cssi/SciSciGPT-SciSciNet huggingface dataset:
Nitric acid emission from the F100 jet engine

[1] A chemical ionization mass spectrometer (CIMS) from the Air Force Research Laboratory at Hanscom AFB was used to measure levels of HNO3 in the exhaust stream of the F100 jet engine both in a test cell at NASA Glenn Research Center (GRC) at simulated altitudes 3–17 km and in flight behind F-16 aircraft at 9–11 km altitude. The HNO3 concentrations have been expressed as emission indices (EI) by normalizing to engine-produced CO2 measured by GRC instruments in the test cell and NASA-Langley Research Center instruments in flight. The test cell data showed that EI(HNO3) is independent of fuel sulfur level, and is highly dependent upon altitude for altitudes at which most commercial aircraft fly (below 12 km), mainly because the emission is a strong function of combustor inlet temperature, which is lower at high altitudes. EI(HNO3) at military power was 0.003 g NO2 kg−1 fuel at low altitude (∼3 km), and increased to 0.02 g kg−1 for altitudes above 11 km. Operating the engine at 85% maximum turbine speed increased the figures above by a factor of about 2.5. At engine idle, EI(HNO3) was typically 0.14 g kg−1. The decrease in EI(HNO3) with combustor inlet temperature is attributed to the temperature dependence of the NO2 + OH reaction producing HNO3. Comparing HNO3 emission indices with those measured at GRC for NO and NOx allowed us to determine the fraction of NO2 which is converted into HNO3 in the combustion process as a function of inlet temperature. Conversion of NO2 to HNO3 is 0.9% at military power for altitudes ≥11 km, and twice that at 85% maximum turbine speed. The conversion fraction changes dramatically in the 8–11 km altitude range, and is only 0.02% at 3 km altitude, for military power, or 0.2% at 85% maximum turbine speed. At engine idle, this fraction was about 8% at all altitudes. The accuracy of the (average) figures quoted above is ±25%. The in situ data, obtained on 10 flights during the NASA Subsonic Near-Interaction Field (SNIF) experiment, are much less definitive but are consistent with the test cell results.
PULMONARY INFARCTS CAN MIMIC PULMONARY METASTASES FROM RENAL CANCER

Abstract Purpose Spontaneous regression of pulmonary metastases from renal cell carcinoma is a rare but well documented event. We present 2 recent cases that were radiographically consistent with pulmonary metastases from renal cell carcinoma but were pathologically shown to be pulmonary infarcts with no evidence of metastatic cells. Stable pulmonary infarcts can be misconstrued as metastatic disease in patients with renal cell carcinoma while resolving pulmonary infarcts may represent a subpopulation of patients with apparent spontaneous regression. Clinical implications of these findings are discussed. Materials and Methods Clinical and pathological data from 2 patients with large primary renal tumors, venous thrombi and lung masses were reviewed. Data from these cases, as well as pertinent urological and pathological literature, are presented. Results Although preoperative assessment was consistent with stage IV renal cell carcinoma, pathological examination of the lung masses in these patients showed no evidence of tumor cells. Conclusions Pulmonary infarcts may mimic resolving or stable pulmonary metastasis in patients with renal cell carcinoma. Accurate clinical staging is crucial for the prognosis and treatment of renal cell carcinoma. Mistaking pulmonary infarcts for metastatic lesions can lead to inaccurate prognoses and inappropriate treatment.
Potassium Deficiency Increases Specific Leaf Weights and Leaf Glucose Levels in Field-Grown Cotton

Potassium deficiency reduces lint yield and causes fiber quality problems for cotton (Gossypium hirsutum L.) producers throughout the U.S. production regions. This deficiency produces plants exhibiting reduced leaf area but increased specific leaf weights (SLW). The objectives of this research were (i) to determine whether the alterations in leaf growth produced by a K deficiency are associated with changes in leaf carbohydrate levels or leaf water status and (ii) to determine if a K deficiency alters the carbohydrate concentration in root tissue. Field studies were conducted in 1993 and 1994 using four genotypes ('DES 119', MD 51 ne', 'Prema', and STV 825') and two levels of K fertilization (0 and 112 kg K ha -1 ). Glucose, fructose, sucrose, and starch concentrations were quantified for leaves collected at three different dates in both years. Root carbohydrate concentrations were determined once in each growing season. Leaf water potential and its components were determined once each growing season using thermocouple psychrometers. Glucose was the only carbohydrate whose leaf concentration was consistently altered by the K deficiency; it was increased an average of 84% across all leaf harvest dates. Leaf concentrations of starch, sucrose, and fructose were inconsistent in their response to variation in K levels. The K deficiency increased root tissue concentrations of starch by 82%, glucose by 14%, and fructose by 27%, averaged across years. Although leaf water potential (ψ 1 ) and leaf osmotic potential (ψ π ) were unaffected by varying the level of K fertilization, leaf turgor (ψ 1 ) averaged across both years was increased 17% in leaves from the K-deficient plants. The elevated carbohydrate concentrations remaining in source tissue, such as leaves, appear to be part of the overall effect of K deficiency in reducing the amount of photosynthate available for reproductive sinks and thereby producing reductions in lint yield and fiber quality seen in cotton.
The E.coli Chromosome is an Internally-Organized, Springy, Helical Ellipsoid, the Shape and Dynamics of Which, Through the Cell Cycle, are Determined by the Mechanical Constraints Associated with Replication-Driven Extrusion of DNA/chromatin into a Confined Space

