cssi/SciSciGPT-SciSciNet huggingface dataset:
A genetic model for human polyglutamine-repeat disease in Drosophila melanogaster

To apply genetics to the problem of human polyglutamine–repeat disease, we recreated polyglutamine–repeat disease in Drosophila melanogaster . To do this, we expressed forms of the human gene encoding spinocerebellar ataxia type 3, also called Machado–Joseph disease (SCA–3/MJD). This gene is responsible for the most common form of human ataxia worldwide. Expression of a normal form of the MJD protein with 27 polyglutamines (MJDtr–Q27) had no phenotype. However, expression of a form of the protein with an expanded run of 78 glutamines (MJDtr–Q78) caused late onset progressive degeneration. In addition, the MJDtr–Q78 formed abnormal protein aggregates, or nuclear inclusions (NIs), whereas the control protein was cytoplasmic. These data indicate that the mechanisms of human polyglutamine–repeat disease are conserved to Drosophila . We are currently using this model to address potential mechanisms by which the mutant disease protein causes neural degeneration, as well as to define genes that can prevent polyglutamine–induced degeneration. By applying the power of Drosophila genetics to the problem of human polyglutamine–induced neural degeneration, we hope to identify ways to prevent and treat these diseases in humans.
Mode coupling and tagged particle correlation functions: the Stokes-Einstein law

Abstract In this paper a mode coupling theory for equilibrium tagged particle correlation functions in simple fluids is developed from molecular considerations. The mode coupling formalism developed in a previous paper [Physica A 181 (1992) 89] to describe equilibrium fluctuations in simple liquids is generalized to include tagged particle correlations. The mode coupling formalism and N ordering approximation scheme used in the previous paper allow a series for the generalized diffusion constant to be obtained which is exact in the thermodynamic limit. The Stokes-Einstein law for a slip Brownian particle is then derived from this series in a systematic fashion. The techniques applied here obviate the need to assume that the simple liquid is incompressible, and allow a self-consistent series of equations for the diffusion constant of the Brownian particle and transport coefficients of the fluid to be obtained which are useful in the study of supercooled liquids.
Does early ultrasonography affect management of pediatric appendicitis? A prospective analysis.

Abstract Background: Appendicitis remains a difficult diagnosis in children. Ultrasonography is increasingly used for the diagnosis of appendicitis, although the proper clinical role for this test remains unclear. Methods: To evaluate the clinical utility of ultrasonography in appendicitis, the authors analyzed prospectively all children evaluated for possible appendicitis from January 1 through December 31, 1997. Children with a high clinical suspicion of appendicitis were referred for surgery (n = 122). Children with equivocal findings of appendicitis were referred for early ultrasonography (EUS) and formed the study cohort (n = 103). An initial management plan was made to operate or observe each patient, and a risk of appendicitis (doubtful, possible, probable) was assigned by a pediatric surgery fellow. EUS was then performed, and its effect on management was assessed. Results: Using clinical judgment to operate at initial presentation, the sensitivity was 38% and specificity was 95%. Using EUS alone, the sensitivity was 87% and specificity was 88%. The management of 30 of 103 patients (30%) was changed after EUS, including a decision to operate in 28 patients and a decision not to operate in two patients. Conclusions: EUS appears to have substantial clinical utility in children with equivocal findings of appendicitis, and its use complements the clinical management. The use of EUS can improve patient care and reduce hospital resource utilization.
Fiber Fabry-Perot filter with passive temperature compensation and its application in a wavelength-division multiple-access computer network

Direct-detection passive networks with optical amplifiers and tunable filters provide sensitivity and selectivity comparable to those of coherent systems and are simpler and more field worthy.1-3 Tunable fiber Fabry–Perot (FFP) filters4 and erbium-doped fiber amplifiers (EDFA’s) offer excellent optical performance and basic compatibility with single-mode optical fibers. This paper describes a tunable fiber FFP filter5 with passive temperature compensation as well as the control circuitry and design detail necessary for its initial application in an IBM research prototype wavelength-division multiple-access (WDMA) computer network called Rainbow.2
Pulsed laser deposition and physical properties of carbon nitride thin films

Carbon nitride thin films were grown using an approach that combines pulsed laser deposition and atomic beam techniques. The composition and phases of the carbon nitride materials obtained from the reaction of laser ablated carbon and atomic nitrogen have been systematically investigated. The nitrogen composition was found to increase to a limiting value of 50% as the fluence was decreased for laser ablation at both 532 and 248 nm. Analysis of these experiments show that the growth rate determines the overall nitrogen composition, and thus suggests that a key step in the growth mechanism involves a surface reaction between carbon and nitrogen. Infrared spectroscopy has also been used to assess the phases present in the carbon nitride thin films. This spectroscopic measurement indicates that a cyanogen-like impurity occurs in films with nitrogen compositions greater than 30%. Investigations of the effects of thermal annealing have been carried out, and show that the impurity phase can be eliminated to yield a single phase material. In addition, systematic measurements of the electrical resistivity and thermal conductivity of the carbon nitride films were made as a function of nitrogen content. The implications of these results are discussed.
Three new species of Spiniloculus (Cestoda: Tetraphyllidea) from Chiloscyllium punctatum (Elasmobranchii: Orectolobiformes) off Borneo with clarification of the identity of the type of the genus.

