TectoRNA: modular assembly units for the construction of RNA nano-objects

Structural information on complex biological RNA molecules can be exploited to design tectoRNAs or artificial modular RNA units that can self-assemble through tertiary interactions thereby forming nanoscale RNA objects. The selective interactions of hairpin tetraloops with their receptors can be used to mediate tectoRNA assembly. Here we report on the modulation of the specificity and the strength of tectoRNA assembly (in the nanomolar to micromolar range) by variation of the length of the RNA subunits, the nature of their interacting motifs and the degree of flexibility of linker regions incorporated into the molecules. The association is also dependent on the concentration of magnesium. Monitoring of tectoRNA assembly by lead(II) cleavage protection indicates that some degree of structural flexibility is required for optimal binding. With tectoRNAs one can compare the binding affinities of different tertiary motifs and quantify the strength of individual interactions. Furthermore, in analogy to the synthons used in organic chemistry to synthesize more complex organic compounds, tectoRNAs form the basic assembly units for constructing complex RNA structures on the nanometer scale. Thus, tectoRNA provides a means for constructing molecular scaffoldings that organize functional modules in three-dimensional space for a wide range of applications.

Efficient construction of long DNA duplexes with internal non-Watson–Crick motifs and modifications

We have developed a semi-synthetic approach for preparing long stretches of DNA (>100 bp) containing internal chemical modifications and/or non-Watson–Crick structural motifs which relies on splint-free, cell-free DNA ligations and recycling of side-products by non-PCR thermal cycling. A double-stranded DNA PCR fragment containing a polylinker in its middle is digested with two restriction enzymes and a small insert (∼20 bp) containing the modification or non-Watson–Crick motif of interest is introduced into the middle. Incorrect products are recycled to starting materials by digestion with appropriate restriction enzymes, while the correct product is resistant to digestion since it does not contain these restriction sites. This semi-synthetic approach offers several advantages over DNA splint-mediated ligations, including fewer steps, substantially higher yields (∼60% overall yield) and ease of use. This method has numerous potential applications, including the introduction of modifications such as fluorophores and cross-linking agents into DNA, controlling the shape of DNA on a large scale and the study of non-sequence-specific nucleic acid–protein interactions.

High-resolution physical mapping by combined Alu-hybridization/PCR screening: construction of a yeast artificial chromosome map covering 31 centimorgans in 3p21-p14.

We describe an integrated approach to large-scale physical mapping using an Alu-PCR hybridization screening strategy in conjunction with direct PCR-based screening to construct a continuous yeast artificial chromosome map covering >20 mb in human chromosome 3, bands p14-p21, composed of 205 loci, connected by 480 yeast artificial chromosomes, with average interlocus distance of approximately equal to 100 kb. We observe an inverse distribution of Alu-PCR and (CA)n markers. These results suggest that the two screening methods may be complementary and demonstrate the utility of Alu-PCR hybridization screening in the closure of high-resolution human physical maps.

The Cultural Construction of Political Action: The Case of the European Community's Single Market Program. CES Germany & Europe Working Papers, No. 04.3, December 1993

Explaining the emergence of the European Community's Single Market Program requires making sense of how that institutional project carne onto the political agenda. I suggest that there are two features of the political process that have been not well understood. First, large-scale institutional projects usually require political opportunities to come to fruition. Second, they require strategic actors who can frame such projects in broad ways in order to attract a wide variety of groups. My basic argument is that the European Commission is an organization whose function is primarily to solve the bargaining game that characterizes interaction within the Community and act as a strategic actor. This does not suggest that they are always successful or are the only source of ideas, but instead that they are the collective actor responsible for trying to frame collective interests in new cultural ways. To illustrate this point, I document how the; Single Market program evolved within the Commission and how other important Community actors carne to sign on to its goals over time.

