Normal ranges and variability of novel urinary renal biomarkers in Sprague-Dawley Rats: comparison of constitutive values between males and females and across assay platforms.

Differences were examined between male and female Sprague-Dawley rats in basal levels of a wide range of urinary biomarkers, including 7 recently qualified biomarkers. The data were generated from urine samples collected on 3 occasions from untreated rats included in a study of the effect of gentamicin nephrotoxicity on urinary renal biomarkers, reported in a companion article in this journal (Gautier et al. 2014). The performance of multiple assays (9 singleplex assays and 2 multiplex platforms from Rules Based Medicine [RBM] and Meso Scale Discovery [MSD]) was evaluated, and normal ranges and variability estimates were derived. While variability was generally greater on the RBM platform than other assays, the more striking difference in the results from different assays was in magnitude. Where differences were observed between assays for an individual biomarker, they were seen in both sexes and consistent across samples collected at different time points. Differences of up to 15-fold were observed for some biomarker values between assays indicating that results generated using different assays should not be compared. For 8 biomarkers, there was compelling evidence for a sex difference. Baseline values in males were significantly higher than in females for total protein, ß2-microglobulin, clusterin, cystatin-C, glutathione-S-transferase (GST-α), tissue inhibitor of metalloproteinases (TIMP-1), and vascular endothelial growth factor (VEGF); female values were significantly higher than that of males for albumin. The largest sex differences (male greater than female by 2- to 11-fold) were seen with ß2-microglobulin, GST-α, and TIMP-1. These data add substantially to the limited body of knowledge in this area and provide a useful framework for evaluation of the potential relevance of sex differences in the diagnostic performance of these biomarkers.

Comparison between male and female Sprague-Dawley rats in the response of urinary biomarkers to injury induced by gentamicin.

Differences were examined between male and female Sprague-Dawley rats in the response of 16 urinary biomarkers (measured using several assay platforms) to renal injury produced by gentamicin administered subcutaneously for 10 days at a dosage of 75 mg/kg. Urinary biomarkers expressed as fold difference from contemporaneous controls and renal histopathology were assessed after 3 and 10 doses. On day 4, minimal proximal tubular changes were observed microscopically in all males but no females; on day 11, more extensive and more severe injury was observed to a similar extent in all animals of both sexes. Modest increases (maximum 5-fold) in all urinary biomarkers (except epidermal growth factor [EGF], which was decreased) on day 4 and marked elevations (maximum 271-fold) on day 11 were seen consistently in both sexes. However, the magnitude of the increases differed between the sexes. On day 4, despite the lack of tubular injury, many biomarkers were more elevated in females than males but this rarely led to statistically significant sex differences; only 2 biomarkers (ß2-microglobulin and total protein) showed a greater increase in males than females in line with the histopathology. On day 11, there were many more biomarkers that showed a statistically significant difference between the sexes in fold change with treatment; in line with the results on day 4, the majority of biomarkers were more increased in females than males. It remains unresolved if sex differences in the magnitude of biomarker response at injury threshold would lead to any difference in diagnostic interpretation between the sexes. These data highlight the need for publication of more studies using animals of both sexes to fully explore the influence of sex on the diagnostic performance of the novel biomarkers.

Exposure to Intermittent Noise Exacerbates the Cardiovascular Response of Wistar-Kyoto Rats to Ozone Inhalation and Arrhythmogenic Challenge.

Noise has become a prevalent public health problem across the world. Although there is a significant amount of data demonstrating the harmful effects of noise on the body, very little is known about how it impacts subsequent responses to other environmental stressors like air pollution, which tend to colocalize in urban centers. Therefore, this study was conducted to determine the effect of intermittent noise on cardiovascular function and subsequent responses to ozone (O3). Male Wistar-Kyoto rats implanted with radiotelemeters to non-invasively measure heart rate (HR) and blood pressure (BP), and assess heart rate variability (HRV) and baroreflex sensitivity (BRS) were kept in the quiet or exposed to intermittent white noise (85-90 dB) for one week and then exposed to either O3 (0.8 ppm) or filtered air. Left ventricular function and arrhythmia sensitivity were measured 24 h after exposure. Intermittent noise caused an initial increase in HR and BP, which decreased significantly later in the regimen and coincided with an increase in HRV and BRS. Noise caused HR and BP to be significantly elevated early during O3 and lower at the end when compared to animals kept in the quiet while the increased HRV and BRS persisted during the 24 h after. Lastly, noise increased arrhythmogenesis and may predispose the heart to mechanical function changes after O3. This is the first study to demonstrate that intermittent noise worsens the cardiovascular response to inhaled O3. These effects may occur due to autonomic changes and dysregulation of homeostatic controls, which persist one day after exposure to noise. Hence, co-exposure to noise should be taken into account when assessing the health effects of urban air pollution.