The type species (Spiniloculus mavensis Southwell, 1925) of the previously monotypic tetraphyllidean genus Spiniloculus Southwell, 1925 is redescribed from the type material from Moreton Bay, Australia. As a consequence the identity of this species is definitively resolved. Three new species in the genus, all collected from Chiloscyllium punctatum Muller et Henle (brownbanded bambooshark), in Borneo, are described. Spiniloculus calhouni sp. n. conspicuously differs from all three of its congeners in its possession of post-poral testes. Spiniloculus fylerae sp. n. and Spiniloculus paigeae sp. n. differ from their two other congeners in that they are relatively small worms (4-6.5 and 2.2-5 mm in total length, respectively) with fewer than 30 proglottids. They can be distinguished from one another in that, while the vitelline follicles are interrupted at the level of its ovary in S. fylerae, this is not the case in S. paigeae. Furthermore, whereas the cirrus sac of the former species is pyriform, it is elongate-oval in the latter species. This brings the total number of species in the genus to four, and lends support to the suggestion that the original identity of the type host of S. mavensis as Mustelus sp. was in error. This work also extends the range of the genus to include the island of Borneo. A key to the species of Spiniloculus is provided. Morphological data generated here, using both light and scanning electron microscopy, support the suggested close affinities between Spiniloculus and Yorkeria Southwell, 1927, both of which parasitize bamboosharks.
Ceramic-Based Nanoparticles Entrapping Water-Insoluble Photosensitizing Anticancer Drugs: A Novel Drug−Carrier System for Photodynamic Therapy

A novel nanoparticle-based drug carrier for photodynamic therapy is reported which can provide stable aqueous dispersion of hydrophobic photosensitizers, yet preserve the key step of photogeneration of singlet oxygen, necessary for photodynamic action. A multidisciplinary approach is utilized which involves (i) nanochemistry in micellar cavity to produce these carriers, (ii) spectroscopy to confirm singlet oxygen production, and (iii) in vitro studies using tumor cells to investigate drug-carrier uptake and destruction of cancer cells by photodynamic action. Ultrafine organically modified silica-based nanoparticles (diameter approximately 30 nm), entrapping water-insoluble photosensitizing anticancer drug 2-devinyl-2-(1-hexyloxyethyl) pyropheophorbide, have been synthesized in the nonpolar core of micelles by hydrolysis of triethoxyvinylsilane. The resulting drug-doped nanoparticles are spherical, highly monodispersed, and stable in aqueous system. The entrapped drug is more fluorescent in aqueous medium than the free drug, permitting use of fluorescence bioimaging studies. Irradiation of the photosensitizing drug entrapped in nanoparticles with light of suitable wavelength results in efficient generation of singlet oxygen, which is made possible by the inherent porosity of the nanoparticles. In vitro studies have demonstrated the active uptake of drug-doped nanoparticles into the cytosol of tumor cells. Significant damage to such impregnated tumor cells was observed upon irradiation with light of wavelength 650 nm. Thus, the potential of using ceramic-based nanoparticles as drug carriers for photodynamic therapy has been demonstrated.
Study design and protocol for a theory-based behavioral intervention focusing on maintenance of weight loss: the Maintenance After Initiation of Nutrition TrAINing (MAINTAIN) study

Abstract Background Obesity is a significant public health problem. Although various lifestyle approaches are effective for inducing significant weight loss, few effective behavioral weight maintenance strategies have been identified. It has been proposed that behavior maintenance is a distinct state that involves different psychological processes and behavioral skills than initial behavior change. Previously, we created a conceptual model that distinguishes behavior initiation from maintenance. This model was used to generate Maintenance After Initiation of Nutrition TrAINing (MAINTAIN), an intervention to enhance weight loss maintenance following initiation. The effectiveness of MAINTAIN is being evaluated in an ongoing trial, the rationale and procedures of which are reported herein. Methods/Design Veterans aged ≤ 75 with body mass index ≥ 30 kg/m 2 participate in a 16-week, group-based weight loss program. Participants who lose ≥ 4 kg by the end of 16 weeks (target n = 230) are randomized 1:1 to receive (a) usual care for 56 weeks or (b) MAINTAIN, a theoretically-informed weight loss maintenance intervention for 40 weeks, followed by 16 weeks of no intervention contact. MAINTAIN involves 3 in-person group visits that transition to 8 individualized telephone calls with decreasing contact frequency. MAINTAIN focuses on satisfaction with outcomes, weight self-monitoring, relapse prevention, and social support. We hypothesize that, compared to usual care, MAINTAIN will result in at least 3.5 kg less regain and better relative levels of caloric intake and physical activity over 56 weeks, and that it will be cost-effective. Discussion If effective, MAINTAIN could serve as a model for redesigning existing weight loss programs. ClinicalTrials.gov Identifier NCT01357551
University Of Texas Electrographic Imaging Laboratory: Mark Ii Camera Performance Update And Current Projects

