cssi/SciSciGPT-SciSciNet huggingface dataset:
Abstract 4500: Normal tissue and data resources for cancer research from the GTEx program

The NIH Common Fund9s Genotype-Tissue Expression (GTEx) project aims to study gene expression and regulation across multiple human tissues from approximately 1000 healthy normal postmortem donors. GTEx will provide valuable insights into gene regulation and its tissue specificity, to identify correlations between genetic variations and variations in gene expression levels as expression quantitative trait loci (eQTLs), and to help understand inherited susceptibility to disease. Initiated in 2010, the GTEx program has generated a large volume of data associated with each donor, including clinical and histopathological, as well as genotyping and gene expression data from whole genome sequencing, whole exome sequencing, expression array, and RNAseq data. The program has published research results in multiple scientific journals over the past year. The following public resources are available from the GTEx program: 1. GTEx Portal: an open access database of GTEx expression data and analysis results: http://www.gtexportal.org 2. Database of Genotypes and Phenotypes (dbGaP): controlled access of comprehensive GTEx clinical data and raw sequencing data: http://www.ncbi.nlm.nih.gov/gap 3. Access to residual GTEx biospecimens for research: http://www.gtexportal.org/home/samplesPage 4. SOPs and best practices from GTEx biospecimen collections: http://biospecimens.cancer.gov/resources/sops/library.asp 5. GTEx histological image viewer: http://biospecimens.cancer.gov/resources/tissue_image_library.asp 6. GTEx donors’ families website: a lay description of the GTEx project tailored to the GTEx donors’ families: http://www.genome.gov/gtex GTEx data can be used in combination with other data sets such as The Cancer Genome Atlas (TCGA) and genome-wide association studies (GWAS) to further explore the genetic causes and biology of cancer. The eQTL data from multiple tissues will help prioritize candidate genes within GWAS-associated loci; allow evaluation of tissue specificity of associated loci, and pinpoint target tissues for disease studies. Researchers are using GTEx resources to: study cancer heterogeneity by subtracting normal tissue expression; identify mutations in protein-truncating variants which may cause cancer; and explore gene activity from multiple donors across multiple tissue types to better understand the age/gender bias in cancer and other diseases. Citation Format: Ping Guan, Abhi Rao, Simona Volpi, Susan Koester, Helen M. Moore, GTEx consortium. Normal tissue and data resources for cancer research from the GTEx program. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4500.
Teaching Sociology Graduate Students to Teach with Techology

In light of the increasing emphasis on the use of instructional technology in higher education, sociology graduate students need to become conversant with instructional technology and its pedagogical implications. Yet, the literature on graduate instructor training has almost completely neglected this issue. This paper directly addresses this important pedagogical issue. After a discussion of the benefits of instructional technology training, we describe how to integrate training in instructional technology into graduate training programs in sociology. Our discussion offers specific suggestions for incorporating instructional technology training throughout the instructor training process. Our recommendations focus on helping graduate students employ effectively instructional technology and to become conversant with its pedagogical implications.
Impact of Thermal and Pressure-Based Technologies on Carotenoid Retention and Quality Attributes in Tomato Juice.

The aim of this study was to investigate the impact of thermal processing (TP) (90 °C, 90 s), high-pressure processing (HPP) (600 MPa, 46 °C, 5 min), and high-pressure homogenization (HPH) (246 MPa, 99 °C, <1 s) on product quality parameters, specifically carotenoid content, and physicochemical attributes of particle size, color, viscosity, total soluble solids, and pH in tomato juice. Unprocessed tomato juice was used as control. The four major species of carotenoids (lycopene, β-carotene, phytoene, and phytofluene) in tomato juice were analyzed by HPLC. The content of total lycopene, all-trans-lycopene, cis-lycopene isomers, phytoene, and phytofluene, in TP-, HPP-, and HPH-treated tomato juice did not significantly differ from that in unprocessed (control) juice. Significant reduction in β-carotene content was observed after TP treatment but not after HPP and HPH treatments. HPH significantly reduced tomato juice particle volume mean diameter from ∼330 μm in control, HPP-, and TP-treated tomato juices to ∼17 μm. A concomitant increase in apparent viscosity was observed in HPH-treated juice versus control. HPH-treated juice had increased redness (a*) and yellowness (b*) than that in control and HPP-treated tomato juices. These results indicate that high-pressure-based technologies (HPP and HPH) can preserve carotenoids as well as improve physicochemical properties.
Contribution from Ising domains overlapping out-of-plane to perpendicular magnetic anisotropy in Mn4N thin films on MgO(001)

