Chemical nanoprinting: a novel method for fabricating DNA microchips

We have developed a novel cost-effective procedure, namely ‘chemical nanoprinting’, for oligonucleotide or cDNA chips manufacture. In this thermo-controlled process, the oligonucleotides, covalently attached to a highly loaded ‘master-chip’ through disulfide bonds, are chemically transferred to the acrylamide layer mounted on a ‘print-chip’. It is demonstrated here that multiple identical print-chips can be produced from a single master-chip. This duplication process is a few hundreds of times faster than any existing methods and the speed of process and cost incurred are independent of the scale of the DNA chips.

Galaxies and large scale structure at high redshifts

It is now straightforward to assemble large samples of very high redshift (z ∼ 3) field galaxies selected by their pronounced spectral discontinuity at the rest frame Lyman limit of hydrogen (at 912 Å). This makes possible both statistical analyses of the properties of the galaxies and the first direct glimpse of the progression of the growth of their large-scale distribution at such an early epoch. Here I present a summary of the progress made in these areas to date and some preliminary results of and future plans for a targeted redshift survey at z = 2.7–3.4. Also discussed is how the same discovery method may be used to obtain a “census” of star formation in the high redshift Universe, and the current implications for the history of galaxy formation as a function of cosmic epoch.

Mineral surfaces and bioavailability of heavy metals: A molecular-scale perspective

There is a continual influx of heavy metal contaminants and pollutants into the biosphere from both natural and anthropogenic sources. A complex variety of abiotic and biotic processes affects their speciation and distribution, including adsorption onto and desorption from mineral surfaces, incorporation in precipitates or coprecipitates, release through the dissolution of minerals, and interactions with plants and microbes. Some of these processes can effectively isolate heavy metals from the biosphere, whereas others cause their release or transformation to different species that may be more (or less) bioavailable and/or toxic to organisms. Here we focus on abiotic adsorption and precipitation or coprecipitation processes involving the common heavy metal contaminant lead and the metalloids arsenic and selenium in mine tailings and contaminated soils. We have used extremely intense x-rays from synchrotron sources and a structure-sensitive method known as x-ray absorption fine structure (XAFS) spectroscopy to determine the molecular-level speciation of these elements at concentrations of 50 to several thousand ppm in the contaminated environmental samples as well as in synthetic sorption samples. Our XAFS studies of As and Pb in the mine tailings show that up to 50% of these contaminants in the samples studied may be present as adsorbed species on mineral surfaces, which makes them potentially more bioavailable than when present in sparingly soluble solid phases. Our XAFS studies of Se(VI) sorption on Fe2+-containing sulfates show that this element undergoes redox reactions that transform it into less bioavailable and less toxic species. This type of information on molecular-level speciation of heavy metal and metalloid contaminants in various environmental settings is needed to prioritize remediation efforts and to assess their potential hazard to humans and other organisms.

Complementation of an Escherichia coli adhE mutant by the Entamoeba histolytica EhADH2 gene provides a method for the identification of new antiamebic drugs.

The pathogenic protozoan parasite Entamoeba histolytica, the cause of amebic dysentery and amebic liver abscess, is an obligate anaerobe, and derives energy from the fermentation of glucose to ethanol with pyruvate and acetyl coenzyme A as intermediates. We have isolated EhADH2, a key enzyme in this pathway, that is a NAD+- and Fe2+-dependent bifunctional enzyme with acetaldehyde dehydrogenase and alcohol dehydrogenase activities. EhADH2 is the only known eukaryotic member of a newly defined family of prokaryotic multifunctional enzymes, which includes the Escherichia coli AdhE enzyme, an enzyme required for anaerobic growth of E. coli. Because of the critical role of EhADH2 in the amebic fermentation pathway and the lack of known eukaryotic homologues of the EhADH2 enzyme, EhADH2 represents a potential target for antiamebic chemotherapy. However, screening of compounds for antiamebic activity is hampered by the cost of large scale growth of Ent. histolytica, and difficulties in quantitating drug efficacy in vitro. To approach this problem, we expressed the EhADH2 gene in a mutant strain of E. coli carrying a deletion of the adhE gene. Expression of EhADH2 restored the ability of the mutant E. coli strain to grow under anaerobic conditions. By screening compounds for the ability to inhibit the anaerobic growth of the E. coli/EhADH2 strain, we have developed a rapid assay for identifying compounds with anti-EhADH2 activity. Using bacteria to bypass the need for parasite culture in the initial screening process for anti-parasitic agents could greatly simplify and reduce the cost of identifying new therapeutic agents effective against parasitic diseases.