The importance of several unique features of the design of the Mark II camera has been proven in use over the past few years. The camera is now completely operational, and the maintenance laboratory has been moved to the observatory at Mount Locke. Recent improvements include: better baking; a new o-ring preparation utilizing high vacuum baking, aluminization, and oxidation; a new rough pumping system that eliminates waiting for pumpdown and reduces the risk of damage due to leaks and user error; a complete users manual; and a cassette magazine for the film. Photocathode lifetimes are now very long, and the photometric and astrometric properties of the camera have been documented. The reliability of the camera is now unsurpassed by any other instrument at McDonald. New projects include: the construction of an already designed motorized tracking guider; completion of the mechanical design and construction of a focal reducer for the 2.1m telescope; the production of K2CsSb(0) photocathodes to increase sensitivity and spectral range; the construction of a new film outgassing bench to allow large numbers of plates to be taken in one night; the installation of a CCD at the electronic focus of the Mark III camera; and the construction of the already designed 9cm., automatic, Mark IV camera.
The carcinogenic potential of cocaine

Analysis of cocaine by CASE, an expert system, results in the prediction that cocaine is a rodent carcinogen. In view of the widespread exposure to cocaine this is cause for alarm, especially as in utero exposure has been widely documented and the developing human fetus is at an increased risk of transplacental cancer induction.
A Note on the Distribution of the Number of Simplex Iterations to Optimality

Abstract In this note, we present a simulation exploring the distribution of the number of simplex iterations required to obtain the optimal solution of a randomly-generated linear programming problem of a given size and type. We use a Chi-square goodness-of-fit test to show that the distribution appears to be well-fit by a gamma distribution.
Multimodal optical microscope for imaging biological systems

A mulitmodal microscope provides a researcher with the ability to capture images with multiple sources of contrast. Previous attempts at multimodal microscopy have been limited to capturing images at different instruments and digitally registering the images empirically using features common in the specimen. Other multimodal microscopes have combined different microscopy techniques, but have been limited in their sources of contrast. We present a unique microscope which containes 5 different imaging modalities, with four different sources of contrast. Quadrature microscopy measures the phase of the electric field of the light transmitted through an optically transparent specimen, by interference with a reference beam, using a polarimetric technique to resolve the ambiguities between phase and amplitude. Differential Interference Contrast (DIC) measures the phase gradient in an optically transparent specimen by combining two spatially separated images interferometrically. Confocal reflectance measures index of refraction changes in a plane or reflection from small scatterers. Confocal fluorescence and 2-photon laser scanning microscopy, measure fluorescent signatures of a specimen. The last three of these are inherently capable of producing three-dimensional images directly, through localized probing.
CRF receptor antagonist attenuates immobilization stress-induced norepinephrine release in the prefrontal cortex in rats

Abstract Neuroanatomical, neurophysiological, and behavioral studies suggest that brain stem nucleus locus coeruleus (LC) plays an important role in stress response. The present study was designed to clarify, whether infusion of CRF antagonist, α hCRF, into LC could attenuate or block stress-induced changes in norepinephrine (NE) concentrations in microdialysates collected from the medial prefrontal cortex (PFM). Rats were implanted with a bilateral cannulae assembly aimed in the LC and a microdialysis probe (4 mm active membrane length) into the LC. Immobilization of animals significantly increased the concentration of NE in microdialysates from PFM to a maximum of 170.8 ± 12.8% of the baseline ten minutes after the onset of stressor. Concentration of NE in dialysates remained significantly elevated for the next 40 min. Infusion of α hCRF into the LC significantly attenuated stress-induced increase in PFM NE concentration in samples collected at 10, 20, 30, and 50 min after the onset of immobilization. Infusion of α hCRF alone (no immobilization) did not change concentrations at any time during sample collection. These results are consistent with other studies and suggest that stress can facilitate NE release in the PFM through the activation of the CRF system in the brain.
Failure Variability in Porous Glasses: Stress Interactions, Crack Orientation, and Crack Size Distributions

