A case-control study of vanishing twin as a risk factor for cerebral palsy.

It has been hypothesized that cerebral palsy of unknown etiology is the result of the death of an unrecognized co-twin--a vanishing twin--in early gestation. We conducted a case-control study of vanishing twin as a risk factor for cerebral palsy of unknown etiology in women who had an obstetric ultrasound during pregnancy. Among mothers of cases, one of 86 had evidence of a vanishing twin on ultrasound, as compared to two of 381 control mothers (odds ratio [OR] 2.2, 95% confidence interval [CI] 0.2-24.8; p = 0.5). Bleeding in early pregnancy, which may indicate the loss of a co-twin, was reported by 14 case mothers and 46 control mothers (OR 1.6, 95% CI 0.8-3.0; p = 0.3). On the basis of results presented here, the vanishing twin syndrome is unlikely to account for a high proportion of cases of cerebral palsy, but there is insufficient statistical power to draw firm conclusions.     

Computational fluid dynamic analysis of flow velocity waveform notching in umbilical arteries

Umbilical artery Doppler velocimetry waveform notching has long been associated with umbilical cord abnormalities, such as distortion, torsion, and/or compression (i.e., constriction). The physical mechanism by which the notching occurs has not been elucidated. Flow velocity waveforms (FVWs) from two-dimensional pulsatile flows in a constricted channel approximating a compressed umbilical cord are analyzed, leading to a clear relationship between the notching and the constriction. Two flows with an asymmetric, semi-elliptical constriction are computed using a stabilized finite-element method. In one case, the constriction blocks 75% of the flow passage, and in the other the constriction blocks 85%. Channel width and prescribed flow rates at the channel inflow are consistent with typical cord diameters and flow rates reported in the literature. Computational results indicate that waveform notching is caused by flow separation induced by the constriction, giving rise to a vortex (core) wave and associated eddies. Notching in FVWs based on centerline velocity (centerline FVW) is directly related to the passage of an eddy over the point of measurement on the centerline. Notching in FVWs based on maximum cross-sectional velocity (envelope FVW) is directly related to acceleration and deceleration of the fluid along the vortex wave. Results show that notching in envelope FVW is not present in flows with less than a 75% constriction. Furthermore, notching disappears as the vortex wave is attenuated at distances downstream of the constriction. In the flows with 75 and 85% constriction, notching of the envelope FVW disappears at ～3.8 and ～4.3 cm (respectively) downstream of the constriction. These results are of significant medical importance, given that envelope FVW is typically measured by commercial Doppler systems.     

A numerical simulation of steady flow fields in a bypass tube.

Steady flow in a complete by-pass tube was simulated numerically. The study was to consider a complete flow field, which included both the by-pass and the host tubes. The changes of the hemodynamics were investigated with three parameters: the inlet flow Reynolds number (Re), anastomotic angle (alpha) and the position of the occlusion in the host tube. The baseline flow field was set up with Re=200, alpha=45 degrees and the centered position of occlusion. The parametric study was then conducted on combination of Re=100, 200, 400, alpha=35 degrees, 45 degrees, 60 degrees, 75 degrees, 90 degrees and three occlusion positions: left, center and right. It was found that in the baseline case, large slow/recirculation flows could be seen in the host tube both upstream and downstream of the occlusion. The separation points were on the opposite walls to the junctions. Recirculation zones were also found near the toe and in the proximal outer wall of the by-pass tube. Their sizes were about one diameter of the tube or smaller. In some cases, pairing vortices could be seen in the host tube upstream of the occlusion. The shear rate distribution associated with the flow fields was presented. The flow pattern obtained was agreeable to those observed experimentally by other investigators. The difference of the flow fields between a complete bypass and simple anastomosis was discussed. The present numerical code provides a preliminary simulation/design tool for bypass graft flows.     

A study of cardiovascular risk in heterozygotes for homocystinuria.

Early atherosclerotic-like lesions and thromboemobolic problems are prominent in homocystinuric patients. Recent evidence suggested that mild homocyst(e)inemia, such as is present in heterozygotes for homocystinuria due to cystathionine synthase deficiency, may cause a marked excess in early ischemic heart disease. To evaluate the risk due to mild homocyst(e)inemia, the frequencies of heart attacks and strokes in parents and grandparents of homocystinuric children were assessed in the present study. No statistically significant increases in the incidence of heart attacks or strokes were consistently detected. The data available are sufficient to virtually exclude an increase in the cardiovascular risk for homocystinuria heterozygotes of as much as fivefold compared to controls, and to make very improbable a relative risk of as much as threefold. Less than 5% of homocystinuria heterozygotes are likely to have a fatal or nonfatal heart attack by age 50. These results fail to suggest that mild homecyst(e)inemia is an important contributory factor in the overall incidence of cardiovascular disease.     