We have used 3-dimensional imaging of E. coli to further our analysis of chromosome dynamics. Using fluorescently labeled histone-like protein HU we can visualize the shape of the E. coli nucleoid in living cells in 3D as a function of time in the cell cycle and monitor the positions of specific chromosomal loci or protein complexes (also fluorescently labeled) with respect to this evolving shape. We find that the E. coli nucleoid in newborn (G1) cells is a football-shaped “feather boa”, denser in the middle and highly compressible at its edges, that is twisted into an asymmetric left-handed helical shape. As replication progresses, one sister is immediately reincorporated back into the “mother” nucleoid while the other sister emerges into the “new pole” of the cell where it also acquires shape. Replication origins, replisome complexes, replication forks and sister loci exhibit specific behaviors that are defined by nucleoid shape, with activity occurring in the periphery and/or the low-density “spaces” created by the shape. These and other findings imply that nucleoid shape and chromosome dynamics are primarily governed by internal mechanical forces rather than via external determinants and that the nucleoid as a whole is stiff but “springy”. Springiness may arise from repulsive interactions between plectonemic supercoiled loops that, after emerging from the replisome, form a series of radial arrays. Given that this stiff structure is confined within a cylindrical cell, energy-minimization may promote twisting of the ellipsoid into a helix, with left-handed bias conferred by the right-handed bias of the component negatively supercoiled plectonemes. Tests of this hypothesis are underway.
Health and the Power of Dance

(2008). Health and the Power of Dance. Journal of Physical Education, Recreation & Dance: Vol. 79, No. 4, pp. 33-36.
High-performance CUDA kernel execution on FPGAs

In this work, we propose a new FPGA design flow that combines the CUDA programming model from Nvidia with the state of the art high-level synthesis tool AutoPilot from AutoESL, to efficiently map the exposed parallelism in CUDA kernels onto reconfigurable devices. The use of the CUDA programming model offers the advantage of a common programming interface for exploiting parallelism on two very different types of accelerators -- FPGAs and GPUs. Moreover, by leveraging the advanced synthesis capabilities of AutoPilot we enable efficient exploitation of the FPGA configurability for application specific acceleration. Our flow is based on a compilation process that transforms the SPMD CUDA thread blocks into high-concurrency AutoPilot-C code. We provide an overview of our CUDA-to-FPGA flow and demonstrate the highly competitive performance of the generated multi-core accelerators.
Automated generation of a four-dimensional model of the liver using warping and mutual information.

The use of mutual information (MI) based alignment to map changes in liver shape and position from exhale to inhale was investigated. Inhale and exhale CT scans were obtained with intravenous contrast for six patients. MI based alignment using thin-plate spine (TPS) warping was performed between each inhale and exhale image set. An expert radiation oncologist identified corresponding vessel bifurcations on the exhale and inhale CTimage and the transformation for identified points was determined. This transformation was then used to determine the accuracy of the MI based alignment. The reproducibility of the vessel bifurcation identification was measured through repeat blinded vessel bifurcation identification. Reproducibility [standard deviation (SD)] in the L/R, A/P, and I/S directions was 0.11, 0.09, and 0.14 cm, respectively. The average absolute difference between the transformation obtained using MI based alignment and the vessel bifurcation in the L/R, A/P, and I/S directions was 0.13 cm (SD=0.10 cm), 0.15 cm (SD=0.12 cm), and 0.15 cm (SD-0.14 cm), respectively. These values are comparable to the reproducibility of bifurcation identification, indicating that MI based alignment using TPS warping is accurate to within measurement error and is a reliable tool to aid in describing deformation that the liver undergoes from the exhale to inhale state.
THE APPLICATION OF GOLAY COLUMNS OF LARGER INTERNAL DIAMETER.

Abstract The application of Golay columns of larger internal diameter is described from a theoretical and practical point of view. The influence of the geometry and of the ratio film thickness to diameter on the admissible sample size is discussed.
Controlling stem cell fate one substrate at a time

Hematopoietic stem cell self-renewal is tightly regulated. Regulation of the stability of c-Myc protein contributes to this control of hematopoietic stem cell quiescence and repopulation.
Teachers’ Coping Strategies for Teaching Science in a “Low-Performing” School District