Produção de energia por mini e micro hidrelétricas na rede de distribuição de água.

A geração de energia hidrelétrica enfrenta uma crescente restrição a sua expansão, diretamente relacionada a fatores ambientais e da limitação de terrenos com potencial economicamente aproveitável. A partir deste fato, é relacionada uma possível fonte de energia hidrelétrica, resultante do aproveitamento dos potenciais presentes na rede de distribuição de água das cidades, ainda sem nenhum aproveitamento. O desenvolvimento desta fonte de energia se dá com a instalação de mini e micro centrais hidrelétricas nos condutos da rede distribuidora de água. Este trabalho tem por objetivo avaliar o potencial de aproveitamento hidrelétrico por mini e micro hidrelétricas por meio de técnicas de modelagem e de otimização, para agilizar e facilitar o procedimento de identificação dos potenciais e a instalação na rede de abastecimento. O trabalho leva em conta as diversas peculiaridades das redes de distribuição de água e dos equipamentos eletro-hidráulicos, discorrendo sobre a possível complementariedade da geração de energia durante os picos de consumo. Discorre também sobre a contribuição para a rede de distribuição elétrica, na logística e nos custos de implantação além de discutir a tipologia das turbinas capazes de aproveitar o potencial energético. É avaliado, com o auxilio de modelos hidráulicos e de otimização, o posicionamento das centrais geradoras na rede e os possíveis benefícios, restrições e impedimentos ao seu uso, desenvolvendo uma metodologia para facilitar a tomada de decisão quanto ao aproveitamento para geração, ou não, em redes diversas. A construção deste procedimento e ferramenta são desenvolvidos a partir do estudo de caso do sistema distribuidor de água do Município de Piquete no estado de São Paulo, Brasil.

Multiple Perspectives on Academic Service-Learning Partnerships at the American University in Cairo: A Mixed Method Study

This mixed method study aimed to redress the gap in the literature on academic service-learning partnerships, especially in Eastern settings. It utilized Enos and Morton's (2003) theoretical framework to explore these partnerships at the American University in Cairo (AUC). Seventy-nine community partners, administrators, faculty members, and students from a diverse range of age, citizenship, racial, educational, and professional backgrounds participated in the study. Qualitative interviews were conducted with members of these four groups, and a survey with both close-ended and open-ended questions administered to students yielded 61 responses. Qualitative analyses revealed that the primary motivators for partners' engagement in service-learning partnerships included contributing to the community, enhancing students' learning and growth, and achieving the civic mission of the University. These partnerships were characterized by short-term relationships with partners' aspiring to progress toward long-term commitments. The challenges to these partnerships included issues pertaining to the institution, partnering organizations, culture, politics, pedagogy, students, and faculty members. Key strategies for improving these partnerships included institutionalizing service-learning in the University and cultivating an institutional culture supportive of community engagement. Quantitative analyses showed statistically significant relationships between students' scores on the Community Awareness and Interpersonal Effectiveness scales and their overall participation in community service activities inside and outside the classroom, as well as a statistically significant difference between their scores on the Community Awareness scale and department offering service-learning courses. The study's outcomes underscore the role of the local culture in shaping service-learning partnerships, as well as the role of both curricular and extracurricular activities in boosting students' awareness of their community and interpersonal effectiveness. Cultivating a culture of community engagement and building support mechanisms for engaged scholarship are among the critical steps required by public policy-makers in Egypt to promote service-learning in Egyptian higher education. Institutionalizing service-learning partnerships at AUC and enhancing the visibility of these partnerships on campus and in the community are essential to the future growth of these collaborations. Future studies should explore factors affecting community partners' satisfaction with these partnerships, top-down and bottom-up support to service-learning, the value of reflection to faculty members, and the influence of students' economic backgrounds on their involvement in service-learning partnerships.