Abstract Single phase e -Mn4N thin and ultrathin films are grown on MgO(001) using molecular beam epitaxy. Reflection high-energy electron diffraction and out-of-plane X-ray diffraction measurements are taken for each sample in order to determine the in- and out-of-plane strain for each sample. Vibrating sample magnetometry and superconducting quantum interference device measurements, which are performed on the thin and ultrathin films respectively, are used to plot the magnetization of each sample versus both in- and out-of-plane H → -fields and to determine the magnitude of perpendicular magnetic anisotropy in these films. Three significant components of perpendicular magnetic anisotropy are observed in these films and are attributed to sample strain (1 component) and shape (2 components). Among these components, the most significant component 0.8 – 4.9 Merg cm 3 is identified as a second term of shape anisotropy, which possesses a negative linear relationship with sample thickness over the range from 9 nm to 310 nm. Atomic (magnetic) force microscopy measurements show the presence of a surface localized magnetic polarization (22–82 % ), which increases with decreasing thickness, when the net magnetizations of the films are zero. The second term of shape anisotropy as well as the surface localized polarization, which each depend on sample thickness, are each regarded as a consequence of Ising domains overlapping out-of-plane in these films.
Systematic Investigation of Multi-TLR Sensing Identifies Regulators of Sustained Gene Activation in Macrophages.

Summary A typical pathogen presents a combination of Toll-like receptor (TLR) ligands during infection. Although individual TLR pathways have been well characterized, the nature of this "combinatorial code" in pathogen sensing remains unclear. Here, we conducted a comprehensive transcriptomic analysis of primary macrophages stimulated with all possible pairwise combinations of four different TLR ligands to understand the requirements, kinetics, and outcome of combined pathway engagement. We find that signal integration between TLR pathways leads to non-additive responses for a subset of immune mediators with sustained expression (>6 hr) properties and T cell polarizing function. To identify the underlying regulators, we conducted a focused RNAi screen and identified four genes— Helz2 , Phf11d , Sertad3 , and Zscan12 —which preferentially affect the late phase response of TLR-induced immune effector expression. This study reveals key molecular details of how contemporaneous signaling through multiple TLRs, as would often be the case with pathogen infection, produce biological outcomes distinct from the single ligands typically used to characterize TLR pathways.
Non-cortical magnitude coding of space and time by pigeons

Considerable research in cognitive science, neuroscience, and developmental science has revealed that the temporal, spatial, and numerical features of a stimulus can interact with one another [1,2], as when larger stimuli are perceived as lasting longer than smaller stimuli. These findings have inspired the prominent hypothesis that time, space, and number are processed by a 'common magnitude system', which represents these dimensions via the same unit of magnitude [3,4]. According to current theorizing, the parietal cortex mediates this system [4]. To test the species generality and neuroanatomical foundations of this hypothesis, we asked whether space-time interactions can be observed in birds. Unlike mammals, birds lack a cortex [5,6]; rather, they possess a neuron-dense pallium that is organized in clusters, in contrast to the laminar structure of the mammalian cortex [7]. Despite these striking neuroanatomical disparities, we observed reliable space-time interactions in pigeons. Our findings suggest that common magnitude systems are more widespread among animals than previously believed and need not be cortically dependent in all species.
Computational Anatomy in the Abdomen: Automated Multi-Organ and Tumor Analysis from Computed Tomography

The interpretation of medical images benefits from anatomical and physiological priors to optimize computer-aided diagnosis (CAD) applications. Diagnosis also relies on the comprehensive analysis of multiple organs and quantitative measures of tissue. This chapter highlights our recent contributions to abdominal multi-organ analysis employing constraints typical to medical images and adapted to patient data. A new formulation for graph-based methods to segment abdominal organs from multi-phase CT data is first presented. The method extends basic graph cuts by using: multi-phases enhancement modeling, shape priors and location constraints. The multi-organ localization is also addressed using maximum a posteriori (MAP) probability estimations of organs’ location, orientation, and scale. The probabilistic framework models the inter-organ spatial relations using a minimum volume overlap constraint. The liver, spleen, left kidney, right kidney and pancreas are concomitantly analyzed in the multi-organ analysis framework. Finally, the automated detection and segmentation of abdominal tumors (i.e., hepatic tumors) from abdominal CT images is presented using once again shape and enhancement constraints. Features are computed for the tumor candidates and machine learning is used to select the optimal features to separate true and false detections. The methods illustrate multi-scale analyses of the abdomen, from multi-organ to organ and tumors and promise to support the processing of large medical data in the clinically oriented integrated analysis of the abdomen.
Complications of Surgery in Glaucoma: Early and Late Bacterial Endophthalmitis Following Glaucoma Filtering Surgery

One case of "early" post-trabeculectomy endophthalmitis and five eyes with "late" endophthalmitis three to nine years after glaucoma filtration surgery are presented. Differentiation of early versus late endophthalmitis is based on the time of onset and pathogenesis. Retrospective analysis of 1100 consecutive trabeculectomies revealed an incidence of less than 0.1% for early and 0.2% for late endophthalmitis. Medical and surgical approaches are discussed. The presumed importance of identifying posterior extension into the vitreous and performing a therapeutic vitrectomy is emphasized.
Urinary Excretion of Amino Acids by Subjects with Renal Calculi

