The evolution of custom microarray manufacture

Given the enormous size of the genome and that there are potentially many other types of measurements we need to do to understand it, it has become necessary to pick and choose one's targets to measure because it is still impossible to evaluate the entire genome all at once. What has emerged is a need to have rapidly customizable microarrays. There are two dominant methods to accomplish custom microarray synthesis, Affymetrix-like microarrays manufactured using light projection rather than semiconductor-like masks used by Affymetrix to mass manufacture their GeneChip/sup TM/ arrays now, or the ink-jet printing method employed by Agilent. The manufacture of these custom Affymetrix-like microarrays can now be done on a digital optical chemistry (DOC) machine developed at the University of Texas Southwestern Medical Center, and this method offers much higher feature numbers and feature density than is possible with ink-jet printed arrays. On a microarray, each feature contains a single genetic measurement. The initial DOC prototype has been described in several publications, but that has now led to a second-generation machine. This machine reliably produces a number of arrays daily, has been deployed against a number of biomedical questions, is being used in new ways and has also led to a number of spin-off technologies.     

Type synthesis of spatial mechanisms on the basis of spatial single loop structural groupsTypensynthese räumlicher mechanismen auf der grundlage räumlicher einfach geschlossener strukturgruppen

This paper describes the basis for a new method of type synthesis of spatial mechanisms with the use of single-loop structural groups having zero degrees of freedom. Applying the binary system, the value 0 is used for R (revolute) and 1 is used for P (prismatic) pairs. The five-link spatial groups are described by codes both in the binary and decimal systems. All other groups are reduced to the basis of five-link spatial groups. In these cases two-degree-of-freedom and three-degree-of-freedom kinematic pairs are transformed to one-degree-of-freedom pairs, and these transformations are also described by codes in the binary and decimal systems. This method of coding can be programmed for digital computation and applied towards the automatic type synthesis in the design of spatial mechanisms. The system is equally clear for alphanumeric or for graphical display. To the designer it defines the diagram of the mechanism, pointing out the frame, the mobile links, the types of the kinematic pairs and their mutual disposition in the mechanism configuration.     

A longitudinal study of green-liver osteomyelitis complex in commercial turkeys

Two flocks of Nicholas tom turkeys from separate farms with histories of above-average condemnations for turkey green-liver osteomyelitis complex (TOC) were studied throughout a 16-week growout. Fifty birds from each farm were necropsied each week for 15 weeks, and birds that had green livers, osteomyelitis in the proximal tibia, or swollen joints were cultured for aerobic bacteria along with an equal number of control birds. At processing, TOC lesions and green livers were obtained for bacterial culture and histopathology. Green-liver-associated TOC was not observed until the turkeys were 9 or 10 weeks of age. The incidence of TOC was higher on one farm, which also had a higher incidence of airsacculitis, higher early and weekly mortality, seroconversion to Newcastle disease virus and Mycoplasma meleagridis, and significantly higher average body weights, relative spleen weights, and relative liver weights. Both farms had a high incidence of intestinal lesions and infestation with Ascaridia dissimilis. Histological evaluation of green livers revealed hyperplasia of bile ducts, dilation of sinusoids, and pigment-containing Kupffer's cells, some of which stained positive for iron. The bacterial isolates most frequently cultured from bones and livers were pleomorphic gram-variable coccobacilli, which grew visible colonies only after a series of subcultures and extended incubation.     

The granulomatous response in murine Schistosomiasis mansoni does not switch to Th1 in IL-4-deficient C57BL/6 mice

IL-4 plays an important role in polarizing inflammation toward a Th2 response. It remains uncertain, however, whether IL-4 also serves to prevent expression of Th1 inflammation. Therefore, using a genetically pure C57BL/6 IL-4-deficient mouse, we studied the role of IL-4 in regulating the production of IFN-gamma and Th1 inflammation in the granulomas of mice infected with Schistosoma mansoni. In contrast to normal animals, IL-4 mutant mice generated smaller liver granulomas that contained fewer eosinophils and no mast cells. Collagenase-dispersed granuloma cells were analyzed by flow cytometry and cultured in vitro to measure cytokine and Ig production. Compared with control granuloma cells, IL-4-/- cells secreted only small quantities of IL-5 and IL-10. Also, there was impaired expression of the IL-4-dependent molecules IgE and IgG1 as well as B cell surface class II and CD23. Yet the granulomas of IL-4 -/- animals produced little IFN-gamma, IgG2a, or other molecules associated with Th1 inflammation even after Ag or anti-CD3 stimulation. Splenocytes from IL-4 -/- animals stimulated with schistosome Ag also failed to produce a Th1 response. Our data show that most aspects of the Th2 response in murine schistosomiasis are highly dependent on IL-4 production. But in the absence of IL-4, neither the natural local granulomatous response to schistosome ova nor the systemic response to soluble egg Ag switches to the type 1 phenotype. Thus the production of IL-4 early in the inflammatory response is not the only factor preventing Th1 expression in inflammation.     

