A new method to predict flowability using a microscale fluid bed

The purpose of this research was to develop a new method to predict the flow behavior of pharmaceutical powders using a multichamber microscale fluid bed. Different amounts of poorly flowing paracetamol were added to various grades of microcrystalline celluloses and silicified microcrystalline cellulose powders. Magnesium stearate was used as a lubricant. Experimental minimum fluidization velocities (u _mf) were defined using 2 to 4 g (equal to 10 mL) of material (Video 1). The reference flowability of the powders was determined using a specific flow meter. Also, the weight variation of the compressed powders, using a single-punch press, was measured. When the amount of paracetamol in the excipients was increased, the experimentalu _mf increased and the fluidization behavior grew worse (Video 2). Principal component analysis (PCA) established that the pressure difference over the bed as a function of fluidization velocity could be used to characterize the behavior of powders. The increase in poor fluidization behavior of the powders was in accordance with the increasing amount of paracetamol and with the increasing weight variation of the tablets. Furthermore, the angle of repose and the flow rate of silicified microcrystalline cellulose powders were predicted using a partial least squares (PLS) model. The developed method to predict flowability is a promising approach for use in the preformulation and formulation stages of new drug candidates, for example.     

Expiratory volume clamping: a new method to assess respiratory mechanics in sedated infants

During breathing under sedation via a two-way valve, airflow (V), volume (delta V), and airway pressure (P) were recorded in eight normal (N) infants, seven with reversible obstructive airway disease (ROAD), and seven with chronic lung disease (CLD). Intermittently, expiratory volume clamping (EVC) was applied, involving selective occlusion of the expiratory valve for three to five breaths. The latter produced cumulative increases in delta V that, due to progressive recruitment of the Hering-Breuer reflex, were accompanied by increasing expiratory plateaus in P (i.e., apneas). The resultant passive inflation delta V-P relationships were closely approximated by the expression: delta V = aP2 + bP + c, wherein a represented the pressure-related changes in chord compliance (Crs), b the Crs at P = 0, and c the difference between the dynamic end-expiratory and relaxation volumes of the respiratory system. Relative to N, the ROAD and CLD infants had significantly reduced weight-specific values of a/kg, their b/kg values were increased, whereas the c/kg measurements did not significantly vary. Moreover, for each subject we determined the net Crs/kg obtaining at P = 20 cmH2O (i.e., Crs20/kg), an estimate of the net deflation compliance; the passive respiratory time constant (tau rs) based on the slope of the expired delta V/V relationship; and the respiratory system conductance (Grs/kg). Relative to N, the mean Crs20/kg was significantly reduced only in the infants with CLD and, due to increases in tau rs, both patient groups depicted significantly diminished values of Grs/kg, suggesting the presence of airways obstruction.(ABSTRACT TRUNCATED AT 250 WORDS)     

Respiratory variations of aortic VTI: a new index of hypovolemia and fluid responsiveness

In 12 mechanically ventilated and anesthetized rabbits, we investigated whether the magnitude of respiratory changes in the aortic velocity time integral (VTI(Ao)), recorded by transthoracic echocardiography (TTE) during a stepwise blood withdrawal and restitution, could be used as a reliable indicator of volume depletion and responsiveness. At each step, left and right ventricular dimensions and the aortic diameter and VTI(Ao) were recorded to calculate stroke volume (SV) and cardiac output (CO). Respiratory changes of VTI(Ao) (maximal - minimal values divided by their respective means) were calculated. The amount of blood withdrawal correlated negatively with left and right ventricular diastolic diameters, VTI(Ao), SV, and CO and correlated directly with respiratory changes of VTI(Ao). Respiratory VTI(Ao) variations (but not other parameters) at the last blood withdrawal step was also correlated with changes in SV after blood restitution (r = 0.83, P < 0.001). In conclusion, respiratory variations in VTI(Ao) using TTE appear to be a sensitive index of blood volume depletion and restitution. This dynamic parameter predicted fluid responsiveness more reliably than static markers of cardiac preload.     