Idiopathic calcareous calculi remains a disorder of unknown cause, or causes. However, this affliction occurs predominantly in nonblack men, is affected by undefined geographic or climatic factors, and may be influenced by dietary habits1. In addition, the familial occurrence of idiopathic calculi has suggested that hereditary factors may exist that increase susceptability to this disorder2. Searching for a possible index of renal tubular dysfunction, McGeown3 investigated the amino acid excretion of 110 patients with calcareous calculi. She reported that, except for 30 patients with some increase in urinary cystine, the amino acid excretion was reduced in the calculous patients as compared with the amino acid excretion of normal subjects. Of these 110 patients, twenty-three had hyperparathyroidism and the mean excretion of amino acid nitrogen was less in these than in the group as a whole. Subsequently, Hum and associates4 reported the urinary amino acid values of 15 patients with calcareous calculi, but they found a reduced excretion only in those patients with impaired renal function.
A multifaceted analysis of social stressors and chronic inflammation.

Abstract Chronic stress has been linked to negative health outcomes, including increased inflammation, which can be measured by high-sensitivity C-reactive protein (CRP). Prior research has focused almost exclusively on relationships between individual social and demographic stressors and CRP. The objective of this study is to assess the role of multiple potential stressors simultaneously to determine which key stressors are related to risk of high CRP, given that sustained stress and resulting inflammation may have long-term health implications. We hypothesized that negative social and environmental factors would be associated with high CRP. Data from two waves of Midlife in the United States were used to predict high CRP with variable selection procedures and logistic regression. Results indicated females, those with greater BMI, those with improvements in family strain, and those with higher A1c had a greater risk of high CRP. There was limited evidence that negative social factors were associated with CRP to the extent seen in prior literature. A key advantage of the study was testing multiple potential determinants of chronic stress and inflammation simultaneously, advancing the existing literature. Results demonstrate the potential usefulness of a multifaceted approach to evaluating the risk of chronic inflammation and high CRP.
Mortality Among Patients With Chronic Hepatitis B Infection: The Chronic Hepatitis Cohort Study (CHeCS).

BACKGROUND According to death certificates, approximately 1800 persons die from hepatitis B annually in the United States; however, this figure may underestimate true mortality from chronic hepatitis B (CHB). METHODS We analyzed data from CHB patients seen in the Chronic Hepatitis Cohort Study (CHeCS) between 1 January 2006 and 31 December 2013. We compared overall and cause-specific death rates and mean ages at death between CHeCS CHB decedents and U.S. decedents from the Multiple Cause of Death (MCOD) file. RESULTS Of 4389 CHB patients followed for a mean of 5.38 years, 492 (11%) CHB patients died after a mean follow-up of 3.00 years. Compared to survivors, decedents were older, more likely to be White (40.6%), African-American (27.1%), or male (74.2%); and more likely to have had cirrhosis (59.8%), diabetes (27.2%), alcohol abuse (17.7%), hepatocellular carcinoma (17.5%), or a liver transplant (5.7%); whereas survivors were more likely to be Asian (48.8%; all P < .001). CHB patients died at an average age of 59.8 years-14 years younger than the general U.S. population-and at higher rates for all causes (relative risk [RR] = 1.85, 95% confidence interval [CI], 1.851-1.857) and liver-related causes (RR = 15.91, 95% CI, 15.81-16.01). Only 19% of CHB decedents and 40% of those dying of liver disease had hepatitis B reported on their death certificates. CONCLUSIONS Compared to the general population, CHB patients die at younger ages and higher rates from all causes and liver-related causes. Death certificates underrepresent the true mortality from CHB.
What Explains Counterterrorism Effectiveness? Evidence from the U.S. Drone War in Pakistan

For years, the U.S. government has been waging counterterrorism campaigns against al-Qaida and other armed groups in safe havens and weak states. What explains the effectiveness of such campaigns? ...
Space-native construction materials for earth-independent and sustainable infrastructure

Abstract A successful space exploration requires establishing permanent and earth-independent infrastructure that are not only resilient to the extreme environment of space but also preferably made of sustainable and indigenous “space-native” construction materials. This review covers feasibility of exploiting in-situ lunar and Martian resources as well as harvesting of elements and compounds, from near Earth objects (NEOs), to produce extraterrestrial materials suitable for construction of space-based infrastructure. This review also details material features and characteristics required to withstand the unique, and harsh, effects of space environment. In essence, this paper reviews past and recent advancements in construction-based materials that could be used in the design and development of space human bases and highlights design consideration for sustainable human settlements. Towards the end of this review, practical and technological challenges associated with development of lunar and Martian indigenous construction materials are identified and examined.
Cystic fibrosis program characteristics associated with adoption of 2013 infection prevention and control recommendations.