Construction of a precise early Eocene orbital cyclostratigraphy for DSDP Site 80-550 from the Goban Spur, North Atlantic

We constructed a precise early Eocene orbital cyclostratigraphy for DSDP Site 550 (Leg 80, Goban Spur, North Atlantic) utilizing precession related cycles as represented in a high resolution X-Ray Fluorescence based Barium core log. Based on counting of those cycles, we constrain the exact timing of two volcanic ash layers in Site 550 which correlate to ashes +19 and -17 of the Fur Formation in Denmark. The ashes, relative to the onset of the Paleocene/Eocene Thermal Maximum (PETM), are offset by 862 kyr and 672 kyr, respectively. When combined with published absolute ages for ash -17, the absolute age for the onset of the PETM is consistent with astronomically calibrated ages. Using the current absolute age of 28.02 Ma for the Fish Canyon Tuff (FCT) standard for calibrating the absolute age of ash -17 is consistent with tuning option 2 in the astronomically calibrated Paleocene time scale of Westerhold et al. (2008) [Westerhold, T., Röhl, U., Raffi, I., Fornaciari, E., Monechi, S., Reale, V., Bowles, J., and Evans, H.F., 2008, Astronomical calibration of the Paleocene time: Palaeogeography, Palaeoclimatology, Palaeoecology, v. 257, p. 377-403]. Using the recently recalibrated absolute age of 28.201 Ma for the FCT standard is consistent with tuning option 3 in the astronomically calibrated Paleocene time scale. The new results do not support the existence of any additional 405-kyr cycle in the early Paleocene astronomically tuned time scale.

Effects of vehicle and region of application on absorption of hydrocortisone through canine skin

Objective-To determine the effects of various vehicles on the penetration and retention of hydrocortisone applied to canine skin. Sample Population-20 canine skin samples obtained from the thorax, neck, and groin regions of 5 Greyhounds. Procedure-Skin was harvested from dogs after euthanasia and stored at -20 degrees C until required. The skin was then defrosted and placed into diffusion cells, which were maintained at approximately 32 degrees C by a water bath. Saturated solutions of hydrocortisone that contained trace amounts of radiolabelled [C-14]-hydrocortisone in each vehicle (ie, PBS solution [PBSS] alone, 50% ethanol [EtOH] in PBSS [wt/wt], and 50% propylene glycol in PBSS [wt/wt]) were applied to the outer (stratum corneum) surface of each skin sample, and aliquots of receptor fluid were collected for 24 hours and analyzed for hydrocortisone. Results-The maximum flux of hydrocortisone was significantly higher for all sites when dissolved in a vehicle containing 50% EtOH, compared with PBSS alone or 50% propylene glycol, with differences more prominent in skin from the neck region. In contrast, higher residues of hydrocortisone were found remaining within the skin when PBSS alone was used as a vehicle, particularly in skin from the thorax and neck. Conclusions and Clinical Relevance-Penetration of topically applied hydrocortisone is enhanced when EtOH is used in vehicle formulation. Significant regional differences (ie, among the thorax, neck, and groin areas) are also found in the transdermal penetration and skin retention of hydrocortisone. Variability in clinical response to hydrocortisone can be expected in relation to formulation design and site of application.

Vehicle effects on the in vitro penetration of testosterone through equine skin

The effects of three vehicles, phosphate-buffered saline (PBS), ethanol (50% in PBS w/w) and propylene glycol (50% in PBS w/w) on in vitro transdermal penetration of testosterone was investigated in the horse. Skin was harvested from the thorax of five Thoroughbred horses after euthanasia and stored at -20 degrees C until required. The skin was then defrosted and placed into Franz-type diffusion cells, which were maintained at approximately 32 degrees C by a water bath. Saturated solutions of testosterone, containing trace amounts of radiolabelled [C-14]testosterone, in each vehicle were applied to the outer (stratum corneum) surface of each skin sample and aliquots of receptor fluid were collected at 0, 2, 4, 8, 16, 20, 22 and 24 h and analysed for testosterone by scintillation counting. The maximum flux (J(max)) of testosterone was significantly higher for all sites when testosterone was dissolved in a vehicle containing 50% ethanol or 50% propylene glycol, compared to PBS. In contrast, higher residues of testosterone were found remaining within the skin when PBS was used as a vehicle. This study shows that variability in clinical response to testosterone could be expected with formulation design.