This study describes how teachers use their personal knowledge of a school district and their students to cope with teaching under stressful situations associated with economic, social, and institutional factors. The 3 teachers dealt with these issues in unique ways, focusing on helping students to overcome negative perceptions, value the importance of an education, and build strong relationships. A model of multicultural science professional development is proposed that complements the strengths that these teachers have. A task for science educators working with teachers and administration in schools and districts that are “critically low performing” is to support everyone in implementing pedagogical methods aimed at empowerment, social justice, and high achievement for all students.
Some Inferences of Eddy Viscosity Associated with Instabilities in the Atmosphere

Abstract Manifestations of both Rayleigh-Taylor instability and Karman vortices in atmospheric flows are recognized, and existing theory is applied to infer some values for the horizontal and vertical eddy transport coefficients for momentum, Kh, and Kz, respectively. Periodic protrusions of cloud material from beneath cirrus bands sometimes associated with warm frontal
Comparison of morning and evening administration of rabeprazole for gastro-oesophageal reflux and nocturnal gastric acid breakthrough in patients with reflux disease: a double-blind, cross-over study.

Summary Aim: To assess the effect of timing of rebeprazole (RB) 20 mg/d administration on oesophageal acid exposure and nocturnal gastric acid breakthrough (NGAB) in patients with GERD. Methods: 20 GERD patients received two 7-day treatments of RB in the morning (a.m.) or in the evening (p.m.) hours. The regimens were randomized in a double-blind fashion and separated by a 7-day washout period. The tablets were taken 30 min before standardized meals. A combined (oesophageal & gastric) 24-hour pH monitoring was performed before and on day 7 of each treatment. Results: Total oesophageal acid exposure was normalized in 10/14 (71.4%) patients with RB p.m. and in 6/15 (42.8%) with RB a.m. RB p.m. significantly decreased the nocturnal supine oesophageal acid exposure vs. RB a.m., 0.2% vs. 3.4%. The mean NGAB duration was significantly shortened with RB a.m. and p.m. vs. the baseline recording, 4.1±1.8 and 3.4±1.5 hours vs. 7.8±1.7 hours. Conclusions: Rabeprazole significantly reduced the NGAB duration and significantly increased the mean nocturnal gastric pH; RB p.m. normalized more effectively the total oesophageal exposure than RB-a.m.; RB p.m. provided significantly better control of nocturnal supine gastro-oesophageal reflux than a.m. dosing. These data suggest that administration of a PPI before the evening meal maximizes acid control and would be the preferred dosing schedule in GERD patients, particularly those with nocturnal symptoms.
Abstract 4422: 2-AAPA: A novel anticancer agent that induces microtubule depolymerization and apoptosis

Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC This study was aimed to investigate the anticancer activities and the mechanism of the anticancer activities of a novel anticancer agent - 2-acetylamino-3-[4-(2-acetylamino-2-carboxyethylsulfanylthiocarbonylamino)phenylthiocarbamoylsulfanyl]propionic acid (2-AAPA). 2-AAPA was found to inhibit various human cancer cell lines with a narrow range of IC50 values (28-75 μM). These cell lines include lung (NCI-H226), prostate (PC-3), breast (MCF-7), skin (A431), melanoma (UACC-62 and SK-MEL-2), and renal (UO-31) cancers, as well as human ovarian cancers (OVCAR-3 and NCI/ADR-RES) which are resistant toward doxorubicin. Flow cytometric studies revealed that 2-AAPA induced cell cycle arrest at G2/M phase and produced significant cell apoptosis in UACC-62 cells. Through immunofluorescence studies, 2-AAPA was found to depolymerize microtubules and cause cell morphological change. An HPLC (high performance liquid chromatography) assay demonstrated that proteins were glutathionylated in both OVCAR-3 and UACC-62 cells when treated with 2-AAPA. A Western blot analysis also showed that a band corresponding to the molecular weight of tubulins was significantly glutathionylated in cell lysate obtained from UACC-62 cells treated with 2-AAPA. Considering the rich thiol content of tubulin proteins and the nature of protein glutathionylation, it is likely that microtubule function might be affected through microtubule glutathionylation resulting in cell cycle arrest at G2/M phase. Immunoprecipitation is being employed to confirm that tubulins are glutathionylated in cells treated with 2-AAPA. Together, our findings could lead to an antimitotic agent with a novel mechanism which is different than those of current antimitotic drugs. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4422.
Surface segregation in binary alloy first wall candidate materials

Abstract We have been studying the conditions necessary to produce a self-sustaining stable lithium monolayer on a metal substrate as a means of creating a low-Z film which sputters primarily as secondary ions. It is expected that because of the toroidal field, secondary ions originating at the first wall will be returned and contribute little to the plasma impurity influx [1,2]. Aluminum and copper have, because of their high thermal conductivity and low induced radioactivity, been proposed [3–5] as first wall candidate materials. The mechanical properties of the pure metals are very poorly suited to structural applications and an alloy must be used to obtain adequate hardness and tensile strength. In the case of aluminum, mechanical properties suitable for aircraft manufacture are obtained by the addition of a few at% Li. In order to investigate alloys of a similar nature as candidate structural materials for fusion machines we have prepared samples of Li-doped aluminum using both a pyro-metallurgical and a vapor-diffusion technique. The sputtering properties and surface composition have been studied as a function of sample temperature and heating time, and ion beam mass. The erosion rate and secondary ion yield of both the sputtered Al and Li have been raonitored by secondary ion mass spectroscopy and Auger analysis providing information on surface segregation, depth composition profiles, and diffusion rates. The surface composition and lithium depth profiles are compared with previously obtained computational results based on a regular solution model of segregation, while the partial sputtering yields of Al and Li are compared with results obtained with a modified version of the TRIM computer program.
Significance of beta116 His (G18) at alpha1beta1 contact sites for alphabeta assembly and autoxidation of hemoglobin