Background The Cystic Fibrosis (CF) Foundation disseminated an updated guideline for infection prevention and control (IP&C) practices for CF care programs in 2013. Assessing adoption rates of IP&C recommendations is crucial to evaluate their impact. Methods CF care programs provided their written IP&C policies for CF. Policies were analyzed to determine adoption of selected recommendations new in 2013, as well as recommendations made in both 2003 and 2013. Weighted adoption scores were analyzed for association with program characteristics. Results The median number of new recommendations adopted by each program was 7 (mean 6.3, range 0-9). The most commonly adopted new recommendations were universal mask use by patients in both inpatient and outpatient settings (85% and 87%, respectively) and contact precautions for CF patients in inpatient and outpatient settings (90% for both). The least frequently adopted new recommendations were the “6-foot rule” in inpatient settings (n = 66, 53%) and auditing disinfection of surfaces in clinic (n = 64, 49%). Larger program size was associated with a higher weighted adoption score (odds ratio [OR] 1.9, P =.02). Conclusions Whereas most programs adopted more than one-half of the selected IP&C recommendations assessed, adoption was variable. Efforts to improve adoption of IP&C recommendations should focus on smaller programs with fewer resources.
Crystal Structures of L-DOPA Dioxygenase from Streptomyces sclerotialus.

Extradiol dioxygenases are essential biocatalysts for breaking down catechols. The vicinal oxygen chelate (VOC) superfamily contains a large number of extradiol dioxygenases, most of which are found as part of catabolic pathways degrading a variety of natural and human-made aromatic rings. The l-3,4-dihydroxyphenylalanine (L-DOPA) extradiol dioxygenases compose a multitude of pathways that produce various antibacterial or antitumor natural products. The structural features of these dioxygenases are anticipated to be distinct from those of other VOC extradiol dioxygenases. Herein, we identified a new L-DOPA dioxygenase from the thermophilic bacterium Streptomyces sclerotialus (SsDDO) through a sequence and genome context analysis. The activity of SsDDO was kinetically characterized with L-DOPA using an ultraviolet-visible spectrophotometer and an oxygen electrode. The optimal temperature of the assay was 55 °C, at which the Km and kcat of SsDDO were 110 ± 10 μM and 2.0 ± 0.1 s-1, respectively. We determined the de novo crystal structures of SsDDO in the ligand-free form and as a substrate-bound complex, refined to 1.99 and 2.31 A resolution, respectively. These structures reveal that SsDDO possesses a form IV arrangement of βαβββ modules, the first characterization of this assembly from among the VOC/type I extradiol dioxygenase protein family. Electron paramagnetic resonance spectra of Fe-NO adducts for the resting and substrate-bound enzyme were obtained. This work contributes to our understanding of a growing class of topologically distinct VOC dioxygenases, and the obtained structural features will improve our understanding of the extradiol cleavage reaction within the VOC superfamily.
Leveraging -omics for asthma endotyping

Asthma is a highly heterogeneous disease, often manifesting with wheeze, dyspnea, chest tightness, and cough as prominent symptoms. The eliciting factors, natural history, underlying molecular biology, and clinical management of asthma vary highly among affected subjects. Because of this variation, many efforts have gone into subtyping asthma. Endotypes are subtypes of disease based on distinct pathophysiologic mechanisms. Endotypes can be clinically useful because they organize our mechanistic understanding of heterogeneous diseases and can direct treatment toward modalities that are likely to be the most effective. Asthma endotyping can be shaped by clinical features, laboratory parameters, and/or -omics approaches. We discuss the application of -omics approaches, including transcriptomics, epigenomics, microbiomics, metabolomics, and proteomics, to asthma endotyping. -Omics approaches have provided supporting evidence for many existing endotyping paradigms and also suggested novel ways to conceptualize asthma endotypes. Although endotypes based on single -omics approaches are relatively common, their integrated multi-omics application to asthma endotyping has been more limited thus far. We discuss paths forward to integrate multi-omics with clinical features and laboratory parameters to achieve the goal of precise asthma endotypes.
Ethnoracial Populism: An Alternative to Neoliberal Globalization?