Fracture behavior of porous glass is investigated through a combined finite element–fracture mechanics approach. In contrast to earlier studies, here, simulations embody flaw size distributions in addition to pore–pore stress interactions and crack orientation along pore surfaces. Fracture strength of porous glass shows a steep decrease up to 20% porosity and then levels off due to interacting pores. Weibull modulus varies because of the decreased probability of interactions in microstructures containing less than 2% porosity or the smallest pore diameter =48 μm. Weibull modulus strongly depends on crack size distributions for porosity less than 2% and pore–pore stress interactions for porosity greater than 5%.
Hormonal contraceptive use and women's risk of HIV acquisition: a meta-analysis of observational studies

Summary Background The evidence from epidemiological research into whether use of hormonal contraception increases women's risk of HIV acquisition is inconsistent. We did a robust meta-analysis of existing data to provide summary estimates by hormonal contraceptive method which can be used to inform contraceptive guidelines, models, and future studies. Methods We updated a recent systematic review to identify and describe studies that met inclusion criteria. To ensure inclusion of more recent research, we searched PubMed for articles published after December, 2011, using the terms "hormonal contraception", "HIV/acquisition", "injectables", "progestin", and "oral contraceptive pills". We assessed statistical heterogeneity for these studies, and, when appropriate, combined point estimates by hormonal contraception formulation using random-effects models. We assessed publication bias and investigated heterogeneity through subgroup and stratified analyses according to study population and design features. Findings We identified 26 studies, 12 of which met inclusion criteria. There was evidence of an increase in HIV risk in the ten studies of depot medroxyprogesterone acetate (pooled hazard ratio [HR] 1·40, 95% CI 1·16–1·69). This risk was lower in the eight studies done in women in the general population (pooled HR 1·31, 95% CI 1·10–1·57). There was substantial between-study heterogeneity in secondary analyses of trials (n=7, I 2 51·1%, 95% CI 0–79·3). Although individual study estimates suggested an increased risk, substantial heterogeneity between two studies done in women at high risk of HIV infection ( I 2 54%, 0–88·7) precluded pooling estimates. There was no evidence of an increased HIV risk in ten studies of oral contraceptive pills (pooled HR 1·00, 0·86–1·16) or five studies of norethisterone enanthate (pooled HR 1·10, 0·88–1·37). Interpretation Our findings show a moderate increased risk of HIV acquisition for all women using depot medroxyprogesterone acetate, with a smaller increase in risk for women in the general population. Whether the risks of HIV observed in our study would merit complete withdrawal of depot medroxyprogesterone acetate needs to be balanced against the known benefits of a highly effective contraceptive. Funding None.
Storytelling in Earth sciences: The eight basic plots

Abstract Reporting results and promoting ideas in science in general, and Earth science in particular, is treated here as storytelling. Just as in literature and drama, storytelling in Earth science is characterized by a small number of basic plots. Though the list is not exhaustive, and acknowledging that multiple or hybrid plots and subplots are possible in a single piece, eight standard plots are identified, and examples provided: cause-and-effect, genesis, emergence, destruction, metamorphosis, convergence, divergence, and oscillation. The plots of Earth science stories are not those of literary traditions, nor those of persuasion or moral philosophy, and deserve separate consideration. Earth science plots do not conform those of storytelling more generally, implying that Earth scientists may have fundamentally different motivations than other storytellers, and that the basic plots of Earth Science derive from the characteristics and behaviors of Earth systems. In some cases preference or affinity to different plots results in fundamentally different interpretations and conclusions of the same evidence. In other situations exploration of additional plots could help resolve scientific controversies. Thus explicit acknowledgement of plots can yield direct scientific benefits. Consideration of plots and storytelling devices may also assist in the interpretation of published work, and can help scientists improve their own storytelling.
Immunization with a Peptide Corresponding to Chlamydial Heat Shock Protein 60 Increases the Humoral Immune Response in C3H Mice to a Peptide Representing Variable Domain 4 of the Major Outer Membrane Protein of Chlamydia trachomatis

C3H (H-2k) mice are susceptible to a vaginal challenge with human strains of Chlamydia trachomatis and thus are a useful strain for testing potential Chlamydia vaccine candidates. However, C3H mice are fairly poor responders in terms of the level of antibody resulting from immunization with potential protective peptides representing variable domains (VDs) of the major outer membrane protein (MOMP). C57BL/6 (H-2b) mice, on the other hand, are moderately resistant to a vaginal challenge but are good responders to the chlamydial MOMP VDs. Peptides representing universal T-cell helper epitopes were employed to determine whether the antibody response to a peptide representing VD4 of the MOMP, which has been shown to contain neutralizing epitopes, could be enhanced in C3H and C57 mice. Universal T-cell helper peptides from tetanus toxin, the pre-S2 region of hepatitis B virus, and the mouse heat shock protein 60, as well as the corresponding segment of the Chlamydia heat shock protein 60 (hspct), were coadministered with the VD4 peptide. Peptides were coencapsulated in liposomes containing the adjuvant monophosphoryl lipid A and administered by using a combination of mucosal and intramuscular injection. The only T-cell helper peptide that improved the immune response as judged by antibody level, in vitro neutralization assays, and T-cell proliferation was hspct. The response in the C57BL/6 strain was not significantly enhanced with hspct over levels achieved with VD4 alone; however, in C3H mice the levels of serum antibody to C. trachomatis increased to that seen in C57 mice. However, the molecular specificity and immunoglobulin subclass distribution differed from those of the C57 response, and the neutralizing titers and T-cell proliferation responses were lower. In both strains of mice, titers of vaginal antibody to C. trachomatis were low. In summary, of the T-helper peptides used, only hspct significantly enhanced the immune response of C3H mice to the VD4 peptide, but it had only a modest effect on the immune response of C57 mice.
Grammatically Judgments and Second Language Acquisition