The role of heterotetramer interaction sites in assembly and autoxidation of hemoglobin is not clear. The importance of beta(116His) (G-18) and gamma(116Ile) at one of the alpha1beta1 or alpha1gamma1 interaction sites for homo-dimer formation and assembly in vitro of beta and gamma chains, respectively, with alpha chains to form human Hb A and Hb F was assessed using recombinant beta(116His)(-->)(Asp), beta(116His)(-->)(Ile), and beta(112Cys)(-->)(Thr,116His)(-->)(Ile) chains. Even though beta chains (e.g., 116 His) are in monomer/tetramer equilibrium, beta(116Asp) chains showed only monomer formation. In contrast, beta(116Ile) and beta(112Thr,116Ile) chains showed homodimer and homotetramer formation like gamma-globin chains which contain 116 Ile. Assembly rates in vitro of beta(116Ile) or beta(112Thr,116Ile) chains with alpha chains were 340-fold slower, while beta(116Asp) chains promoted assembly compared to normal beta-globin chains. These results indicate that amino acid hydrophobicity at the G-18 position in non-alpha chains plays a key role in homotetramer, dimer, and monomer formation, which in turn plays a critical role in assembly with alpha chains to form Hb A and Hb F. These results also suggest that stable dimer formation of gamma-globin chains must not occur in vivo, since this would inhibit association with alpha chains to form Hb F. The role of beta(116His) (G-18) in heterotetramer-induced stabilization of the bond with oxygen in hemoglobin was also assessed by evaluating autoxidation rates using recombinant Hb tetramers containing these variant globin chains. Autoxidation rates of alpha(2)beta(2)(116Asp) and alpha(2)beta(2)(116Ile) tetramers showed biphasic kinetics with the faster rate due to alpha chain oxidation and the slower to the beta chain variants whose rates were 1.5-fold faster than that of normal beta-globin chains. In addition, NMR spectra of the heme area of these two hemoglobin variant tetramers showed similar resonance peaks, which are different from those of Hb A. Oxygen-binding properties of alpha(2)beta(2)(116His)(-->)(Asp) and alpha(2)beta(2)(116His)(-->)(Ile), however, showed slight alteration compared to Hb A. These results suggest that the beta116 amino acid (G18) plays a critical role in not only stabilizing alpha1beta1 interactions but also in inhibiting hemoglobin oxidation. However, stabilization of the bonds between oxygen and heme may not be dependent on stabilization of alpha1beta1 interactions. Tertiary structural changes may lead to changes in the heme region in beta chains after assembly with alpha chains, which could influence stability of dioxygen binding of beta chains.
Cuban Internationalism, Che Guevara, and the Survival of Cuba's Socialist Regime:

Two of the most important factors that have contributed to the survival of Cuba's socialist regime are its commitment to its socialist ideals and its policies of internationalism. Cuba's socialist regime has provided substantial support for national liberation struggles against imperialism in every region of the world, humanitarian assistance to people in at least 90 countries, and solidarity with progressive governments and a wide array of progressive international movements and organizations around the globe. Cuba's socialist regime, like Che Guevara's ideas and example of socialist internationalism, will survive if the regime continues to support socialist revolutions and to struggle against imperialism. Moreover, Cuba's revolutionary example and its internationalist support for the Bolivarian Revolution in Venezuela will be a fundamental factor in determining the outcome of the current trends toward the radical left in Latin American politics.
Numerical Procedure for Analyzing Langmuir Probe Data

A numerical procedure is proposed for analyzing Langmuir probe data in the presence of a two-group plasma containing both primary and Maxwellian electrons. The procedure is known as a least-squares differential-correction technique for determining the unknown coefficients of the governing equation. It is shown that for a given set of input data the results of the analysis are unique and independent of the initial estimate of electron temperature, that convergence is fastest when electron temperature is overestimated, that the results are sensitive to the region of the curve used as input and also to the voltage increment, and that plasma properties determined by the proposed numerical procedure are either consistent with those determined graphically or closer to expected values. With a suitable data acquisition system, the Fortran IV program worked out for this procedure could be used to provide real-time plasma diagnostic information for an operating ion thruster.
Respiratory gas exchange of high altitude adapted chick embryos