ABSTRACTWorldwide emergence of strongmen leaderships and eroded or failed democracies suggest that the era of unchallenged neoliberal hegemony may be winding down and that alternatives are rising. ...
Imagining a more just world: critical arts pedagogy and youth participatory action research

Current conceptualizations of youth impact the ways in which youth are understood and shape and limit the questions and policy solutions that educational theorists, practitioners and researchers ca...
Low-Complexity Energy Methods for Discretization

One potential difficulty that arises in numerical generation of near-optimal configurations is the computational complexity of the energy sums and their derivatives. One way of dealing with this issue is to minimize weighted energy sums, where the weight varies with N and vanishes if the points x and y are further away from each other than a certain threshold distance \(r_N\). A natural question arises whether the limiting distribution of asymptotically optimal sequences of N-point configurations and the leading term of the minimal energy with the varying weight coincide with the ones of the energy with some fixed weight.
Is soy protein effective in reducing cholesterol and improving bone health

Hyperlipidemia associated with cardiovascular health, and bone loss with regard to osteoporosis contribute to increased morbidity and mortality and are influenced by diet. Soy protein has been shown to reduce cholesterol levels, and its isoflavones may improve bone health. The objective of this study was to determine the effects of soy protein on lipid profiles and biomarkers of bone metabolism and inflammation. Ninety men and women (aged 27–87) were randomly assigned to consume 40 g of soy or casein protein daily for three months. Both soy and casein consumption significantly reduced bone alkaline phosphatase (P = 0.011) and body fat % (P < 0.001), tended to decrease tartrate-resistant acid phosphatase (P = 0.066), and significantly increased serum insulin-like growth factor-I (IGF-1) (P < 0.001), yet soy increased IGF-1 to a greater extent (P = 0.01) than casein. Neither treatment affected total cholesterol, HDL cholesterol, LDL cholesterol, or C-reactive protein. These results demonstrate that daily supplementation of soy and casein protein may have positive effects on indices of bone metabolism and body composition, with soy protein being more effective at increasing IGF-1, an anabolic factor, which may be due to soy isoflavones’ role in upregulating Runx2 gene expression, while having little effect on lipid profiles and markers of inflammation.
Elucidating ecological complexity: Unsupervised learning determines global marine eco-provinces

An unsupervised learning method is presented for determining global marine ecological provinces (eco-provinces) from plankton community structure and nutrient flux data. The systematic aggregated eco-province (SAGE) method identifies eco-provinces within a highly nonlinear ecosystem model. To accommodate the non-Gaussian covariance of the data, SAGE uses t-stochastic neighbor embedding (t-SNE) to reduce dimensionality. Over a hundred eco-provinces are identified with the density-based spatial clustering of applications with noise (DBSCAN) algorithm. Using a connectivity graph with ecological dissimilarity as the distance metric, robust aggregated eco-provinces (AEPs) are objectively defined by nesting the eco-provinces. Using the AEPs, the control of nutrient supply rates on community structure is explored. Eco-provinces and AEPs are unique and aid model interpretation. They could facilitate model intercomparison and potentially improve understanding and monitoring of marine ecosystems.
On-Chip Single-Layer Integration of Diamond Spins with Microwave and Plasmonic Channels

On-chip scalable integration represents a major challenge for practical quantum devices. One particular challenge is to implement on-chip optical readout of spins in diamond. This readout requires ...
Compiling symbolic execution with staging and algebraic effects

Building effective symbolic execution engines poses challenges in multiple dimensions: an engine must correctly model the program semantics, provide flexibility in symbolic execution strategies, and execute them efficiently. This paper proposes a principled approach to building correct, flexible, and efficient symbolic execution engines, directly rooted in the semantics of the underlying language in terms of a high-level definitional interpreter. The definitional interpreter induces algebraic effects to abstract over semantic variants of symbolic execution, e.g., collecting path conditions as a state effect and path exploration as a nondeterminism effect. Different handlers of these effects give rise to different symbolic execution strategies, making execution strategies orthogonal to the symbolic execution semantics, thus improving flexibility. Furthermore, by annotating the symbolic definitional interpreter with binding-times and specializing it to the input program via the first Futamura projection, we obtain a "symbolic compiler", generating efficient instrumented code having the symbolic execution semantics. Our work reconciles the interpretation- and instrumentation-based approaches to building symbolic execution engines in a uniform framework. We illustrate our approach on a simple imperative language step-by-step and then scale up to a significant subset of LLVM IR. We also show effect handlers for common path selection strategies. Evaluating our prototype's performance shows speedups of 10~30x over the unstaged counterpart, and ~2x over KLEE, a state-of-the-art symbolic interpreter for LLVM IR.
Ecological adaptation drives wood frog population divergence in life history traits.