Sargramostim (rhu GM-CSF) Improves Survival of Non-Human Primates with Severe Bone Marrow Suppression after Acute, High-Dose, Whole-Body Irradiation.

Exposure to acute, high-dose, whole-body ionizing radiation results in bone marrow failure (hematopoietic acute radiation syndrome with resultant infection, bleeding, anemia, and increased risk of death). Sargramostim (yeast-derived rhu GM-CSF), a yeast-derived, molecularly cloned, hematopoietic growth factor and pleiotropic cytokine supports proliferation, differentiation, maturation and survival of cells of several myeloid lineages. We evaluated the efficacy of sargramostim in non-human primates (rhesus macaques) exposed to whole-body ionizing radiation at a 50-60% lethal dose. The primary end point was day 60 survival. Non-human primates received daily subcutaneous sargramostim (7 mcg/kg/day) or control. To reflect the anticipated setting of a nuclear or radiologic event, treatment began 48 h postirradiation, and non-human primates received only moderate supportive care (no whole blood transfusions or individualized antibiotics). Sargramostim significantly increased day 60 survival to 78% (95% confidence interval, 61-90%) vs. 42% (26-59%; P = 0.0018) in controls. Neutrophil, platelet and lymphocyte recovery rates were accelerated and infection rates decreased. Improved survival when sargramostim was started 48 h postirradiation, without use of intensive supportive care, suggests sargramostim may be effective in treating humans exposed to acute, high-dose whole-body, ionizing radiation in a scenario such as a mass casualty event.

Interaction between charged surfaces mediated by rodlike counterions: the influence of discrete charge distribution in the solution and on the surfaces.

The interaction between two charged surfaces, with discrete or uniform charge distributions, embedded in a solution of rodlike counterions has been studied. Monte Carlo simulations and density functional theory have been applied to study the concentration profiles of counterions and the force between the charged surfaces. We show that for low surface charge densities the repulsive force between like-charged surfaces is observed regardless of the rod length. Where high surface charge densities are present, attractive forces at surface separations related to the rod length are observed.

Microfluidic chips for the crystallization of biomacromolecules by counter-diffusion and on-chip crystal X-ray analysis.

Microfluidic devices were designed to perform on micromoles of biological macromolecules and viruses the search and the optimization of crystallization conditions by counter-diffusion, as well as the on-chip analysis of crystals by X-ray diffraction. Chips composed of microchannels were fabricated in poly-dimethylsiloxane (PDMS), poly-methyl-methacrylate (PMMA) and cyclo-olefin-copolymer (COC) by three distinct methods, namely replica casting, laser ablation and hot embossing. The geometry of the channels was chosen to ensure that crystallization occurs in a convection-free environment. The transparency of the materials is compatible with crystal growth monitoring by optical microscopy. The quality of the protein 3D structures derived from on-chip crystal analysis by X-ray diffraction using a synchrotron radiation was used to identify the most appropriate polymers. Altogether the results demonstrate that for a novel biomolecule, all steps from the initial search of crystallization conditions to X-ray diffraction data collection for 3D structure determination can be performed in a single chip.

Statistical Analysis of Quantitative RT-PCR Results.

Quantitative real-time reverse transcription polymerase chain reaction (RT-PCR) represents a benchmark technology in the detection and quantification of mRNA. Yet, accurate results cannot be realized without proper statistical analysis of RT-PCR data. Here we examine some of the issues concerning RT-PCR experiments that would benefit from rigorous statistical treatment including normalization, quantification, efficiency estimation, and sample size calculations. Examples are used to illustrate the methods.

An evaluation of fit factors and dissolution efficiency for the comparison of in vitro dissolution profiles.