Study of gas exchange by embryos from chickens acclimatized to an altitude of 3800 m. The oxygen partial pressure and carbon dioxide partial pressure differences across the egg shell were measured and found to be less than the values previously reported for sea-level eggs by about a factor of two. Further measurements of embryonic oxygen consumption and shell conductivity to oxygen indicated that, compared to eggs at sea level, oxygen consumption was reduced by a factor of 0.58 while conductivity to oxygen was increased only by a factor of 1.07 in the high-altitude eggs. These independent measurements predict the change in oxygen partial pressure across the egg shell of the high-altitude eggs to be only 0.54 times that of sea-level eggs; the directly measured factor was 0.53. The authors conclude that at high altitude, a major adaptation of the chick embryo is a reduced metabolism which decreases the change in oxygen partial pressure across the egg shell since its gas conductivity remains essentially unchanged.
Towards Self-Adaptive Cloud Collaborations

In multi-tenant collaborative cloud systems, the choice of cloud providers is based on pre-negotiated terms and conditions to help meet Service Level Agreements (SLAs) and streamline resource provisioning. However, these collaborations are not self-adaptive to accommodate changes in tenancy requirements, quality of resources and provider capabilities as provider collaborations remain static over tenancy period. In our paper, we present an approach towards achieving self-adaptive cloud collaborations. Our model selects the best possible cloud collaborations from amongst multiple possible dependent cloud provider collaboration links. The formation of cloud provider collaborations is broadly based on cloud provider capabilities, tenancy requirements, cost modeling of each cloud provider andits functional ability at the Software as a Service (SaaS) layer. We present an algorithm to form dynamic cloud collaborations and thereby determine the most appropriate linkages within the providers. We also illustrate our approach throughout our paper with a realistic running example, and present detailed experimental evaluation via a proof-of-concept prototype implementation.
Predictive factors for long-term survival in patients with advanced ovarian cancer

Abstract A total of 107 patients with carcinoma of the ovary were entered in a study combining extensive primary surgery and intensive chemotherapy. Because of evidence supporting the effectiveness of both single agent platinum (P) and the combination of cyclophosphamide and doxorubicin (CA), patients were treated with alternating cycles of CA and CP. Primary surgery to remove the bulk of tumor to less than 2 cm was possible in 45% of the 85 eligible patients, and an additional 17% had similar surgery after two to four cycles of chemotherapy. Fifteen percent of patients progressed on chemotherapy. Of the 68 who were clinically and radiologically without disease at the completion of chemotherapy, 91% had second-look surgery. Forty-eight percent of these women had residual disease. All patients but one are at risk for >60 months, with a median follow-up of 86 months. Overall 5-year survival is 26%, with a median survival of 33 months. Twenty patients survived over 5 years with 11 continuing to be free of disease (13% of all eligible patients). Patients with modified Broder's grade I,II tumors have not yet reached a median survival. Grade, stage, and primary mass size were the only variables with independent prognostic value in a Cox multivariate analysis.
EVIDENCE OF ADAPTIVE DIVERGENCE IN PLASTICITY: DENSITY- AND SITE-DEPENDENT SELECTION ON SHADE-AVOIDANCE RESPONSES IN IMPATIENS CAPENSIS

We investigated the conditions under which plastic responses to density are adaptive in natural populations of Impatiens capensis and determined whether plasticity has evolved differently in different selective environments. Previous studies showed that a population that evolved in a sunny site exhibited greater plasticity in response to density than did a population that evolved in a woodland site. Using replicate inbred lines in a reciprocal transplant that included a density manipulation, we asked whether such population differentiation was consistent with the hypothesis of adaptive divergence. We hypothesized that plasticity would be more strongly favored in the sunny site than in the woodland site; consequently, we predicted that selection would be more strongly density dependent in the sunny site, favoring the phenotype that was expressed at each density. Selection on internode length and flowering date was consistent with the hypothesis of adaptive divergence in plasticity. Few costs or benefits of plasticity were detected independently from the expressed phenotype, so plasticity was selected primarily through selection on the phenotype. Correlations between phenotypes and their plasticity varied with the environment and would cause indirect selection on plasticity to be environment dependent. We showed that an appropriate plastic response even to a rare environment can greatly increase genotypic fitness when that environment is favorable. Selection on the measured characters contributed to local adaptation and fully accounted for fitness differences between populations in all treatments except the woodland site at natural density.
Environmental justice: insights from an interdisciplinary instructional workshop

Environmental justice recognizes the connections between social and environmental concerns and interrogates power dynamics related to environmental issues. Courses in environmental studies and the geosciences provide an opportunity, and perhaps an obligation to explore environmental justice, but few resources exist to help instructors do so effectively. A 2013 interdisciplinary workshop at Carleton College sponsored by InTeGrate—Interdisciplinary Teaching of Geoscience for a Sustainable Future—convened instructors interested in environmental justice as a topic of instruction and produced a series of insights and challenges for doing so. Environmental justice instruction provides opportunities to tackle tough issues of race, class, and privilege in a variety of disciplinary contexts particularly in geoscience courses, where course content regarding hazards, climate change, and other topics may contain social justice components which are not often included in instruction. Teaching environmental justice, though, presents a number of challenges: how can instructors teach the conceptual and theoretical explanations of environmental justice while giving students the necessary tools to address environmental injustices? The InTeGrate workshop provided insights for addressing these challenges and developing materials for future pedagogical use in a variety of higher education contexts.
Introduction to the Proceedings of the Avian Genomics and Gene Ontology Annotation Workshop