TMKink: a method to predict transmembrane helix kinks

A hallmark of membrane protein structure is the large number of distorted transmembrane helices. Because of the prevalence of bends, it is important to not only understand how they are generated but also to learn how to predict their occurrence. Here, we find that there are local sequence preferences in kinked helices, most notably a higher abundance of proline, which can be exploited to identify bends from local sequence information. A neural network predictor identifies over two-thirds of all bends (sensitivity 0.70) with high reliability (specificity 0.89). It is likely that more structural data will allow for better helix distortion predictors with increased coverage in the future. The kink predictor, TMKink, is available at http://tmkinkpredictor.mbi.ucla.edu/.     

基于模糊理论预测CpG岛新方法

启动子区域的CpG岛的异常甲基化是识别癌症的重要标志之一。目前已经建立的一些CpG岛的预测思想和方法都有自身的缺点,基于模糊理论的预测思想从贴进度的角度来判定CpG岛,能更容易地找到被以往方法所忽略的具有更多生物学意义的CpG岛。本研究通过构建属于CpG岛集合的隶属函数,计算候选序列的隶属度,找出所有的可接受隶属程度的CpG岛。将该方法应用于UCSC数据库中的一段序列（hg18．chr1．31618510.31623510.-1000）进行预测,发现提高了预测的精确度。可见应用模糊理论预测CpG岛具有一定的可行性,利用选取不同的截集,可以得到更为精确的CpG岛。     

A new method to predict the consensus secondary structure of a set of unaligned RNA sequences

MOTIVATION: To predict the consensus secondary structure, possibly including pseudoknots, of a set of RNA unaligned sequences. RESULTS: We have designed a method based on a new representation of any RNA secondary structure as a set of structural relationships between the helices of the structure. We refer to this representation as a structural pattern. In a first step, we use thermodynamic parameters to select, for each sequence, the best secondary structures according to energy minimization and we represent each of them using its corresponding structural pattern. In a second step, we search for the repeated structural patterns, i.e. the largest structural patterns that occur in at least one sequence, i.e. included in at least one of the structural patterns associated to each sequence. Thanks to an efficient encoding of structural patterns, this search comes down to identifying the largest repeated word suffixes in a dictionary. In a third step, we compute the plausibility of each repeated structural pattern by checking if it occurs more frequently in the studied sequences than in random RNA sequences. We then suppose that the consensus secondary structure corresponds to the repeated structural pattern that displays the highest plausibility. We present several experiments concerning tRNA, fragments of 16S rRNA and 10Sa RNA (including pseudoknots); in each of them, we found the putative consensus secondary structure.     

MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs

The identification of cis-regulatory modules (CRMs) can greatly advance our understanding of eukaryotic regulatory mechanism. Current methods to predict CRMs from known motifs either depend on multiple alignments or can only deal with a small number of known motifs provided by users. These methods are problematic when binding sites are not well aligned in multiple alignments or when the number of input known motifs is large. We thus developed a new CRM identification method MOPAT (motif pair tree), which identifies CRMs through the identification of motif modules, groups of motifs co-occurring in multiple CRMs. It can identify 'orthologous' CRMs without multiple alignments. It can also find CRMs given a large number of known motifs. We have applied this method to mouse developmental genes, and have evaluated the predicted CRMs and motif modules by microarray expression data and known interacting motif pairs. We show that the expression profiles of the genes containing CRMs of the same motif module correlate significantly better than those of a random set of genes do. We also show that the known interacting motif pairs are significantly included in our predictions. Compared with several current methods, our method shows better performance in identifying meaningful CRMs.     

Food-web models predict species abundances in response to habitat change

Plant and animal population sizes inevitably change following habitat loss, but the mechanisms underlying these changes are poorly understood. We experimentally altered habitat volume and eliminated top trophic levels of the food web of invertebrates that inhabit rain-filled leaves of the carnivorous pitcher plant Sarracenia purpurea. Path models that incorporated food-web structure better predicted population sizes of food-web constituents than did simple keystone species models, models that included only autecological responses to habitat volume, or models including both food-web structure and habitat volume. These results provide the first experimental confirmation that trophic structure can determine species abundances in the face of habitat loss.     

