key player in tumor metastasis. However, little is known about the mechanisms of regulation of BAR domain-containing proteins in general and IRSp53 in particular. Here, we show a structural mechanism for IRSp53 regulation, which involves the release of autoinhibitory interactions by Cdc42. Central to this mechanism is a semi-conserved CRIB-PR motif that is rich in prolines (CRIB-PR) that joins the N-terminal BAR domain to the C-terminal SH3 domain. We have employed several biophysical techniques to confirm that both GTP-Cdc42 and the SH3 domain can bind to a CRIB-PR motif. Furthermore, we have used FRET to show IRSp53 undergoes a conformational change upon Cdc42 binding, consistent with the release of an autoinhibitory interaction. A crystal structure of a complex between activated Cdc42 and the CRIB-PR motif shows that proline-rich region binds to a region on Cdc42, not previously seen by conventional CRIB domains. Mutagenesis studies not only confirm this binding in solution and in cells, but also indicate that the SH3 domain is required for autoinhibition. In conclusion, we show a structural mechanism for IRSp53 regulation that involves a uniquely adapted CRIB motif that serves as a Cdc42-dependent switch for IRSp53 function, which helps to explain it's indispensible role in cell migration.
Keeping the psyche in psychiatry: eight years later.

My first column as editor of this journal’s psychotherapy columns declared my prime objective in taking on the task: “Keeping the Psyche in Psychiatry.” 1,2 I am concerned about the practice by psychiatrists of well founded forms of psychotherapy in all psychiatric settings. I am a senior psychiatrist and psychoanalyst in private practice with a longstanding involvement in medical education and in professional organizations. To counterbalance my own perspective, I have often tried to write in more general terms than my own psychodynamic orientation. Invited guest columnists have written from the perspective of other schools of psychotherapy as well as other professional environments. Of course, I have not been alone in this quest. Numerous psychiatrists in leadership positions—from widely varying practice settings and all parts of the country, as well as academic psychiatrists and even some leaders in managed care—have expressed their concern about the fading role of psychotherapy and the decreasing interest in the patient’s personal narrative 3 in psychiatric practice. They lament the decline of the psychotherapy skill set in many recentlytrained psychiatrists. In my initial column, I highlighted the American Psychiatric Association’s Commission on Psychotherapy by Psychiatrists (COPP), of which I had been chair. COPP is now a committee of the same name reporting to the Council on Quality Care. It comments frequently on psychotherapy issues, writes or revises position statements, reviews practice guidelines, contributes to the design of psychiatric practice surveys, makes presentations at scientific meetings of the American Psychiatric Association, and has completed a paper differentiating the common, often supportive denominators of psychotherapies and their divergence into distinctively psychodynamic and cognitive-behavioral methodologies. COPP continues to be a respected voice for psychotherapy by psychiatrists in the American Psychiatric Association. However, it is only one of many forces at work to advance the cause. Now, almost 8 years later, what has been accomplished? In the past year, several major, longstanding efforts have come to fruition with beneficial implications for psychotherapy by psychiatrists. On the down side, a recent study shows that the trend continues for psychiatrists to provide psychotherapy for a smaller proportion of their patients, with more psychiatrists doing no psychotherapy at all. The well-rounded psychiatrist skilled in the full armamentarium of treatments is still an endangered species. Like the proverbial three-legged stool, the viability of psychotherapy by psychiatrists rests on the complex interaction of three bases—scientific support, availability of training, and financial reimbursement. However, in the new healthcare environment, a fourth leg is equally essential—privacy.
Decreased aortic growth and middle aortic syndrome in patients with neuroblastoma after radiation therapy

Background Long-term CT follow-up studies are required in pediatric patients who have received intraoperative radiation therapy (IORT) and external beam radiation therapy (EBRT) to assess vascular toxicities and to determine the exact complication rate. Objective To analyze with CT the effects of radiation therapy (RT) on the growth of the aorta in neuroblastoma patients. Materials and methods Abdominal CT scans of 31 patients with intraabdominal neuroblastoma (stage II–IV), treated with RT (20 IORT±EBRT, 11 EBRT alone), were analyzed retrospectively. The diameter of the abdominal aorta was measured before and after RT. These data were compared to normal and predicted normal aortic diameters of children, according to themodelofFitzgerald,DonaldsonandPoznanski (aortic diameter in centimeters=0.844+0.0599×age in years), and to the diameters of a control group of children who had not undergone RT. Statistical analyses for the primary aims were performed using the chi-squared test, t-test, Mann-Whitney test, nonparametric Wilcoxon matched-pairs test and analysis of variance for repeated measures. Clinical files and imaging studies were evaluated for signs of late vascular complications of neuroblastoma patients who had received RT. Results The mean diameter before and after RT and the growth of the aorta were significantly lower than expected in patients with neuroblastoma (P<0.05 for each) and when compared to the growth in a control group with normal and nonirradiated aortas. Among the patients who had received RT, there was no difference due to the type of RT. Seven patients from the IORT±EBRT group developed vascular complications, which included hypertension (five), middle aortic syndrome (two), death due to mesenteric ischemia (one) and critical aortic stenosis, which required aortic bypass surgery (two). Conclusion Patients with neuroblastoma who had received RT showed impaired growth of the abdominal aorta. Significant long-term vascular complications occurred in seven patients who received IORT±EBRT. Thus, CT evaluation of patients with neuroblastoma who receive RT should include not only reports of changes in tumor extension, but also documentation of perfusion, and the size and growth of the aorta and its branches over time.
Cochlear implants: current status

This article reviews the current and evolving status of cochlear implants, including technology, design, candidacy, outcomes and future directions. It examines these variables in terms of their present and future impact on clinical outcomes in pediatric and adult populations.
The spectral shape and the components of the background in in vivo neutron capture prompt gamma ray analysis

Abstract The shape of the background spectrum and the different contributions to the background in in vivo neutron capture prompt gamma ray analysis have been studied using a 252Cf neutron source. Since the source of background and its contribution varies for different energy regions, the detector shielding and the facility construction materials may be different for each analyzed element. Limits of detection for in vivo measurement of Hg, Ca and N were determined.
On the Asymptotic Behavior of Least-Squares Estimators in AR Time Series with Roots Near the Unit Circle

Some asymptotic properties of the least-squares estimator of the parameters of an AR model of order p, p ? 1, are studied when the roots of the characteristic polynomial of the given AR model are on or near the unit circle. Specifically, the convergence in distribution is established and the corresponding limiting random variables are represented in terms of functionals of suitable Brownian motions. Further, the preceding convergence in distribution is strengthened to that of convergence uniformly over all Borel subsets. It is indicated that the method employed for this purpose has the potential of being applicable in the wider context of obtaining suitable asymptotic expansions of the distributions of leastsquares estimators.