Comparison of the clinical efficacy of twice-daily Ritalin and once-daily Equasym XL with placebo in children with Attention Deficit/Hyperactivity Disorder

Objective To compare the efficacy and safety of two methylphenidate (MPH) formulations—once-daily modified-release MPH (EqXL, Equasym™ XL) and twice-daily immediate-release methylphenidate (MPH-IR, Ritalin®)—and placebo in children with Attention Deficit/Hyperactivity Disorder (ADHD). Methods Children aged 6–12 years on a stable dose of MPH were randomized into a double-blind, three-arm, parallel-group, multi-center study and received 3 weeks of EqXL (20, 40, or 60 mg qd), MPH-IR (10, 20, or 30 mg bid) or placebo. Non-inferiority of EqXL to MPH-IR was assessed by the difference in the inattention/overactivity component of the overall teacher’s IOWA Conners’ Rating Scale on the last week of treatment (per protocol population). Safety was monitored by adverse events, laboratory parameters, vital signs, physical exam, and a Side Effect Rating Scale. Results The lower 97.5% confidence interval bound of the difference between MPH groups fell above the non-inferiority margin (−1.5 points) not only during the last week of treatment but during all three treatment weeks. Both MPH-treatment groups experienced superior benefit when compared to placebo during all treatment weeks (P < 0.001). All treatments were well tolerated. Conclusions EqXL given once-daily was non-inferior to MPH-IR given twice-daily. Both treatments were superior to placebo in reducing ADHD symptoms.

Penetration of chlorhexidine into human skin

This study evaluated a model of skin permeation to determine the depth of delivery of chlorhexidine into full-thickness excised human skin following topical application of 2% (wt/vol) aqueous chlorhexidine digluconate. Skin permeation studies were performed on full-thickness human skin using Franz diffusion cells with exposure to chlorhexidine for 2 min, 30 min, and 24 h. The concentration of chlorhexidine extracted from skin sections was determined to a depth of 1,500 µm following serial sectioning of the skin using a microtome and analysis by high-performance liquid chromatography. Poor penetration of chlorhexidine into skin following 2-min and 30-min exposures to chlorhexidine was observed (0.157 ± 0.047 and 0.077 ± 0.015 µg/mg tissue within the top 100 µm), and levels of chlorhexidine were minimal at deeper skin depths (less than 0.002 µg/mg tissue below 300 µm). After 24 h of exposure, there was more chlorhexidine within the upper 100-µm sections (7.88 ± 1.37 µg/mg tissue); however, the levels remained low (less than 1 µg/mg tissue) at depths below 300 µm. There was no detectable penetration through the full-thickness skin. The model presented in this study can be used to assess the permeation of antiseptic agents through various layers of skin in vitro. Aqueous chlorhexidine demonstrated poor permeation into the deeper layers of the skin, which may restrict the efficacy of skin antisepsis with this agent. This study lays the foundation for further research in adopting alternative strategies for enhanced skin antisepsis in clinical practice.

Design and construction of an ultrasonic probe for use in a Cryo-Magnet NMR Spectrometer

SINNMR (Sonically Induced Narrowing of the Nuclear Magnetic Resonance spectra of solids), is a novel technique that is being developed to enable the routine study of solids by nuclear magnetic resonance spectroscopy. SINNMR aims to narrow the broad resonances that are characteristic of solid state NMR by inducing rapid incoherent motion of solid particles suspended in a support medium, using high frequency ultrasound in the range 2-10 MHz. The width of the normal broad resonances from solids are due to incomplete averaging of several components of the total spin Hamiltonian caused by restrictions placed on molecular motion within a solid. At present Magic Angle Spinning (MAS) NMR is the classical solid state technique used to reduce line broadening, but: this has associated problems, not least of which is the appearance of many spinning side bands which confuse the spectra. It is hoped that SlNNMR will offer a simple alternative, particularly as it does not reveal spinning sidebands The fundamental question concerning whether the use of ultrasound within a cryo-magnet will cause quenching has been investigated with success, as even under the most extreme conditions of power, frequency and irradiator time, the magnet does not quench. The objective of this work is to design and construct a SINNMR probe for use in a super conducting cryo-magnet NMR spectrometer. A cell for such a probe has been constructed and incorporated into an adapted high resolution broadband probe. It has been proved that the cell is capable of causing cavitation, up to 10 MHz, by running a series of ultrasonic reactions within it and observing the reaction products. It was found that the ultrasound was causing the sample to be heated to unacceptable temperatures and this necessitated the incorporation of temperature stabilisation devices. Work has been performed on the investigation of the narrowing of the solid state 23Na spectrum of tri-sodium phosphate using high frequency ultrasound. Work has also been completed on the signal enhancement and T1 reduction of a liquid mixture and a pure compound using ultrasound. Some preliminary "bench" experiments have been completed on a novel ultrasonic device designed to help minimise sample heating. The concept involves passing the ultrasound through a temperature stabilised, liquid filled funnel that has a drum skin on the end that will enable the passage of ultrasound into the sample. Bench experiments have proved that acoustic attenuation is low and that cavitation in the liquid beyond the device is still possible.