This article takes a critical look at grammaticality judgment tasks in second language acquisition research. It begins by examining the theoretical assumptions that underlie grammaticality judgment tasks, pointing out that previous studies have reported considerable differences between the results obtained from grammaticality judgment tasks and from other, production-oriented tasks. A description of the design features of grammaticality judgment tasks that have been used to date is then provided. There follows an account of a small-scale study designed to investigate the nature of learner judgments. Twenty-one adult advanced Chinese learners of English were asked to judge sentences designed to test their knowledge of dative alternation. The results indicated that the learners rarely used the “not sure” option in the test. Eight of these subjects were then administered a reduced version of the original test as a think-aloud task 1 week later. The results showed that these learners were inconsistent in 22.5% of their judgments. The think-aloud protocols showed that they resorted to a variety of strategies in making judgments. The article concludes by arguing that grammaticality judgment tasks elicit a particular kind of performance that needs to be understood much more thoroughly before it is used as a basis for investigating second language acquisition.
Impact of Metformin on Peak Aerobic Capacity

Individually, exercise and the drug metformin have been shown to prevent or delay type 2 diabetes. Metformin mildly inhibits complex I of the electron transport system and may impact aerobic capacity in people exercising while taking metformin. The purpose of the study was to evaluate the effects of metformin on maximal aerobic capacity in healthy individuals without mitochondrial dysfunction. Seventeen healthy, normal-weight men (n=11) and women (n=6) participated in a double-blind, placebo-controlled, cross-over design. Peak aerobic capacity was measured twice using a continuous, incrementally graded protocol; once after 7-9 d of metformin (final dose=2000 mg/d) and once with placebo, with 1 week between tests. The order of the conditions was counterbalanced. Peak oxygen uptake (VO2 peak), heart rate (HR), ventilation (VE), respiratory exchange ratio (RER), rating of perceived exertion (RPE), and test duration were compared across conditions using paired t tests with the R statistical program. VO2 peak (-2.7%), peak heart rate (-2.0%), peak ventilation (-6.2%), peak RER (-3.0%), and exercise duration (-4.1%) were all reduced slightly, but significantly, with metformin (all p<0.05). There was no effect of metformin on RPE or ventilatory breakpoint. Correlations between the decrement in VO2 peak and any of the other outcome variables were weak (r2<0.20) and not significant. Short-term treatment with metformin has statistically significant, but physiologically subtle, effects that reduce key outcomes related to maximal exercise capacity. Whether this small but consistent effect is manifested in people with insulin resistance or diabetes who already have some degree of mitochondrial dysfunction remains to be determined.
Fast Quantum Algorithms for Handling Probabilistic and Interval Uncertainty

In many real-life situations, we are interested in the value of a physical quantity y that is difficult or impossible to measure directly. To estimate y, we find some easier-to-measure quantities x1, … , xn which are related to y by a known relation y = f(x1, … , xn). Measurements are never 100% accurate; hence, the measured values are different from xi, and the resulting estimate is different from the desired value y = f(x1, … , xn). How different can it be? Traditional engineering approach to error estimation in data processing assumes that we know the probabilities of different measurement errors . In many practical situations, we only know the upper bound Δi for this error; hence, after the measurement, the only information that we have about xi is that it belongs to the interval . In this case, it is important to find the range y of all possible values of y = f(x1, … , xn) when xi ∈ xi. We start the paper with a brief overview of the computational complexity of the corresponding interval computation problems: Most of the related problems turn out to be, in general, at least NP-hard. In this paper, we show how the use of quantum computing can speed up some computations related to interval and probabilistic uncertainty. We end the paper with speculations on whether (and how) “hypothetic” physical devices can compute NP-hard problems faster than in exponential time. Most of the paper's results were first presented at NAFIPS'2003 [30]. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Effects of Lowhead Dams on the Ephemeropterans, Plecopterans, and Trichopterans Group in a North American River