Pol III proofreading activity prevents lesion bypass as evidenced by its molecular signature within E.coli cells

Replication of genomes that contain blocking DNA lesions entails the transient replacement of the replicative DNA polymerase (Pol) by a polymerase specialized in lesion bypass. Here, we isolate and visualize at nucleotide resolution level, replication intermediates formed during lesion bypass of a single N-2-acetylaminofluorene-guanine adduct (G-AAF) in vivo. In a wild-type strain, a ladder of replication intermediates mapping from one to four nucleotides upstream of the lesion site, can be observed. In proofreading-deficient strains (mutD5 or dnaQ49), these replication intermediates disappear, thus assigning the degradation ladder to the polymerase-associated exonuclease activity. Moreover, in mutD5, a new band corresponding to the insertion of a nucleotide opposite to the lesion site is observed, suggesting that the polymerase and exonuclease activities of native Pol III enter a futile insertion-excision cycle that prevents translesion synthesis. The bypass of the G-AAF adduct located within the NarI sequence context requires the induction of the SOS response and involves either Pol V or Pol II in an error-free or a frameshift pathway, respectively. In the frameshift mutation pathway, inactivation of the proofreading activity obviates the need for SOS induction but nonetheless necessitates a functional polB gene, suggesting that, although proofreading-deficient Pol III incorporates a nucleotide opposite G-AAF, further extension still requires Pol II. These data are corroborated using a colony-based bypass assay.     

A systematic search for protein signature sequences.

Signature sequences are contiguous patterns of amino acids 10-50 residues long that are associated with a particular structure or function in proteins. These may be of three types (by our nomenclature): superfamily signatures, remnant homologies, and motifs. We have performed a systematic search through a database of protein sequences to automatically and preferentially find remnant homologies and motifs. This was accomplished in three steps: 1. We generated a nonredundant sequence database. 2. We used BLAST3 (Altschul and Lipman, Proc. Natl. Acad. Sci. U.S.A. 87:5509-5513, 1990) to generate local pairwise and triplet sequence alignments for every protein in the database vs. every other. 3. We selected "interesting" alignments and grouped them into clusters. We find that most of the clusters contain segments from proteins which share a common structure or function. Many of them correspond to signatures previously noted in the literature. We discuss three previously recognized motifs in detail (FAD/NAD-binding, ATP/GTP-binding, and cytochrome b5-like domains) to demonstrate how the alignments generated by our procedure are consistent with previous work and make structural and functional sense. We also discuss two signatures (for N-acetyltransferases and glycerol-phosphate binding) which to our knowledge have not been previously recognized.     

An in vitro fluid dynamic study of pediatric cannulae: the value of animal studies to predict human flow

A challenge to the development of pediatric ventricular assist devices (PVADs) is the use of the aortic cannulae attached to the devices. Cannulae used for pediatric application have small diameters and large pressure drops. Furthermore, during the development of the 12cc Penn State pediatric PVAD, particle image velocimetry (PIV) illustrated that hematocrit levels, through changes in blood viscoelasticity, affected the fluid dynamics. The objective of this study is to compare the fluid dynamics of a pediatric viscoelastic blood analog and a goat viscoelastic blood analog within the PVAD aortic cannula. Two acrylic models were manufactured to model the aortic cannula (6 mm and 8 mm diameters). PIV data was collected to examine the flow at the outlet of the VAD and in the aortic cannula at heart rates of 50 and 75 beats per minute (bpm). Three planes of data were taken, one at the centerline and two 1.5 mm above and below the centerline. Three more planes of data were taken orthogonal to the original planes. While a 75 bpm heart rate was used to represent normal operating conditions, a 50 bpm heart rate represented use of the PVAD during weaning. At 75 bpm, differences were evident between the two different fluids and the two models. Separation zones developed in the plane below the centerline for the higher hematocrit pediatric blood analog. This study raises question to the usefulness of animal testing results in regard to how well they predict the outcome of pediatric patients.     

A dynamic inline sample thermoregulation unit for flow cytometry

BACKGROUND: Flow cytometry is a valuable tool for the study of cellular and molecular interactions. We sought to develop instrumentation that would allow accurate and precise inline dynamic temperature control of flow cytometry samples in order to expand the analytical capabilities of flow cytometry. METHODS: Using a temperature controller, DC power supply, and a Peltier module, we designed a temperature control circuit that regulates the temperature of a heat transfer block. The heat transfer block surrounds the sample line to efficiently heat and cool the sample. We attached DNA oligomers to microspheres and observed the denaturation of fluorescently labeled complementary oligomers to verify that the sample was achieving the desired temperature. RESULTS: The inline thermoregulation unit can ramp between 30 and 95 degrees C (>2 degrees C per second) within 30 s repeatedly. The accuracy of the instrument was verified by comparing the observed melting temperatures of the oligomer sets to the predicted values. These values varied within 6% of the predicted and were reproducible over a variety of conditions. CONCLUSIONS: The apparatus we constructed accurately and dynamically controls the sample temperature of inline samples. Flow cytometers equipped with our inline thermoregulation unit will be able to conveniently use temperature as a robust experimental parameter.     