Design, modeling and construction of a novel ablative fast pyrolysis reactor and product collection system

The objective of this work was to design, construct and commission a new ablative pyrolysis reactor and a high efficiency product collection system. The reactor was to have a nominal throughput of 10 kg/11r of dry biomass and be inherently scalable up to an industrial scale application of 10 tones/hr. The whole process consists of a bladed ablative pyrolysis reactor, two high efficiency cyclones for char removal and a disk and doughnut quench column combined with a wet walled electrostatic precipitator, which is directly mounted on top, for liquids collection. In order to aid design and scale-up calculations, detailed mathematical modelling was undertaken of the reaction system enabling sizes, efficiencies and operating conditions to be determined. Specifically, a modular approach was taken due to the iterative nature of some of the design methodologies, with the output from one module being the input to the next. Separate modules were developed for the determination of the biomass ablation rate, specification of the reactor capacity, cyclone design, quench column design and electrostatic precipitator design. These models enabled a rigorous design protocol to be developed capable of specifying the required reactor and product collection system size for specified biomass throughputs, operating conditions and collection efficiencies. The reactor proved capable of generating an ablation rate of 0.63 mm/s for pine wood at a temperature of 525 'DC with a relative velocity between the heated surface and reacting biomass particle of 12.1 m/s. The reactor achieved a maximum throughput of 2.3 kg/hr, which was the maximum the biomass feeder could supply. The reactor is capable of being operated at a far higher throughput but this would require a new feeder and drive motor to be purchased. Modelling showed that the reactor is capable of achieving a reactor throughput of approximately 30 kg/hr. This is an area that should be considered for the future as the reactor is currently operating well below its theoretical maximum. Calculations show that the current product collection system could operate efficiently up to a maximum feed rate of 10 kg/Fir, provided the inert gas supply was adjusted accordingly to keep the vapour residence time in the electrostatic precipitator above one second. Operation above 10 kg/hr would require some modifications to the product collection system. Eight experimental runs were documented and considered successful, more were attempted but due to equipment failure had to be abandoned. This does not detract from the fact that the reactor and product collection system design was extremely efficient. The maximum total liquid yield was 64.9 % liquid yields on a dry wood fed basis. It is considered that the liquid yield would have been higher had there been sufficient development time to overcome certain operational difficulties and if longer operating runs had been attempted to offset product losses occurring due to the difficulties in collecting all available product from a large scale collection unit. The liquids collection system was highly efficient and modeling determined a liquid collection efficiency of above 99% on a mass basis. This was validated due to the fact that a dry ice/acetone condenser and a cotton wool filter downstream of the collection unit enabled mass measurements of the amount of condensable product exiting the product collection unit. This showed that the collection efficiency was in excess of 99% on a mass basis.

Using secondary knowledge to support decision tree classification of retrospective clinical data

Retrospective clinical data presents many challenges for data mining and machine learning. The transcription of patient records from paper charts and subsequent manipulation of data often results in high volumes of noise as well as a loss of other important information. In addition, such datasets often fail to represent expert medical knowledge and reasoning in any explicit manner. In this research we describe applying data mining methods to retrospective clinical data to build a prediction model for asthma exacerbation severity for pediatric patients in the emergency department. Difficulties in building such a model forced us to investigate alternative strategies for analyzing and processing retrospective data. This paper describes this process together with an approach to mining retrospective clinical data by incorporating formalized external expert knowledge (secondary knowledge sources) into the classification task. This knowledge is used to partition the data into a number of coherent sets, where each set is explicitly described in terms of the secondary knowledge source. Instances from each set are then classified in a manner appropriate for the characteristics of the particular set. We present our methodology and outline a set of experiential results that demonstrate some advantages and some limitations of our approach. © 2008 Springer-Verlag Berlin Heidelberg.