The Avian Genomics Conference and Gene Ontology Annotation Workshop brought together researchers and students from around the world to present their latest research addressing the delivery of value from the billions of base-pairs of Archosaur sequence that have become available in the last few years. This editorial describes the conference itself and introduces the ten peer-reviewed manuscripts accepted for publications in the proceedings. These manuscripts address issues ranging from the poultry industry view of USDA genomics policy to the genomics of a wide variety of Archeosaur species including chicken, duck, alligator, and condors and their pathogens.
Probing the early universe with inflationary gravitational waves

Near comoving wave number $k$, the gravitational-wave background (GWB) from inflation carries information about the physical conditions near two moments in cosmic history: the moment when $k$ ``left the horizon'' during inflation, and the moment when it ``re-entered the horizon'' after inflation. We investigate the extent to which this information can be extracted if the GWB is measured by a combination of cosmic-microwave-background polarization experiments on large scales and space-based laser-interferometer experiments on small scales. To disentangle this information, we derive a new gravitational-wave transfer function that incorporates a number of physical effects that were treated less accurately, less generally, or were missing altogether in previous treatments. In particular, it incorporates: (i) dark energy with time-varying equation of state $w(z)$; (ii) tensor anisotropic stress due to free-streaming relativistic particles in the early universe; and (iii) a variety of physical effects that cause deviations from the standard equation of state $w=1/3$ during the radiation era. Based on this transfer function, we consider the degree to which the GWB can be used to test inflation and to probe the ``primordial dark age'' between the end of inflation and the electroweak phase transition.
Peronospora species in Arizona

One might not expect to find an abundance of downy mildews in the southwestern desert. That this surmise may be wrong is amply demonstrated by collections made during the period of March 7 to April 11, 1968. No special effort was made to search for downy mildews. Nevertheless, several collecting trips yielded 23 specimens involving six species of Peronospora on 10 different wild hosts. One of these, Peronospora eriogoni, is described as new. All of these collections were made in Pima County. Most are from the general vicinity of Tucson but a few are from west of the Baboquivari Mountains. An additional species, Peronospora destructor (BERK.) CASP. on onion (Allium cepa L.), was collected by RICHARD B. HINE in Dome Valley, Yuma County, March 13, 1968. No doubt the profuse development of these fungi was due to very favorable moisture conditions. The winter of 1967-68 was characterized by considerably higher precipitation than normal. In addition the temperatures were relatively cool, resulting in high humidity, at least at night and during the morning. These conditions could lead to a rich development of these fungi only if ample inoculum in the form of zoospores or conidia or both was present. It would be interesting to knowhowthese fungi survive through dry spring periods for several years and whether or not parasitization of tile several hosts is of annual occurrence. In addition to the species of Peronospora collected in 1968, two specimens of P. tri/oliorum DEBY. on alfalfa (Medicago sativa L.) from earlier years are included in this report. Other species of Peronospora, as well as other host species, no doubt occur in Arizona but are at present not represented in the mycological herbarium of the University of Arizona.
The Use of Concept Mapping to Identify Community-Driven Intervention Strategies for Physical and Mental Health

Research that partners with youth and community stakeholders increases contextual relevance and community buy-in and therefore maximizes the chance for intervention success. Concept mapping is a mixed-method participatory research process that accesses the input of the community in a collaborative manner. After a school-wide health needs assessment at a low-income, minority/immigrant K-8 school identified bullying and obesity as the most important health issues, concept mapping was used to identify and prioritize specific strategies to address these two areas. Stakeholders including 160 K-8 students, 33 college students working in the school, 35 parents, 20 academic partners, and 22 teachers/staff brainstormed strategies to reduce and prevent obesity and bullying. A smaller group of stakeholders worked individually to complete an unstructured sorting of these strategies into groups of similar ideas, once for obesity and again for bullying. Multidimensional scaling and cluster analysis was applied to the sorting data to produce a series of maps that illustrated the stakeholders' conceptual thinking about obesity and bullying prevention strategies. The maps for both obesity and bullying organized specific strategies into themes that included education, parental role, teacher/school supervision, youth role, expert/professional role, and school structure/support.
Lead discovery using molecular docking

As the structures of more and more proteins and nucleic acids become available, molecular docking is increasingly considered for lead discovery. Recent studies consider the hit-rate enhancement of docking screens and the accuracy of docking structure predictions. As more structures are determined experimentally, docking against homology-modeled targets also becomes possible for more proteins. With more docking studies being undertaken, the 'drug-likeness' and specificity of docking hits is also being examined.
Global Financial Reporting: Implications for U.S. Academics