Phenotypic variation among populations is thought to be generated from spatial heterogeneity in environments that exert selection pressures that overcome the effects of gene flow and genetic drift. Here, we tested for evidence of isolation by distance or by ecology (i.e., ecological adaptation) to generate variation in early life history traits and phenotypic plasticity among 13 wood frog populations spanning 1200 km and 7° latitude. We conducted a common garden experiment and related trait variation to an ecological gradient derived from an ecological niche model (ENM) validated to account for population density variation. Shorter larval periods, smaller body weight, and relative leg lengths were exhibited by populations with colder mean annual temperatures, greater precipitation, and less seasonality in precipitation and higher population density (high-suitability ENM values). After accounting for neutral genetic variation, the QST–FST analysis supported ecological selection as the key process generating population divergence. Further, the relationship between ecology and traits was dependent upon larval density. Specifically, high-suitability/high-density populations in the northern part of the range were better at coping with greater conspecific competition, evidenced by greater postmetamorphic survival and no difference in body weight when reared under stressful conditions of high larval density. Our results support that both climate and competition selection pressures drive clinal variation in larval and metamorphic traits in this species. Range-wide studies like this one are essential for accurate predictions of population’s responses to ongoing ecological change.
Comparative study of multiwall carbon nanotube nanocomposites by Raman, SEM, and XPS measurement techniques

Abstract Substantial research efforts are under way to optimize the production of composites enhanced by the incorporation of nanomaterial fillers such as multiwall carbon nanotubes (MWCNTs). It is therefore critical to develop robust methods to detect and characterize MWCNTs in nanocomposites to measure product performance and potential risks from release of the MWCNTs. In this study, the effectiveness of X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, and scanning electron microscopy (SEM) methods is assessed on a series of MWCNT-epoxy nanocomposites samples. A general trend of positive correlation between signal intensity and MWCNT mass loading was observed by both Raman spectroscopy and XPS. Raman spectroscopy was capable of detecting MWCNTs at the lowest nominal concentration tested (0.01%), while for XPS, MWCNTs were detected down to a threshold of approximately 0.5%. Analysis of the same locations of two nanocomposite samples with nominal MWCNT mass fractions of 0.3% and 1% using Raman chemical imaging and SEM revealed a similar detectability of MWCNT clusters and with the higher mass loading sample having a greater number of MWCNT-rich domains. Overall, these results show a good comparability among the different techniques and therefore provide comprehensive, nondestructive microscopy methods to characterize nanocomposites.
Hydropower development potential at non-powered dams: Data needs and research gaps

Abstract Hydropower plays a key role in the evolving energy grid. In the United States, thousands of non-powered dams (NPDs) represent untapped opportunities for new energy production. This paper reviews past NPD resource assessments, with a particular focus on those in the United States, and evaluates where there is room for improving methods, data, and assumptions for estimating development potential. Through this review, we catalog the types of information that are available to stakeholders involved in NPD development. Past assessments have generally focused on interests of project developers (i.e. how much hydropower development potential is available); however, needs of other stakeholders are not adequately addressed in literature. We thus suggest specific actions for improving methods and data used in assessing development potential: establishing consistency among datasets, accounting for uncertainties, representing technology in a more robust way, and accounting for a broader suite of factors that affect potential. To support development at NPDs, future research should consider emerging technologies, explore co-development strategies, and incorporate socio-economic incentives and constraints. Additionally, we survey recent NPD retrofit projects in the United States and identify patterns at successful projects (restrictions on additional flow alterations and water quality/ecological requirements are common) and unsuccessful projects (surrendered licenses often cite lack of economic feasibility). A comparison between retrofits and the remaining population of NPDs highlights that certain characteristics are disproportionately observed in successful retrofits (i.e. concrete dams with the primary purpose of navigation). Understanding the current state of the literature and recent patterns in NPD development will help improve future analyses of potential and support broader development-related interests.
Effect of growth twins on strength and microstructural evolution of nanocrystalline aluminum

The effect of growth-twins on friction, wear, and microstructural evolution of nanocrystalline (NC) aluminum is investigated using molecular dynamics simulations. NC Al with growth-twins has been previously synthesized experimentally, but the role of twins in deformation of this material has remained unknown. We find that twins increase strength and wear resistance of NC Al. The main reason is the anisotropy of plastic deformation since dislocations preferentially propagate along twin boundaries and therefore it is more difficult to nucleate dislocations in twinned sample with randomly oriented grains. The strengthening that comes from the increased stress required to nucleate dislocations in twinned samples can be off-set by the lower rate of strain hardening associated with the reduced dislocation densities. The balance of these effects is expected to depend on the grain size and twin spacing. Finally, our simulations reveal that dislocations in the neighboring twin layers move together, leading to a concerted confined layer slip.
TechCheck-K: A Measure of Computational Thinking for Kindergarten Children