ABSTRACT We assessed the effects of lowhead dams on the EPT group (ephemeropterans, plecopterans, and trichopterans) by sampling habitat and macroinvertebiates monthly from November 2000 to October 2001 at eight gravel bars centered around two lowhead dams on the Neosho River, Lyon County, Kansas. Sites included a reference and treatment site upstream and downstream from each dam. Percent EFT was greater at reference sites than upstream treatment sites, and was positively correlated with stream velocity and %gravel in the substrate, but negatively correlated with substrate compaction and %boulder in the substrate. These results are similar to those for large dams and suggest that differences in habitat around these lowhead dams are unfavorable for EPT taxa, a finding important to the conservation and restoration of biotic integrity in riverine ecosystems.
MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing

Although the costs of next generation sequencing technology have decreased over the past years, there is still a lack of simple-to-use applications, for a comprehensive analysis of RNA sequencing data. There is no one-stop shop for transcriptomic genomics. We have developed MAP-RSeq, a comprehensive computational workflow that can be used for obtaining genomic features from transcriptomic sequencing data, for any genome. For optimization of tools and parameters, MAP-RSeq was validated using both simulated and real datasets. MAP-RSeq workflow consists of six major modules such as alignment of reads, quality assessment of reads, gene expression assessment and exon read counting, identification of expressed single nucleotide variants (SNVs), detection of fusion transcripts, summarization of transcriptomics data and final report. This workflow is available for Human transcriptome analysis and can be easily adapted and used for other genomes. Several clinical and research projects at the Mayo Clinic have applied the MAP-RSeq workflow for RNA-Seq studies. The results from MAP-RSeq have thus far enabled clinicians and researchers to understand the transcriptomic landscape of diseases for better diagnosis and treatment of patients. Our software provides gene counts, exon counts, fusion candidates, expressed single nucleotide variants, mapping statistics, visualizations, and a detailed research data report for RNA-Seq. The workflow can be executed on a standalone virtual machine or on a parallel Sun Grid Engine cluster. The software can be downloaded from http://bioinformaticstools.mayo.edu/research/maprseq/ .
Relationships Between Intergroup Contact and Prejudice Among Minority and Majority Status Groups

Considerable research has shown that greater intergroup contact corresponds with lower intergroup prejudice, yet little is known regarding how the relationships between contact and prejudice may vary for members of minority and majority status groups. The present research examined differences in contact-prejudice relationships among members of minority and majority status groups, using data from a larger meta-analytic study of the effects of intergroup contact. Results indicate that the relationships between contact and prejudice tend to be weaker among members of minority status groups than among members of majority status groups. Moreover, establishing Allport's (1954) proposed conditions for optimal intergroup contact significantly predicts stronger contact-prejudice relationships among members of majority status groups, but not among members of minority status groups. Implications of these findings for future research on contact between minority and majority status groups are discussed.
On regression adjustments to experimental data

Regression adjustments are often made to experimental data. Since randomization does not justify the models, almost anything can happen. Here, we evaluate results using Neyman's non-parametric model, where each subject has two potential responses, one if treated and the other if untreated. Only one of the two responses is observed. Regression estimates are generally biased, but the bias is small with large samples. Adjustment may improve precision, or make precision worse; standard errors computed according to usual procedures may overstate the precision, or understate, by quite large factors. Asymptotic expansions make these ideas more precise.
Influence of Overstimulation on Temporary Threshold Shift and the Onset of Aural Overload

This investigation sought to examine the sensitivity of pure tone thresholds and the onset of aural overload to the fatiguing effects of broad band noise. Noise levels ranging from 35 to 110 dB SPL were presented to 8 normal hearers. Post-exposure pure tone thresholds were determined for octave frequencies 500—4000 Hz while aural overload thresholds were obtained for the fundamental frequencies of 500 and 2000 Hz. Aural overload thresholds were found to decline following exposure levels insufficient to produce measurable TTS. This was particularly evident for low-frequency stimuli (below 2000 Hz). Results suggested that the aural overload test may be a more effective indication of cochlear damage than is the traditional temporary threshold shift procedure. These findings are discussed in terms of the “injured hair cell” hypothesis proffered by Wever & Lawrence (1955).
Shrink-Induced Single-Cell Plastic Microwell Array

The ability to interrogate and track single cells over time in a high-throughput format would provide critical information for fundamental biological understanding of processes and for various applications, including drug screening and toxicology. We have developed an ultrarapid and simple method to create single-cell wells of controllable diameter and depth with commodity shrink-wrap film and tape. Using a programmable CO(2) laser, we cut hole arrays into the tape. The tape then serves as a shadow mask to selectively etch wells into commodity shrink-wrap film by O(2) plasma. When the shrink-wrap film retracts upon briefly heating, high-aspect plastic microwell arrays with diameters down to 20 μm are readily achieved. We calibrated the loading procedure with fluorescent microbeads. Finally, we demonstrate the utility of the wells by loading fluorescently labeled single human embryonic stem cells into the wells.
Justinian, Malalas, and the End of Athenian Philosophical Teaching in A.D. 529

