A versatile maskless microscope projection photolithography system and its application in light-directed fabrication of DNA microarrays

We present a maskless microscope projection lithography system (MPLS), in which photomasks have been replaced by a Digital Micromirror Device type spatial light modulator (DMD, Texas Instruments). Employing video projector technology high resolution patterns, designed as bitmap images on the computer, are displayed using a micromirror array consisting of about 786000 tiny individually addressable tilting mirrors. The DMD, which is located in the image plane of an infinity corrected microscope, is projected onto a substrate placed in the focal plane of the microscope objective. With a 5x(0.25 NA) Fluar microscope objective, a fivefold reduction of the image to a total size of 9 mm2 and a minimum feature size of 3.5 microns is achieved. Our system can be used in the visible range as well as in the near UV (with a light intensity of up to 76 mW/cm2 around the 365 nm Hg-line). We developed an inexpensive and simple method to enable exact focusing and controlling of the image quality of the projected patterns. Our MPLS has originally been designed for the light-directed in situ synthesis of DNA microarrays. One requirement is a high UV intensity to keep the fabrication process reasonably short. Another demand is a sufficient contrast ratio over small distances (of about 5 microns). This is necessary to achieve a high density of features (i.e. separated sites on the substrate at which different DNA sequences are synthesized in parallel fashion) while at the same time the number of stray light induced DNA sequence errors is kept reasonably small. We demonstrate the performance of the apparatus in light-directed DNA chip synthesis and discuss its advantages and limitations.Comment: 12 pages, 9 figures, journal articl

The influence inclination of supply pipe to the Q/H characteristic of measuring flume PARS P3

Tato bakalářská práce se zabývá vlivem přívodního potrubí na Q/H charakteristiku měrného žlabu PARS P3. Byla provedena měření Q/H charakteristik pod různými sklony přívodního potrubí a měrného žlabu. Následně pak byly tyto měření zpracovány a z výsledků byly stanoveny korekce a nejistoty měření.This bachelor thesis deals with the influence of the inlet pipe on the Q / H characteristic of the measuring flume PARS P3. Measurements of Q / H characteristics were performed under different inclination of the inlet pipe and the measuring flume. Subsequently, these measurements were processed and the corrections and uncertainties of the measurements were determined from the results.

Sports hall with facilities and restaurants, Valašské Klobouky

Diplomová práce se týká novostavby samostatně stojící sportovní haly se zázemím a restaurací ve Vlašských Kloboukách. Sportovní hala má jedno podlaží částečně zapuštěné pod terénem, obsahuje tribunu pro 340 diváků. Druhá část, tj. zázemí sportovní haly je v podzemním podlaží, v nadzemním podlaží je restaurace s kuchyní. Objekt je navržen v půdorysném tvaru dvou obdélníků. Střecha je sedlová a pultová. Obvodové konstrukce u haly jsou provětrávané, část se zázemím a restaurací je kontaktně zateplen. Zázemí zaměstnanců restaurace jsou situovány v nadzemním podlaží, strojovny VZT jsou celkem 3, v části haly, v 1S a v 1NP. Pro vytápění je navrhnut výměník, ke kterému je přiveden horkovod. Povrchovou úpravu tvoří keramická dlažba a v hale je použita dvojitá palubovka. Nosnou konstrukci nad 1S tvoří prefabrikované dílce spiroll.This thesis covers brand new detached sports hall with facilities and restaurants in Walnut Klobouky. Sports hall has a floor partly sunk below the surface, contains grandstand for 340 spectators. The second part, ie background sports hall is in the basement, the ground floor is a restaurant kitchen. The building is designed in plan shape of two rectangles. The roof is gabled and desk. Cladding the halls are ventilated, part of the facilities and restaurants are contact-insulated. Staff restaurant facilities are located in the floor, engine room ventilation are 3, in the hall, first underground floor and first floor. The heat exchanger is designed, which is applied hot water. The finish consists of ceramic tiles in the lobby is used double wood board flooring. The supporting structure consists of prefabricated unit first underground floor SPIROLL.

Understanding fractional equivalence and the differentiated effects on operations with fractions

This study compared two representations for teaching fraction equivalence. It traced the implications of both representations on the students comprehension of fractions as well as their ability to perform operations with fractions. The participants in the study included 65 sixth grade students in three extant classrooms. Two classes were instructed using the textbook representation while the third class received instruction using a representation presented by Van de Walle and recommended by the National Council for Teaching Mathematics. Data were collected from pre-tests, post-tests, student work samples, field notes and a semi-structured interview. Qualitative analyses were used to analyze the data. Items were coded for procedural and conceptual understanding and categorized into levels of proficiency. Additionally, items involving operations with fractions were coded for error patterns. Conclusions were drawn about how the different representations affected student comprehension and faculty with fractions

Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies

Infections early in life can have enduring effects on an organism's development and immunity. In this study, we show that this equally applies to developing ‘superorganisms’––incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen's immune system to suppress pathogen proliferation. Early-life queen pathogen exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen's pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism

Provider-facing ehealth tool for transitioning youth with special health care needs from pediatric to adult care: Mixed methods, user-engaged usability study

Background: There is a need for medical education on health care transitions for youth with special health care needs. The Texas Transition Toolkit (the tool) supports providers through a one-stop shop for researching literature on care transitions, a catalog of care transition tools, and guides for developing care transition programs. Objective: This study aims to assess the functionality and usability of the tool with providers working with transition-aged children and youth with special health care needs (representative users). Methods: The tool was evaluated using a triangulated mixed methods case study approach consisting of a concurrent think-aloud phase, a satisfaction survey, and a survey of problem relevance and task performance to operationalize and capture functionality and usability. Our mixed methods deep dive into the functionality and usability of the tool focused on 10 representative users from one medical home in Texas and 5 website design experts. Results: Representative users found the tool to be highly relevant, as demonstrated by the satisfaction score for relevance (138/150, 92%). According to the users, the tool provided comprehensive information related to health care transitions for youth with special health care needs, with a satisfaction score of 87.3% (131/150) for comprehensive. Overall satisfaction with the tool was high at 81.92% (1065/1300) with a cutoff score of 73.33% (953.4/1300) indicating high satisfaction, but users reported relatively lower satisfaction with search (114/150, 76%) and navigation (ease of use: 114/150, 76%; hyperlinks: 163/200, 81.5%; structure: 159/200, 79.5%). They experienced search- and navigation-related problems (total problems detected: 21/31, 68%) and, based on quality checks, had a relatively low task completion rate for tasks involving finding information (60/80, 75%), which required searching and navigation. The problems identified around search and navigation functionality were relevant (relevance scores ranging from 14.5 to 22, with a cutoff score of 11.7 indicating relevance). Conclusions: The tool may help bridge the gaps in training on health care transitions for youth with special health care needs in US medical education. The tool can be used to create structured protocols to help improve provider knowledge, collaboration across pediatric and adult care providers, and the continuity of care as youth with special health care needs transition from pediatric to adult care. The results provided a road map for optimizing the tool and highlighted the importance of evaluating eHealth technologies with representative users.Community Health Sciences, Counseling and Counseling Psycholog

Nonequilibrium effects in DNA microarrays: a multiplatform study

It has recently been shown that in some DNA microarrays the time needed to reach thermal equilibrium may largely exceed the typical experimental time, which is about 15h in standard protocols (Hooyberghs et al. Phys. Rev. E 81, 012901 (2010)). In this paper we discuss how this breakdown of thermodynamic equilibrium could be detected in microarray experiments without resorting to real time hybridization data, which are difficult to implement in standard experimental conditions. The method is based on the analysis of the distribution of fluorescence intensities I from different spots for probes carrying base mismatches. In thermal equilibrium and at sufficiently low concentrations, log I is expected to be linearly related to the hybridization free energy $\Delta G$ with a slope equal to $1/RT_{exp}$, where $T_{exp}$ is the experimental temperature and R is the gas constant. The breakdown of equilibrium results in the deviation from this law. A model for hybridization kinetics explaining the observed experimental behavior is discussed, the so-called 3-state model. It predicts that deviations from equilibrium yield a proportionality of $\log I$ to $\Delta G/RT_{eff}$. Here, $T_{eff}$ is an effective temperature, higher than the experimental one. This behavior is indeed observed in some experiments on Agilent arrays. We analyze experimental data from two other microarray platforms and discuss, on the basis of the results, the attainment of equilibrium in these cases. Interestingly, the same 3-state model predicts a (dynamical) saturation of the signal at values below the expected one at equilibrium.Comment: 27 pages, 9 figures, 1 tabl

Position dependent mismatch discrimination on DNA microarrays – experiments and model

<p>Abstract</p> <p>Background</p> <p>The propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microarray hybridization and PCR. Yet our understanding of oligonucleotide hybridization, in particular in presence of surfaces, is rather limited. Here we use oligonucleotide microarrays made in-house by optically controlled DNA synthesis to produce probe sets comprising all possible single base mismatches and base bulges for each of 20 sequence motifs under study.</p> <p>Results</p> <p>We observe that mismatch discrimination is mostly determined by the defect position (relative to the duplex ends) as well as by the sequence context. We investigate the thermodynamics of the oligonucleotide duplexes on the basis of double-ended molecular zipper. Theoretical predictions of defect positional influence as well as long range sequence influence agree well with the experimental results.</p> <p>Conclusion</p> <p>Molecular zipping at thermodynamic equilibrium explains the binding affinity of mismatched DNA duplexes on microarrays well. The position dependent nearest neighbor model (PDNN) can be inferred from it. Quantitative understanding of microarray experiments from first principles is in reach.</p