In this pilot study we created and evaluated a new version of the TechCheck Computational Thinking (CT) assessment designed specifically for kindergarten students. The original version of TechCheck was validated in first and second graders and consists of 15 multiple choice unplugged challenges drawn from six CT domains. The kindergarten version, called TechCheck-K, consists of similar unplugged challenges but reduces the number of response choices from four to three and uses exclusively non-verbal material in the responses to accommodate younger, pre-literate children. We administered TechCheck-K to N =89 kindergarten students from four schools, including 45 boys and 44 girls with no coding experience. Participants completed the assessment in an average of 23.43 minutes. TechCheck-K scores were normally distributed (M =8.26, SD =2.33). Mean scores were numerically higher in boys (M =8.71, SD = 2.69) than girls (M =8.05, SD = 2.07). The difference between genders was not significant. The pattern of correct responses to the 15 TechCheck-K items correlated (r =.76) with the pattern observed in first and second graders on the original TechCheck, providing evidence that comparable CT constructs are measured by the two versions of the instrument. Results of this pilot study indicate that TechCheck-K has acceptable characteristics for assessment of CT in kindergarten children.
Urban vegetation and songbird nesting guilds: Relationships and implications for conservation and management

Abstract Urban environments are heavily anthropogenic and often species depauperate. Many bird species, however, persist in cities, facilitated in part by the vegetated habitats cities provide. Urban vegetation management is likely to be key to bird conservation in cities, but supporting such conservation requires a more complete understanding of the relationships between urban birds and different aspects of urban vegetation than we currently possess. We sought to identify relationships between the species richness and abundance of songbird nesting guilds and attributes of urban vegetation to help build this understanding. We used guild richness and abundance and urban vegetation data compiled via point-count and urban-forest surveys in the Cedar Rapids and Iowa City corridor of Iowa, USA to construct binomial N-mixture models. We used our models to evaluate relationships between the abundance and richness of native songbird nesting guilds and different attributes of urban forests and understory vegetation. Relationships between nesting guilds and urban vegetation differed among guilds, although relationships with some attributes of urban vegetation (e.g., impervious and lawn cover) were more similar. Our models indicate that some characteristics of urban vegetation (e.g., tree height, evergreen trees, standing dead trees) are related to the richness or abundance of only one guild, while others (e.g., low vegetation) are important predictors for multiple guilds, but with different relationships. These findings suggest that some attributes such as lawn and impervious cover could be managed city-wide to support conservation, but few vegetation management approaches could be applied uniformly across cities to support species in all nesting guilds. These results thus indicate that urban conservation in the study area and beyond is likely to require vegetation management that is targeted to specific settings within cities and to the requirements of different groups of species that occur within those settings to support a diversity of bird species.
What Do Capuchin Monkeys Tell Us about Cooperation

Nature may be red in tooth and claw, but working together with one’s group mates can be an efficient way to increase fitness. Cooperation is common, for example, among capuchin monkeys. These monkeys are not only willing to help others obtain resources, but are more likely to share with individuals who help them. Cooperation can be risky, however, and not surprisingly capuchins are much less likely to cooperate when a partner is able to monopolize the reward. However, they also pay attention to the partner’s behavior; monkeys that share with their partners promote successful cooperation, and thus actually receive more benefits over the long term than those who always claim the best rewards for themselves. The ability to recognize inequity may be a mechanism by which the monkeys determine which partners are the best collaborators. The study of capuchin monkeys can tell us quite a lot about how, when, and with whom to cooperate, perhaps providing insight into the design and implementation of our own human cooperative institutions.
Southeast Asian Perceptions of U.S. and Japanese Imports: a Cross-National Comparison of Country-Of-Origin Effects

When countries differ in the perceived quality of their exports, country-of-origin labeling influences consumer choice. The influx of U.S. and Japanese products in Southeast Asia markets (SEA) offers a testing frame suitable for investigating perceived differences between imports produced in the two nations.
Terahertz Non-destructive Evaluation of Layered Media with the Maximum Likelihood Estimator

Terahertz (THz) non-destructive evaluation (NDE) has shown great promise for applications in manufacturing, security screening, and medical imaging. However, interpretation of the THz A-scans is complicated by a number of factors. Other researchers have applied signal processing techniques that improve object boundary detection, but still rely on human interpretation without a statistical framework that provides automated detection. This work presents a statistical signal processing algorithm to detect boundaries/defects in THz NDE data based on techniques that have traditionally been used to detect targets in radar/sonar applications. It is demonstrated that this method provides better signal-to-noise ratio (SNR) in the processed waveform along with a mature mathematical framework for analysis of measured data.
Negative-index polarization-independent metamaterial

We introduce a polarization-independent left-handed metamaterial, and describe its electromagnetic properties using numerical techniques. Conventional mirrored S-shaped resonators are shown to exhibit a negative refractive index; and in this work a crossed design based on these resonators is demonstrated as a polarization insensitive metamaterial with negative effective index.
The Role of the Software Enigneer in Real-Time Software Development: An Introductory Course