Large-scale clustering measurements with photometric redshifts: comparing the dark matter haloes of X-ray AGN, star-forming and passive galaxies at z ≈ 1

We combine multi-wavelength data in the AEGIS-XD and C-COSMOS surveys to measure the typical dark matter halo mass of X-ray selected active galactic nuclei (AGN) [L_X(2–10 keV) > 10^42 erg s^− 1] in comparison with far-infrared selected star-forming galaxies detected in the Herschel/PEP survey (PACS Evolutionary Probe; L_IR > 10^11 L_⊙) and quiescent systems at z ≈ 1. We develop a novel method to measure the clustering of extragalactic populations that uses photometric redshift probability distribution functions in addition to any spectroscopy. This is advantageous in that all sources in the sample are used in the clustering analysis, not just the subset with secure spectroscopy. The method works best for large samples. The loss of accuracy because of the lack of spectroscopy is balanced by increasing the number of sources used to measure the clustering. We find that X-ray AGN, far-infrared selected star-forming galaxies and passive systems in the redshift interval 0.6 < z < 1.4 are found in haloes of similar mass, log M_DMH/(M_⊙ h^−1) ≈ 13.0. We argue that this is because the galaxies in all three samples (AGN, star-forming, passive) have similar stellar mass distributions, approximated by the J-band luminosity. Therefore, all galaxies that can potentially host X-ray AGN, because they have stellar masses in the appropriate range, live in dark matter haloes of log M_DMH/(M_⊙ h^−1) ≈ 13.0 independent of their star formation rates. This suggests that the stellar mass of X-ray AGN hosts is driving the observed clustering properties of this population. We also speculate that trends between AGN properties (e.g. luminosity, level of obscuration) and large-scale environment may be related to differences in the stellar mass of the host galaxies.

The effect of the geomagnetic field on cosmic ray energy estimates and large scale anisotropy searches on data from the Pierre Auger Observatory

We present a comprehensive study of the influence of the geomagnetic field on the energy estimation of extensive air showers with a zenith angle smaller than 60 degrees, detected at the Pierre Auger Observatory. the geomagnetic field induces an azimuthal modulation of the estimated energy of cosmic rays up to the similar to 2% level at large zenith angles. We present a method to account for this modulation of the reconstructed energy. We analyse the effect of the modulation on large scale anisotropy searches in the arrival direction distributions of cosmic rays. At a given energy, the geomagnetic effect is shown to induce a pseudo-dipolar pattern at the percent level in the declination distribution that needs to be accounted for.

Development of The Readiness To Teach Online Scale

Despite the growing importance of online education, faculty acceptance has remained unchanged. Training programs developed for faculty to teach online have often focused on assessing their cognitive rather than affective and behavioral outcomes. The Readiness To Teach Online scale was developed as part of a multiphase mixed method research project to measure faculty perceptions and motivations toward teaching online. Items in the subcategory Teaching and Learning measured perceptions of technology and online teaching, and motivations regarding resources and other external factors. Items in the subcategories Social and Student Engagement, Faculty and Technology Support, Course Development and Instructional Design, and Evaluation and Assessment collected baseline data for current practices. The pilot study of this scale demonstrated strong internal consistency reliability estimates and support for validity, showing moderately to highly correlated significant relationships between faculty perceptions and motivation to teach online; both perception and motivation constructs were moderately to highly correlated with Social and Student Engagement.

Large scale SLAM with visual features

Comunicación presentada en el X Workshop of Physical Agents, Cáceres, 10-11 septiembre 2009.

Development and psychometric testing of the clinical learning environment, supervision and nurse teacher evaluation scale (CLES+T): The Spanish version

Background: The Clinical Learning Environment, Supervision and Nurse Teacher scale is a reliable and valid instrument to evaluate the quality of the clinical learning process in international nursing education contexts. Objectives: This paper reports the development and psychometric testing of the Spanish version of the Clinical Learning Environment, Supervision and Nurse Teacher scale. Design: Cross-sectional validation study of the scale. Setting: 10 public and private hospitals in the Alicante area, and the Faculty of Health Sciences (University of Alicante, Spain). Participants: 370 student nurses on clinical placement (January 2011–March 2012). Methods: The Clinical Learning Environment, Supervision and Nurse Teacher scale was translated using the modified direct translation method. Statistical analyses were performed using PASW Statistics 18 and AMOS 18.0.0 software. A multivariate analysis was conducted in order to assess construct validity. Cronbach’s alpha coefficient was used to evaluate instrument reliability. Results: An exploratory factorial analysis identified the five dimensions from the original version, and explained 66.4% of the variance. Confirmatory factor analysis supported the factor structure of the Spanish version of the instrument. Cronbach’s alpha coefficient for the scale was .95, ranging from .80 to .97 for the subscales. Conclusion: This version of the Clinical Learning Environment, Supervision and Nurse Teacher scale instrument showed acceptable psychometric properties for use as an assessment scale in Spanish-speaking countries.