To historians of the ancient world, the closing of the Athenian Neoplatonic school by the emperor Justinian stands as one of the best known, and most debated, events of the later Roman Empire. To some, it is an event of little consequence with only an ephemeral impact upon subsequent developments. To others, it represents nothing less than the death of classical philosophy. Nevertheless, this modern scholarly interest belies ancient attitudes. The only direct statement about the end of Athenian philosophical teaching comes from the Chronicle of John Malalas, and all other ancient sources, including those that rely upon Malalas, are silent about the incident. This silence hints at a fact that this study will make clear. To contemporaries, the closing of the Athenian school was an unremarkable occurrence that represented neither a tyrannical use of imperial power nor an attack upon the valued cultural tradition of philosophical teaching. Like all else in the later Roman world, it occurred within the confines of a political system that, when working properly, matched imperial initiative to the specific needs of a province or city. As a result, the causes and significance of the closing of the Athenian school are best appreciated by understanding how the event developed out of its local political setting.
Learning During the Integration Phase of Mergers and Acquisitions: Perspectives From Learning and Development Professionals

Learning stands as most promising for future mergers and acquisitions (MA Marks & Mirvis, 2011). The purpose of this study was to describe the learning that occurred during the integration phase as perceived by learning and development (L&D) professionals. To strengthen the link among L&D professionals and learning, this study used the organizational learning frameworks posited by Huber (1991) and Crossan, Lane, and White (1999). The findings revealed that four major learning events occurred during the integration. These events encompassed learning about the change, learning how to manage the change, learning for work, and learning from experiences. Although the events are presented in a linear fashion, their occurrences were nonlinear. The results indicated that the work of L&D professionals is instrumental to organizational learning.
The relationship between negative life events and suicidal behavior: moderating role of basic psychological needs.

Background: Individuals who experience negative life events may be at increased risk for suicidal behavior. Intrapersonal characteristics, such as basic psychological needs, however, may buffer this association. Aims: To assess the potential moderating role of overall basic psychological needs, and the separate components of autonomy, competence, and relatedness, on the association between negative life events and suicidal behavior. Method: Our sample of 439 college students (311 females, 71%) completed the following self-report surveys: Life Events Scale, Basic Psychological Needs Scale, Beck Depression Inventory – II, and the Suicide Behaviors Questionnaire-Revised. Results: In support of our hypotheses, negative life events were associated with greater levels of suicidal ideation and attempts, and satisfaction of basic psychological needs, including autonomy, relatedness, and competence, significantly moderated this relationship, over and above the effects of the covariates of age, sex, and depressive ...
Issues on the design and implementation of an intelligent database inference controller

The authors discuss the issues involved in designing and implementing an intelligent database inference controller, referred to as a knowledge-based inference controller. An inference controller is a device that prevents and/or detects security violations via inference. The knowledge-based inference controller, called XINCON, is able to deduce unauthorized inferences that users could make via logical deduction, certain types of non-classical logical deduction, and analogical reasoning. The need for knowledge-based inference control and the functions of an ideal knowledge-based inference controller are considered. The modules of XINCON, knowledge representation, reasoning strategies, and a preliminary prototype implementation are described. >
Slotted Wavelength Scheduling for Bulk Transfers in Research Networks

The advancement of optical network technologies has enabled data-intensive e-science collaborations, which often require the transfer of large files with predictable performance. To support such applications, we design and evaluate two algorithms for scheduling time-constrained bulk transfers on wavelength-based optical research networks. The first one seeks to maximize the network throughput while maintaining a level of fairness among the jobs. The second algorithm works in an overloaded network and serves as an alternative to the first algorithm. It seeks to extend the end times by the smallest possible proportion and complete all the jobs by the extended end times. The main challenge is that the underlying problems are integer optimization problems for wavelength assignment, which have no known fast optimal solutions. We present a heuristic sub-algorithm called LPDAR, which converts fractional solutions from linear programming into integer solutions. LPDAR is the key component used in both aforementioned algorithms. Evaluation shows that LPDAR leads to very good algorithms with a performance level and speed both comparable to those of the LP fractional solutions.
Transaction Level Economics of Cloud Applications

Cloud computing provides many benefits to users including the elimination of up front infrastructure investment plus lower overall infrastructure costs due to increased resource usage efficiency. Cloud applications can also make use of outside services on demand. Since cloud computing operates on a pay-as-you-go model, application developers must understand the economics of their software in finer detail. They must understand how much their software costs to run and how much revenue they earn as their software runs. This understanding comes from knowing how the application uses infrastructure and services for which costs accumulate. We explore some fundamental concepts of cloud application economics at the transaction level.
Threats to Parental and Romantic Attachment Figures' Availability and Adult Attachment Insecurity