ABSTRACT: This paper identifies challenges and opportunities created by global financial reporting for the education and research activities of U.S. academics. Relating to education, after overviewing the relation between global financial reporting and U.S. GAAP, it offers suggestions for topics to be covered in global financial reporting curricula and clarifies common misunderstandings about the concepts underlying financial reporting. Relating to research, it explains how and why research can provide meaningful input into standard-setting, and identifies questions that can motivate research related to topics on the International Accounting Standards Board’s technical agenda and to the globalization of financial reporting.
Mother knows best: Psychological control, child disclosure, and maternal knowledge in emerging adulthood

Although perceived parental knowledge of children's behaviors, whereabouts, and companions in emerging adulthood has been linked with less engagement in risk behaviors [Journal of Youth and Adolescence, 37 (2008) 847-859], much remains unknown about how parents gain this knowledge during this time period. Because parents tend to have less direct control over their children's comings and goings in emerging adulthood, child disclosure may play a particularly important role in the knowledge parents have of their children's lives. The purpose of this study was to examine: (1) whether aspects of the mother - child relationship were related to child disclosure, (2) whether child disclosure was related to maternal knowledge, and (3) whether child disclosure and maternal knowledge were related to a child's involvement in risk behaviors during emerging adulthood. Data collected from 252 emerging adults attending college in the United States (77 males, 175 females), and their mothers, were analyzed using structural equation modeling. Results suggested that: (a) satisfaction with the current relationship between emerging adults and their mothers was positively related to child disclosure, (b) maternal psychological control was negatively related to child disclosure, (c) child disclosure was positively related to maternal knowledge, and (d) child disclosure was indirectly and maternal knowledge was directly related to lower levels of risk behaviors.
Defining psychological maltreatment: The relationship between questions and answers

Over the past 30 years, hundreds of millions, perhaps billions, of dollars have been spent on research related to child maltreatment. Yet, with some notable exceptions, this research has produced disappointingly little information that is relevant to policy-makers. In part, this reflects the difficulty of doing policy-relevant research, a problem exacerbated by the unwillingness of most funding sources to support the types of large-scale research projects needed to answer many policy questions. However, part of the blame lies with the research community itself. Too often, researchers have failed to understand the policy issues at stake. As a result, they have not asked the right questions or utilized appropriate research designs. In fact, they often have failed to conceptualize adequately the questions they were trying to address.
Internal model predictive control (IMPC)

A computationally simple model predictive control algorithm incorporates the attractive features of the internal model control (IMC) law. The algorithm first computes the IMC control effort via a model state feedback implementation which automatically compensates for past control effort saturation. Before applying the calculated control, the algorithm checks to see if this control effort, when applied over a single sampling interval and followed by a control effort at the opposite limit (relative to its steady state level), will cause the model output to exceed its desired trajectory. If not, the calculated control is applied. Otherwise the control is reduced appropriately.
Simulation of Housing Market Dynamics

Developed over the past decade by the Urban Studies Croup of the National Bureau of Economic Research, the NBER Urban Simulation Model is primarily a model of the urban housing market. It represents other urban phenomena such as industrial location, transportation systems, and changes in the demographic structure of the population, but the behavior of the housing “market” is its central focus. This paper provides a brief description of the NBER Urban Simulation Model and presents illustrative results from a series of baseline simulations for the period 1960 to 1970 for the Chicago and Pittsburgh SMSAs.
Predicting readiness to return to work in a population with multiple sclerosis

Return to work is a key concept in vocational rehabilitation. Predicting readiness to return to work is salient to the process of vocational rehabilitation for individuals with Multiple Sclerosis. An individual's readiness to return to work has been shown to be an effective predictor of that person's actual return to work. A survey of a population of persons with MS (N=663) was analyzed using correlation and multiple regression analyses. Severity of symptoms appeared to predict reported readiness to return to work over other factors. Issues including the relationship of self-efficacy to readiness to return to work are discussed. Further research is recommended.
Functional morphology of the caudal region of certain clupeiform and perciform fishes with reference to the taxonomy.

The caudal anatomy (caudal skeleton, musculature, vascularization, innervation, and urohypophysis) and swimming behavior of three clupeiform and three perciform fishes: Elops hawaiensis (Cupeiformes: Elopidae), Oncorhynchus nerka (Cupeiformes: Salmonidae), Chanos chanos (Clupeiformes: Chanidae), Kuhlia sandvicensis (Perciformes: Kuhlidae), Apogon menesemus (Perciformes: Apogonidae), and Gnathanodon speciousus (Perciformes: Carangidae), were studdied. The taxonomic significance of caudal structures was determined and evaluated by detailed examination of differences in caudal anatomy. An interpretation of functional significance of these differences was attempted by relating them to observed differences in swimming behavior. The swimming behavior was studied by the observation of swimming activities of fish while resting or cruising and while feeding in the aquarium, and by an analysis of each frame of an 8 mm movie film of swimming activities. There are certain consistent and basic differences between all three species of the order Clupeiformes and all three species of the order Perciformes in respect to caudal structures. Although certain caudal structures show overlapping in number and/or complexity of arrangement, they seem to indicate more complex structural organization in Clupeiformes than Perciformes. The differences confirm the conclusion of others that the order Clupeiformes is more “primitive” than the order Perciformes. With respect to caudal structures of the three clupeiform species studied, E. hawaiensis is the most “primitive” and, of the three perciform species studied, K. sandvicensis is the most “primitive.” Caudal structural variations from one species to another are related to the mode of adaptation to swimming as well as to the evolutionary status of the species.
Multi-resolution indexing for XML data