Towards the understanding of the interfacial pH scale at Pt(1 1 1) electrodes

The determination of the potentials of zero total and free charge, pztc and pzfc respectively, were made in a wide pH range by using the CO displacement method and the same calculation assumptions used previously for Pt(1 1 1) electrodes in contact with non-specifically adsorbing anions. Calculation of the pzfc involves, in occasions, long extrapolations that lead us to the introduction of the concept of potential of zero extrapolated charge (pzec). It was observed that the pztc changes with pH but the pzec is independent of this parameter. It was observed that the pztc > pzec at pH > 3.4 but the opposite is true for pH > 3.4. At the latter pH both pzec and pztc coincide. This defines two different pH regions and means that adsorbed hydrogen has to be corrected in the “acidic” solutions at the pztc while adsorbed OH is the species to be corrected in the “alkaline” range. The comparison of the overall picture suggests that neutral conditions at the interface are attained at significantly acidic solutions than those at the bulk.

Calcareous plankton response to orbital and millennial-scale climate changes from ODP Leg 161-975

The paleoenvironmental conditions through MIS 15-9 at the Mediterranean Ocean Drilling Program (ODP) Site 975 were interpreted by high resolution study of calcareous plankton assemblages compared with available d18O and d13C records and high resolution paleoclimate proxies from the Atlantic Ocean. Sea Surface Temperatures (SSTs) have been estimated from planktonic foraminiferal assemblages using the artificial neural networks method. Calcareous plankton varied dominantly on a glacial-interglacial scale as testified by the SST record, foraminiferal diversity, total coccolith abundance and changes in warm-water calcareous nannofossil taxa. A general increase in foraminiferal diversity and of total coccolith abundance is observed during interglacials. Warmest SSTs are reached during MIS 11, while MIS 12 and MIS 10 represent the coldest intervals of the studied record. During MIS 12, one of the most extreme glacials of the last million years, occurrence of Globorotalia inflata and of neogloboquadrinids indicates a shoaling of the interface between Atlantic inflowing and Mediterranean outflowing waters. Among calcareous nannofossils the distribution of Gephyrocapsa margereli-G. muellerae > 4 µm also supports a reduced Atlantic-Mediterranean exchange during MIS 12. Superimposed on glacial-interglacial variability, six short-terms coolings are recognized during MIS 12 and 10, which appear comparable in their distribution and amplitude to the Heinrich - type events documented in the Atlantic Ocean in the same interval. During these H-type events, N. pachyderma (s) and G. margereli-G. muellerae > 4 µm increase as a response to the enhanced inflow of cold Atlantic water into the Mediterranean via the Strait of Gibraltar. Mediterranean surface water hydrography appears to have been most severely affected at Termination V during the H-type event Ht4, possibly as a response to a large volume of Atlantic meltwater inflow via the Strait of Gibraltar and/or to freshwater/terrigenous input deriving from local mountain glaciers. Three additional SST coolings are recorded through MIS 14-16, but these are not well correlated with Heinrich - type events documented in the Atlantic Ocean in the same interval; during these cooling episodes only the subpolar Turborotalita quinqueloba increases. These results highlight the sensitive response of the Mediterranean basin to millennial-scale climate variations related to Northern Hemisphere ice-sheet instability and support the hypothesis that the tight connection between high latitude climate dynamics and Mediterranean sea surface water features can be traced through the Middle Pleistocene.

A. S. T. M. viscosity index tables, based on and amplified from A. S. T. M. tentative method for calculating viscosity index (D 567-40 T)

"Acknowledgment is hereby given to E.W. Dean and G. H. B. Davis for the development of the viscosity index scale (Journal of Industrial and engineering chemistry, vol. 32, p. 102 (1940)) and to the Standard oil development co., for the compilation of these tables."

A Kinetic Vlasov Model for Plasma Simulation Using Discontinuous Galerkin Method on Many-Core Architectures

Thesis (Ph.D.)--University of Washington, 2016-03