This study tested hypotheses based on the theoretical idea that threats to parental availability would have a direct effect on later adult attachment insecurity and that this relationship would be partially, but not fully, mediated by threats to the availability of a romantic partner. Participants were 1,063 individuals in a married or unmarried romantic relationship. Individuals completed a questionnaire on threats to attachment figures' availability and completed another questionnaire about attachment insecurity (avoidance and anxiety) approximately 1 year later. In both models, the greater the threats to attachment figures' (parents' or current partners') availability, the greater the attachment avoidance and attachment anxiety. Consistent with theorizing in the literature, the impact of remembered threats to parental availability on adult attachment avoidance and anxiety, although not eliminated, was greatly reduced by the inclusion of current partner's availability in the model.
Inhibition of estradiol-induced endosteal-bone formation after intrafemoral implantation of testosterone propionate into mice.

1. One hundred and sixty-seven mice had cavities drilled into their right femora and were divided into seven groups with or without intrafemoral placement of hormones or placebos. 2. Mice which had cavities drilled only into their femora or had cholesterol placebos or testosterone propionate pellets implanted intrafemorally showed little endosteal bone proliferation in the distal metaphyses and callus formation at the drilled sites four weeks after implantation. 3. Both intrafemoral and systemic applications of ninety micrograms of estradiolbenzoate induced localized hyperostosis in the traumatized regions. However, four weeks after hormone implantation the distal metaphyses of both femora were endosteally proliferated to approximately the same degree, due to the systemic effects of estradiol benzoate. 4. Over eighty micrograms of intrafemorally placed testosterone propionate was needed to inhibit the effects produced by ninety-microgram pellets of estradiol benzoate placed subcutaneously. However, the androgen inhibited the estrogenic activity not only in the drilled femur, but also in the contralateral one. 5. No sexual differences were observed in response to the dosages of hormones given. Differences in femoral changes between castrated and non-castrated mice were not seen.
Effects of maturation and acute hypoxia on receptor-IP3 coupling in ovine common carotid arteries

Whereas previous studies have established that many mechanisms mediating pharmacomechanical coupling are subject to regulation, evidence of physiological regulation of the coupling efficiency between receptor activation and second-messenger production is scarce. The present studies address the hypothesis that acute hypoxia and maturation can influence the mass of second-messenger production for each activated agonist-bound receptor (“receptor gain”). For this assessment, receptor density and agonist affinity values were used to calculate 5-hydroxytryptamine (5-HT) concentrations that would produce standardized numbers of bound receptors (8.5 fmol/mg protein) in each experimental group and thus minimize effects of age or hypoxia on receptor density or agonist affinity. After 3 min of exposure to these 5-HT concentrations, normoxic magnitudes of contraction were similar (as %potassium maxima) in fetal (50 ± 14%) and adult (40 ± 9%) arteries, but hypoxia (Po 2 ≈ 9–12 Torr for 30 min) depressed contractile tensions with a significantly different time course and magnitude in fetal (30 ± 10%) and adult (17 ± 11%) arteries ( P < 0.05). Basal inositol 1,4,5-trisphosphate (IP3) values (in pmol/mg protein) were significantly greater in fetal (94 ± 16) than in adult (44 ± 6) arteries, and integrated areas above baseline for the IP3 time courses (in nmol-s/mg protein) were significantly greater in fetal than in adult arteries both in normoxic (14.3 ± 1.8 vs. 9.1 ± 1.6) and hypoxic (15.0 ± 2.1 vs. 8.6 ± 1.2) conditions ( P < 0.05). Hypoxia altered the IP3 time courses both in the fetus and the adult but had no significant effect on IP3 mobilization or receptor gain. These data demonstrate that for the 5-HT2areceptor predominant in this preparation, receptor gain can be experimentally determined, is not influenced by acute hypoxia, but is greater in fetal than in adult ovine carotid arteries.
Review of Kurian Kachappilly (ed.), 2009,Process, Religion, and Society.

Alfred North Whitehead (1861–1947) proposed one of the boldest and most thoroughgoing efforts to rethink cosmology of the last century. His philosophy of organism has had a strong, though controversial, influence on Christian theology in North America and beyond, with interest growing in some circles in South and East Asia. While Whitehead is strongly rooted in the Western philosophical tradition, including Plato, the British and American empiricists, and the English Romantic poets, his thought also has strong resonances with aspects of Hindu, Buddhist, and Taoist thought. The two volumes under review are collections of essays that were presented at the Seventh International Whitehead Conference that took place in India in January 2009. In his keynote address at the beginning of volume 1, John B. Cobb, Jr., a Methodist Christian who is one of the most influential process theologians of the last halfcentury, sets the tone for the entire discussion by stressing the primacy of relationships in process and th...