As the Extendible Markup Language (XML) becoming a de facto standard for representing and exchanging data over the Internet, it is critical to be able to retrieve XML data efficiently. One way to achieve this is to use indexing, just like we index data stored in relational databases. In this paper, we present a multi-resolution structural index (MRI) method to facilitate fast retrieval of XML data. The indexing method is based on a new coding scheme that assigns unique numbers to the elements on all possible paths of the tree representing the XML document. The coding scheme is based on the DTD (data type definition) of the XML file. Elements are stored in internal data structures in such a way that they can be directly accessed via the unique coding. The ancestor-descendant relationships among the tree elements are easily identified to help fast process of user's queries. Our experiments show that the MRI indexing approach is effective, both in time and space.
Initial Results of a Positron Tomograph for Prostate Imaging

We present the status and initial images of a positron tomograph for prostate imaging that centers a patient between a pair of external curved detector banks (ellipse: 45 cm minor, 70 cm major axis). The distance between detector banks adjusts to allow patient access and to position the detectors as closely as possible for maximum sensitivity with patients of various sizes. Each bank is composed of two axial rows of 20 CTI PET Systems HR+ block detectors for a total of 80 detectors in the camera. Compared to an ECAT HR PET system operating in 3D mode, our camera uses about one-quarter the number of detectors and has approximately the same sensitivity for a central point source, because our detectors are close to the patient. The individual detectors are angled in the plane to point towards the prostate to reduce resolution degradation in that region. The detectors are read out by modified CTI data acquisition electronics. We have completed construction of the gantry and electronics, have developed detector calibration and data acquisition software, and are taking coincidence data. We demonstrate that we can clearly visualize a "prostate" in a simple phantom. Reconstructed images of two phantoms are shown
The control of alternative splicing at genes regulating sexual differentiation in D. melanogaster

The transformer (tra) and doublesex (dsx) genes produce sex-specific transcripts that are generated by differential RNA processing. We have examined the effects of mutants in other regulatory genes controlling sexual differentiation on the patterns of processing of the tra and dsx RNA transcripts. Our results demonstrate that the genes suggested by genetic studies to act upstream of tra or dsx in the sex determination hierarchy regulate these two loci at the level of RNA processing. Our data suggest that the order of interaction of the factors controlling sex is X:A greater than Sxl greater than tra greater than tra-2 greater than dsx greater than or equal to ix greater than terminal differentiation. While these results cannot preclude regulatory interactions at other levels, the regulation of RNA splicing revealed by these experiments is sufficient to account for all of the known functional interactions between the regulatory genes in this hierarchy.
Political Theory Simulations in the Classroom: Simulating John Locke’s Second Treatise of Government

Political scientists frequently use in-class simulations as teaching tools. However, few such exercises have been developed to assist in teaching pre-modern political theories. This is unfortunate because simulations effectively promote active learning and excite students about course material. This article develops a new simulation to teach Locke's Second Treatise of Government in an introductory general education or political science course. Surveys of participants indicate that the Locke simulation promotes active learning, as well as understanding of course concepts, teamwork, and interest in the material.
Evolution of the GST Omega Gene Family in 12 Drosophila Species

Gene families provide a unique system to study the evolutionary relationships between related genes both within and between organisms. We can ascertain whether members of a gene family in different species are orthologs or paralogs. We may also search for evidence that may explain why duplicate genes are present. The availability of genome sequences for 12 Drosophila species allows us to address these questions with respect to the evolution of one gene family, the glutathione S transferase (GST) omega class. This gene family is of particular interest because of its relationship with human disease and its presence in a wide range of species.
TMR and squeeze at gigabit areal densities

The track misregistration (TMR) required to achieve gigabit areal densities is calculated for a set of components based on the average bit error rate for a file. The average error rate is a statistical average, based on the TMR of the file, of the on-track and off-track error rate. The on-track and off-track error rates are dependent on squeeze from adjacent tracks. In this analysis, the average error rate is calculated using measured error rate profiles of the center track. For a file average soft error rate of 1*10/sup -6/, the results show, for a particular head/disk combination designed for gigabit recording and operating at a linear density of 158 kbpi, that a track pitch of 4.0 mu m (3.35 ktpi) can be achieved with a TMR of 0.635 mu m. Obtaining this TMR value in a file is one of the challenges to recording of 1 Gb/in/sup 2/ in magnetic storage products. >