Identification by parameter bounds in adaptive control

Approximate solutions are suggested for receding horizon dual control to guarantee acceptable control performance of a plant with large a priori parameter uncertainties under poor excitation by the output reference and to satisfy the requirement of very fast adaptation using knowledge available on sensor and performance in industrial applications of adaptive control. the aim of the paper is to present several levels of interaction between on-line identification and control performance using parameter bounds. an interesting theorem shows that parameter bounding is a necessary part of the solution of the dual control problem. Starting from the complete separation of identification and control, various approximations are presented at different levels of optimality. Finally, the exact solution of the dual control problem is found for static gain adaptation, which implicitly involves a parameter-bounding identification procedure.     

New aspects in cationization of lignocellulose materials. IX. Flame retardancy effect of modification with nitrogen and sulfur containing groups

Lignocellulose materials were modified with 3-chlor-2-hydroxypropyltrimethylammoniumchloride, 1,3-bis(3-chlor-2-hydroxypropyl)imidazoliumhydrogensulphate, and 2-chlorethyl-sodiumsulphonate and the flame-retardant properties of materials obtained were studied. The flame-retardant effect was proved using the limited oxygen index (LOI) method and values up to 32.8 vol % of oxygen were determined. The LOI values were higher when the modification was done without using NaOH for activation, but in that case the alkylating groups were not chemically bonded to the material. The NaOH activation was necessary to obtain material with flame-retardant properties stable against washing. No synergistic effects were observed when the material was modified with both nitrogen- and sulfur-containing groups.     

Influence of anionic form on thermooxidation of TMAHP–cellulose

With the help of DTA, DTG elementary analysis of carbonized residues and ESR spectroscopy the influence of anionic form on thermooxidation of trimethylammoniumhydroxyprophyl (TMAHP)–cellulose was studied. At 300°C the percentage of carbon in carbonized residue thermolyzed in oxidative atmosphere is higher than for the sample degraded in inert atmosphere. The percentage of hydrogen decreases simultaneously. The concentration of free radicals in thermolyzed residue also increases due to the presence of oxygen. We propose that oxygen is abstracting the hydrogen atoms from polysaccharide and unpaired electrons on carbon atoms are produced. At 400°C the percentage of carbon in residues prepared at inert atmosphere is higher than for residue formed at oxidative atmosphere. Also the concentration of free radicals in thermolyzed residues obtained in inert atmosphere is greater than for those from oxidative ones. That is why suppose that at this temperature oxygen is bonded to polysaccharide residue and free radicals are terminated. From the semiquantitative DTA we can make the following sequence of samples according to their increasing thermooxidative effect: unmodified cellulose < A–HSO < A–Br^? < A–I^? < A–NO < A–H₂PO < A–CH₃COO^? < A–HCO < A–F^? < A–Cl^?1 < A–OH^p?.     

Visually Perceived Distance Judgments: Tablet-Based Augmented Reality Versus the Real World

Does visually perceived distance differ when objects are viewed in augmented reality (AR), as opposed to the real world? What are the differences? These questions are theoretically interesting, and the answers are important for the development of many tablet- and phone-based AR applications, including mobile AR navigation systems. This article presents a thorough literature review of distance judgment experimental protocols, and results from several areas of perceptual psychology. In addition to distance judgments of real and virtual objects, this section also discusses previous work in measuring the geometry of virtual picture space and considers how this work might be relevant to tablet AR. Then, the article presents the results of two experiments. In each experiment, observers bisected egocentric distances of 15 and 30 m in tablet-based AR and in the real world, in both indoor corridor and outdoor field environments. In AR, observers bisected the distances to virtual humans, while in the real world, they bisected the distances to real humans. This is the first reported research that directly compares distance judgments of real and virtual objects in a tablet AR system. Four key findings were: (1) In AR, observers expanded midpoint intervals at 15 m, but compressed midpoints at 30 m. (2) Observers were accurate in the real world. (3) The environmental setting—corridor or open field—had no effect. (4) The picture perception literature is important in understanding how distances are likely judged in tablet-based AR. Taken together, these findings suggest the depth distortions that AR application developers should expect with mobile and especially tablet-based AR.     

Coriolis acceleration analysis of planar mechanisms by complex-number algebra

One of the pitfalls in current methods of acceleration analysis of planar mechanisms is the difficulty in identifying the different types of acceleration components such as the “sliding” acceleration and the Coriolis contribution. Furthermore, the latter is often missed by the analyst altogether which then leads to completely false results in dynamic analysis. Even distinguished authors have on the record actual numerical examples where the wrong angular velocity was used in computing the Coriolis component. The present article demonstrates the acceleration analysis of planar mechanisms using complex-number algebra. This technique, when programmed for digital computation using complex-arithmetic, or using hand calculation, provides the magnitude and direction of all the acceleration components, including the Coriolis term, automatically without resort to such crutches as a “rule of thumb” for determining whether or not the latter is present, “traditional sign conventions”, and without the risk of using the wrong angular velocity. The procedure, derived here, is illustrated by examples.