Toward the atomistic simulation of T cell epitopes automated construction of MHC:peptide structures for free energy calculations

Epitopes mediated by T cells lie at the heart of the adaptive immune response and form the essential nucleus of anti-tumour peptide or epitope-based vaccines. Antigenic T cell epitopes are mediated by major histocompatibility complex (MHC) molecules, which present them to T cell receptors. Calculating the affinity between a given MHC molecule and an antigenic peptide using experimental approaches is both difficult and time consuming, thus various computational methods have been developed for this purpose. A server has been developed to allow a structural approach to the problem by generating specific MHC:peptide complex structures and providing configuration files to run molecular modelling simulations upon them. A system has been produced which allows the automated construction of MHC:peptide structure files and the corresponding configuration files required to execute a molecular dynamics simulation using NAMD. The system has been made available through a web-based front end and stand-alone scripts. Previous attempts at structural prediction of MHC:peptide affinity have been limited due to the paucity of structures and the computational expense in running large scale molecular dynamics simulations. The MHCsim server (http://igrid-ext.cryst.bbk.ac.uk/MHCsim) allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale.

Social construction of Geographic Information Systems. (Volumes I and II)

Geographic Information Systems (GIS) is an emerging information technology (IT) which promises to have large scale influences in how spatially distributed resources are managed. It has had applications in the management of issues as diverse as recovering from the disaster of Hurricane Andrew to aiding military operations in Desert Storm. Implementation of GIS systems is an important issue because there are high cost and time involvement in setting them up. An important component of the implementation problem is the "meaning" different groups of people who are influencing the implementation give to the technology. The research was based on the theory of (theoretical stance to the problem was based on the) "Social Construction of Knowledge" systems which assumes knowledge systems are subject to sociological analysis both in usage and in content. An interpretive research approach was adopted to inductively derive a model which explains how the "meanings" of a GIS are socially constructed. The research design entailed a comparative case analysis over two county sites which were using the same GIS for a variety of purposes. A total of 75 in-depth interviews were conducted to elicit interpretations of GIS. Results indicate that differences in how geographers and data-processors view the technology lead to different implementation patterns in the two sites.

Characteristics of effective clinical and theory instructors as perceived by LPN to RN versus generic students in an associate degree nursing program

The purpose of this study was to compare the characteristics of effective clinical and theory instructors as perceived by LPN/RN versus generic students in an associate degree nursing program.^ Data were collected from 508 students during the 1996-7 academic year from three NLN accredited associate degree nursing programs. The researcher developed instrument consisted of three parts: (a) Whitehead Characteristics of Effective Clinical Instructor Rating Scale, (b) Whitehead Characteristics of Effective Theory Instructor Rating Scale, and (c) Demographic Data Sheet. The items were listed under five major categories identified in the review of the literature: (a) interpersonal relationships, (b) personality traits, (c) teaching practices, (d) knowledge and experience, and (e) evaluation procedures. The instrument was administered to LPN/RN students in their first semester and to generic students in the third semester of an associate degree nursing program.^ Data was analyzed using a one factor mutivariate analysis of variance (MANOVA). Further t tests were carried out to explore for possible differences between type of student and by group. Crosstabulations of the demographic data were analyzed.^ There were no significant differences found between the LPN/RN versus generic students on their perceptions of either effective theory or effective clinical instructor characteristics. There were significant differences between groups on several of the individual items. There was no significant interaction between group and ethnicity or group and age on the five major categories for either of the two instruments. There was a significant main effect of ethnicity on several of the individual items.^ The differences between the means and standard deviations on both instruments were small, suggesting that all of the characteristics listed for effective theory and clinical instructors were important to both groups of students. Effective teaching behaviors, as indicated on the survey instruments, should be taught to students in graduate teacher education programs. These behaviors should also be discussed by faculty coordinators supervising adjunct faculty. Nursing educators in associate degree nursing programs should understand theories of adult learning and implement instructional strategies to enhance minority student success. ^