Dissolution efficiency (D.E.), the area under a dissolution curve between defined time points, and the fit factors (f1 and f2) have been compared for the characterisation of dissolution profiles, using data from three batches of a product in nine different packs stored under two conditions. The factors f1 and f2 offer ease of calculation and a simple measure of similarity between pairs of dissolution profiles. This is well suited to the qualitative determination of 'similarity' as required by the FDA's SUPAC Guide. However, they do not provide information on individual batches, including their consistency. In contrast, D.E. does provide such information is well-suited to making quantitative comparisons amongst batches. Because D.E. has a simple physical meaning, it is easier to interpret D.E. data then corresponding f1 and f2 results. The confidence limits in D.E. values provide a useful measure of the variability in batch dissolution and allow the statistical significance of difference in D.E. between pairs of batches to be determined. Both of the above measures lead to the same conclusions regarding the similarity in protective power amongst the nine packs under test and to the value of added desiccant in maintaining the dissolution profile of the product when stored under high humidity conditions. It is concluded that D.E. offers a suitable alternative to the single point dissolution measurement for QC of immediate release products.

Determination of the equilibrium charge distribution for polyampholytes of different compactness in a single computer experiment.

The conformational properties of charge-balanced polyampholytes described by the end-to-end distance or radius of gyration depend on parameters such as the temperature and pH as well as on the detailed charge distribution along the backbone. In this work we present a method to determine the charge distribution along a semi-stiff polyampholyte backbone which will result in a thermodynamically stable structure for the compactness of interest, from several loops to an uncoiled structure, performed in a single computer experiment.

Statistical analysis of quantitative RT-PCR results.

Real-time reverse transcription polymerase chain reaction (RT-PCR) represents a benchmark technology in the detection and quantification of mRNA. Yet, accurate results cannot be realized without proper statistical analysis of RT-PCR data. Here, we examine some of the issues concerning RT-PCR experiments that would benefit from rigorous statistical treatment, including normalization, quantification, efficiency estimation, and sample size calculations. Examples are used to illustrate the methods.

Method for sampling compact configurations for semistiff polymers.

The sampling of compact configurations is crucial when investigating structural properties of semistiff polymers, like proteins and DNA, using Monte Carlo methods. A sampling scheme for a continuous model based on configuration biasing is introduced, tested, and compared with conventional methods. The proposed configuration biased Monte Carlo method, used together with the Wang-Landau sampling scheme, enables us to obtain any thermodynamic property within the statistical ensemble in use. Using the proposed method, it is possible to collect statistical data of interest for a wide range of compactions (from stretched up to several toroid loops) in a single computer experiment. A second-order-like stretched-toroid phase transition is observed for a semistiff polymer, and the critical temperature is estimated.

Number fluctuations of the condensing agent affects the coil-toroid coexistence for semi-stiff polyelectrolytes.

A semi-stiff charged polymer with counterions and salt was investigated using a Monte Carlo method with the Wang-Landau sampling scheme. Simulations show the coexistence of thermodynamically stable structures-prolonged and compact (toroidal-like). The transition between the two states is accompanied by concentration fluctuations for the condensing agent. Compact structures are accompanied by more multivalent counterions than prolonged ones.

Decreased osmotic pressure via interfacial charge clustering.

Behaviors of a model interfacial system featuring the clustering of discrete, mobile wall charges and a counterion solution are investigated. The results demonstrate that even very small localized charge clusters produce significant effects for the osmotic pressure, effects that are not adequately represented in common colloidal models. We observe a pronounced decrease in osmotic pressure where a certain level of clustering is attained, with potentially significant implications for theories of colloidal stability and biochemical processes at microscopic length scales. The stable level of wall charge clustering, and thus the osmotic pressure, is found to be variable in the addition of an attractive potential, as measured via the excess free energy of clustering.

Effects of Discrete Charge Clustering in Simulations of Charged Interfaces.