Computational fluid dynamic simulation of aggregation of deformable cells in a shear flow

We present computational fluid dynamic (CFD) simulation of aggregation of two deformable cells in a shearflow. This work is motivated by an attempt to develop computational models of aggregation of red blood cells (RBCs). Aggregation of RBCs is a major determinant of blood viscosity in microcirculation under physiological and pathological conditions. Deformability of the RBCs plays a major role in determining their aggregability. Deformability depends on the viscosity of the cytoplasmic fluid and on the rigidity of the cell membrane, in a macroscopic sense. This paper presents a computational study of RBC aggregation that takes into account the rheology of the cells as well as cell-cell adhesion kinetics. The simulation technique considered here is two dimensional and based on the front tracking/immersed boundary method for multiple fluids. Results presented here are on the dynamic events of aggregate formation between two cells, and its subsequent motion, rolling, deformation, and breakage. We show that the rheological properties of the cells have significant effects on the dynamics of the aggregate. A stable aggregate is formed at higher cytoplasmic viscosity and membrane rigidity. We also show that the bonds formed between the cells change in a cyclic manner as the aggregate rolls in a shearflow. The cyclic behavior is related to the rolling orientation of the aggregate. The frequency and amplitude of oscillation in the number of bonds also depend on the rheological properties.     

Interstitial fluid flow as a factor in decubitus ulcer formation

Decubitus ulcers form as a result of prolonged excessive external pressure on soft tissue. The mechanisms of ulcer formation are poorly understood. In this preliminary study, the effects of external pressure on interstitial fluid dynamics are analysed, using a simple mathematical model. Calculations revealed that an inverse relationship exists, between the intensity and duration of external pressure required for the interstitial fluid volume in the pressurized region to reach a given portion of its initial volume, which is similar to the experimentally observed relationship between the intensity and duration of external pressure required to produce threshold damage. The preliminary analysis suggests that interstitial fluid flow may play an important role in the ulcer formation.     

Fluorescence energy transfer in two dimensions. A numeric solution for random and nonrandom distributions.

A method of Monte Carlo calculations has been applied to the problem of fluorescence energy transfer in two dimensions in order to provide a quantitative measure of the effects of nonideal mixing of lipid and protein molecules on the quenching profiles of membrane systems. These numerical techniques permit the formulation of a detailed set of equations that describes in a precise manner the quenching and depolarization properties of planar donor-acceptor distributions as a function of specific spectroscopic and organizational parameters. Because of the exact nature of the present numeric method, these results are used to evaluate critically the validity of previous approximate treatments existing in the literature. This method is also used to examine the effects of excluded volume interactions and distinct lattice structures on the expected transfer efficiencies. As a specific application, representative quenching profiles for protein-lipid mixtures, in which donor groups are covalently linked to the protein molecules and acceptor species are randomly distributed within lipid domains, have been obtained. It is found that the existence of phase-separated protein domains gives rise to a shielding effect that significantly decreases the transfer efficiencies with respect to those expected for an ideal distribution of protein molecules. The results from the present numerical study indicate that the experimental application of fluorescence energy transfer measurements in multicomponent membrane systems can be used to obtain organizational parameters that accurately reflect the lateral distribution of protein and lipid molecules within the bilayer membrane.     

A study of the Coriolis effect on the fluid flow profile in a centrifugal bioreactor

Increasing demand for tissues, proteins, and antibodies derived from cell culture is necessitating the development and implementation of high cell density bioreactors. A system for studying high density culture is the centrifugal bioreactor (CCBR), which retains cells by increasing settling velocities through system rotation, thereby eliminating diffusional limitations associated with mechanical cell retention devices. This article focuses on the fluid mechanics of the CCBR system by considering Coriolis effects. Such considerations for centrifugal bioprocessing have heretofore been ignored; therefore, a simpler analysis of an empty chamber will be performed. Comparisons are made between numerical simulations and bromophenol blue dye injection experiments. For the non‐rotating bioreactor with an inlet velocity of 4.3 cm/s, both the numerical and experimental results show the formation of a teardrop shaped plume of dye following streamlines through the reactor. However, as the reactor is rotated, the simulation predicts the development of vortices and a flow profile dominated by Coriolis forces resulting in the majority of flow up the leading wall of the reactor as dye initially enters the chamber, results are confirmed by experimental observations. As the reactor continues to fill with dye, the simulation predicts dye movement up both walls while experimental observations show the reactor fills with dye from the exit to the inlet. Differences between the simulation and experimental observations can be explained by excessive diffusion required for simulation convergence, and a slight density difference between dyed and un‐dyed solutions. Implications of the results on practical bioreactor use are also discussed. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009