A noteworthy feature of the computing industry is the increasing demand for application-specific software. For example, software to control a factory in real-time involves timing, fault-tolerance, and safety constraints. These requirements differ from those one would encounter in the design of a software interface to a database. Software engineers who architect real-time systems need to know how to apply basic principles about real-time computing, but there is a gap between real-time computing theory and industrial engineering practice. The subject of this report is a full-semester course, Introduction to Real-Time Software and Systems, which bridges this gap by focusing on the role of the software engineer in real-time software development. This course shows how real-time computing theory can be incorporated into software engineering practice. The report describes the rationale, structure, and content of the course. It also relates the author's experiences in teaching the course.
Espaço de Convivência Digital virtual (ECODI): o acoplamento estrutural no processo de interação

Pre-service teacher education occurs in the stream of interactions among the human beings in congruence with the environment (constituted in the VDLS). Thus, in the process of teaching-learning we consider: the ontogeny of the human beings, the dynamic of relations in the social systems, the congruence among the human beings and digital technologies (DT), the pedagogical practice when teaching and the pedagogical mediation established in the process. During the pre-service education, the teachers represent their perception (through relationships of acceptation, legitimization and mutual respect), establish the disruptions in the auto-poetic social systems, compensate the disruptions incongruence with the environment and establish different structural couplings. The reflecion about the problems occurred during courses of initial formation of the teacher, in the context of VDLS – hybrid digital technology comprised of the DT: Virtual Environment of Learning (VEL); Instantaneous Communicator; Blog and Metaverse. The empiric data, used to reflect on the domains of structural coupling, resulted from the process of interaction of the initial formation courses, developed in Brazil and France, and have been submitted to the methodology of context analysis. The analysis of the data has made it possible to identify, in the courses developed in the context of hybrid digital technological, structural couplings of three domains: structural coupling, technological structural coupling, and structural coupling of virtual digital nature. In this context, it was possible to amplify the reflections on the pedagogical practices developed in the Higher Education by means of DT; to identify the teaching action that is established in the pedagogical mediation; and the proposal of courses that may represent an innovation in the process of teaching-learning.
Structural genomics and structural biology: compare and contrast

A report on the Keystone Symposium 'Structural Genomics', held concurrently with the 'Frontiers in Structural Biology' symposium, Snowbird, USA, 13-19 April 2004.
Maspin and tumor metastasis

For most cancer cell types, the acquisition of metastatic activity leads to clinically incurable disease. Improvements in surgery and radiotherapy, and the development of new chemotherapeutic agents or their use in new combinations, have, so far, only incrementally improved patient survival. Despite the obvious importance of metastasis, the process remains incompletely characterized at the molecular and biochemical levels. Tumor metastasis is a complex process and requires multiple cellular functions over time. From cellular invasion, extravasation from the primary tumor, intravasation to the secondary organs, to successful colonization, tumor cells utilize many cellular or biochemical mechanisms to complete the metastatic spread. During the process of metastasis, there are consistent changes in gene expression. Studies of genes that are reduced or silenced have yielded surprising insights into in vivo mechanisms of regulating tumor metastasis. This review describes a tumor suppressor gene, Maspin, which is often silenced in cancer cells and exhibits suppressing activity against tumor growth and metastasis. Maspin has been shown to be involved in processes that are important to both tumor growth and metastasis such as cell invasion, angiogenesis, and more recently apoptosis. Hence, many efforts have been devoted to deciphering the molecular mechanism of maspin. While some insights have come from the protease inhibitory effect of maspin, more perceptive results on how maspin may function in suppressing tumor metastasis have come from studies of gene manipulation, protein interactions and global protein profiling.
Energy and greenhouse gas emission savings of biofuels in Spain's transport fuel. The adoption of the EU policy on biofuels

Using Life Cycle Assessment (LCA) the fossil energy benefits and avoided global warming emissions have been evaluated for the EU Biofuels goals in Spain. The Biofuels considered are cereal ethanol, biodiesel from residual oils, and from palm, sunflower, soybeans and rapeseed vegetable oils. Our findings are that the source of the cereal and vegetable oil influences the efficacy of the Biofuels and that results greatly depend on whether or not electricity has been produced as co-product in bioethanol plants and that without CHP the energy balance of ethanol is negative with few greenhouse gas offsets.
The NOD/SCID chimeric mouse model of human B cell development: studies on the VH4 family immunoglobulin repertoire and implications for SLE.

The use of the NOD=SCID mouse as a transplant recipient for human cord blood B cell progenitorsas a tool for investigations into the development of human B cells has become an exciting reality. The characteristics of the immunoglobulin repertoire in such a model is important to investigate, as it is possiblethat normal or skewed representationscould be produced.Here we reviewour current work in which we describe a normal VH4 repertoire produced in this chimeric mouse model and describe the differences in combinatorial diversity between the human cells that were isolated from the bone marrow and spleen. The implications of this model for studies of systemic lupus erythematosus are also discussed.