A system of counterions between charged surfaces is investigated, with the surfaces represented by uniform charged planes and three different arrangements of discrete surface charges - an equispaced grid and two different clustered arrangements. The behaviors of a series of systems with identical net surface charge density are examined, with particular emphasis placed on the long ranged corrections via the method of "charged slabs" and the effects of the simulation cell size. Marked differences are observed in counterion distributions and the osmotic pressure dependent on the particular representation of the charged surfaces; the uniformly charged surfaces and equispaced grids of discrete charge behave in a broadly similar manner, but the clustered systems display a pronounced decrease in osmotic pressure as the simulation size is increased. The influence of the long ranged correction is shown to be minimal for all but the very smallest of system sizes.

Laser processing for bio-microfluidics applications (part II).

This paper reviews applications of laser-based techniques to the fabrication of microfluidic devices for biochips and addresses some of the challenges associated with the manufacture of these devices. Special emphasis is placed on the use of lasers for the rapid prototyping and production of biochips, in particular for applications in which silicon is not the preferred material base. This review addresses applications and devices based on ablation using femtosecond lasers, infrared lasers as well as laser-induced micro-joining, and the laser-assisted generation of micro-replication tools, for subsequent replication of polymeric chips with a technique like laser LIGA.

Laser processing for bio-microfluidics applications (part I).

This paper reviews applications of laser-based techniques to the fabrication of microfluidic devices for biochips and addresses some of the challenges associated with the manufacture of these devices. Special emphasis is placed on the use of lasers for the rapid prototyping and production of biochips in particular for applications in which silicon is not the preferred material base. Part I of this review addresses applications and devices using UV lasers for laser ablation and surface treatment of microchannels, in particular in polymers.

A scalable parallel Monte Carlo method for free energy simulations of molecular systems.

We present a method of parallelizing flat histogram Monte Carlo simulations, which give the free energy of a molecular system as an output. In the serial version, a constant probability distribution, as a function of any system parameter, is calculated by updating an external potential that is added to the system Hamiltonian. This external potential is related to the free energy. In the parallel implementation, the simulation is distributed on to different processors. With regular intervals the modifying potential is summed over all processors and distributed back to every processor, thus spreading the information of which parts of parameter space have been explored. This implementation is shown to decrease the execution time linearly with added number of processors.

The influence of discrete surface charges on the force between charged surfaces.

The force between two parallel charged flat surfaces, with discrete surface charges, has been calculated with Monte Carlo simulations for different values of the electrostatic coupling. For low electrostatic coupling (small counterion valence, small surface charge, high dielectric constant, and high temperature) the total force is dominated by the entropic contribution and can be described by mean field theory, independent of the character of the surface charges. For moderate electrostatic coupling, counterion correlation effects lead to a smaller repulsion than predicted by mean field theory. This correlation effect is strengthened by discrete surface charges and the repulsive force is further reduced. For large electrostatic coupling the total force for smeared out surface charges is known to be attractive due to counterion correlations. If discrete surface charges are considered the attractive force is weakened and can even be turned into a repulsive force. This is due to the counterions being strongly correlated to the discrete surface charges forming effective, oppositely directed, dipoles on the two walls.

A review of microfabrication technologies: application to x-ray optics.

We present an outline of various microfabrication techniques and processes, particularly for applications to x-ray optics. Emphasis is placed on both high resolution diffractive components such as gratings and zone plates and multidimensional reflective diffracting structures using multilayer interference mirrors. Some selected examples are also discussed.

Swelling behaviour of poly(methylmethacrylate) thick resist layers in deep X-ray lithography.

The understanding and optimization of lithographic conditions are particularly important for irradiation of thick resist layers in deep X-ray lithography. The causes and consequences of radiation-induced formation and accumulation of gaseous species inside the poly(methylmethacrylate) (PMMA) resist matrix are discussed. Thick PMMA layers were exposed to high-energy photons from a bending-magnet beamline at the Center for Advanced Microstructures and Devices (CAMD). The focus of this work was to explore the swelling behaviour of PMMA resist of thickness between 50 micro m and 1.6 mm. The influence of various exposure parameters, such as photon energy, filtering conditions, electron current in the storage ring, scan length and scan speed, exposure atmosphere etc., on the swelling of the resist are discussed. The effect of pre-exposure annealing of the PMMA sheets and of temperature variation during irradiation was also investigated. Exposure with optimized X-ray spectral distribution, incident power density, absorbed dose and rate of energy deposition inside the resist allowed swelling of the resist to be minimized during exposure.