The neighbor-joining method: a new method for reconstructing phylogenetic trees

A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.      

The evolution of function: a new method to assess the phylogenetic value of ribosomal sensitivity to antibiotics.

Thirty-five archaeal, bacterial and eukaryotic translational systems have been proved against forty different protein synthesis inhibitors with diverse domain and functional specificities. The inhibition curves generated in every ribosome-antibiotic combination had previously shown interesting similarities among organisms belonging to the same phylogenetic group. This opened the possibility of using such functional information for developing evolutionary studies. A new mathematical method based on the main data components analysis has been developed to extract most of the information contained in the inhibition curves. The phenograms obtained closely resemble those generated by the small ribosomal subunit rRNA sequence comparison and such functional clustering is also congruent when a particular subset of organisms and/or antibiotics is used. These results prove the phylogenetic value of our functional analysis and suggest that the ribosome represents an interesting intersection between genotypic and phenotypic (functional) information stored in organisms.     

In vitro-generated respiratory mucosa: a new tool to study inhalational anthrax

We generated a three-dimensional (3-D) model of human airway tissues in order to study initiation of inhalational form of anthrax infection. The system was designed to model the air-blood barrier of the respiratory tract represented by epithelial cells and macrophages. When grown on collagen/fibronectin gel support at an air-liquid interface, airway epithelial cells formed cell layers morphologically resembling those in vivo. These preformed epithelial cell cultures were further supplemented with monocytes/macrophages isolated from human blood. After 2-5 days of co-culture, monocytes differentiated into a phenotype of resident macrophages, which was evaluated by the expression of specific cell surface markers. This model allowed sorting out the role of each type of cell found at the air surface of the lung. The interdependence of macrophages and epithelial cells in the clearance of anthrax spores from airways and the capacity of the airway epithelial cells to protect from anthrax infection was demonstrated.     

The repeated replacement method: a pure lagrangian meshfree method for computational fluid dynamics

In this paper we describe the repeated replacement method (RRM), a new meshfree method for computational fluid dynamics (CFD). RRM simulates fluid flow by modeling compressible fluids' tendency to evolve towards a state of constant density, velocity, and pressure. To evolve a fluid flow simulation forward in time, RRM repeatedly "chops out" fluid from active areas and replaces it with new "flattened" fluid cells with the same mass, momentum, and energy. We call the new cells "flattened" because we give them constant density, velocity, and pressure, even though the chopped-out fluid may have had gradients in these primitive variables. RRM adaptively chooses the sizes and locations of the areas it chops out and replaces. It creates more and smaller new cells in areas of high gradient, and fewer and larger new cells in areas of lower gradient. This naturally leads to an adaptive level of accuracy, where more computational effort is spent on active areas of the fluid, and less effort is spent on inactive areas. We show that for common test problems, RRM produces results similar to other high-resolution CFD methods, while using a very different mathematical framework. RRM does not use Riemann solvers, flux or slope limiters, a mesh, or a stencil, and it operates in a purely Lagrangian mode. RRM also does not evaluate numerical derivatives, does not integrate equations of motion, and does not solve systems of equations.     

C5-blocking antibody reduces fluid requirements and improves responsiveness to fluid infusion in hemorrhagic shock managed with hypotensive resuscitation.

Hypotensive resuscitation strategies and inhibition of complement may both be of benefit in hemorrhagic shock. We asked if C5-blocking antibody (anti-C5) could diminish the amount of fluid required and improve responsiveness to resuscitation from hemorrhage. Awake, male Sprague-Dawley rats underwent controlled hemorrhage followed by prolonged (3 h) hypotensive resuscitation with lactated Ringer's or Hextend, with or without anti-C5. Anti-C5 treatment led to an estimated 62.3 and 58.5% reduction in the volume of Hextend and lactated Ringer's, respectively. In the subgroup of animals with a positive mean arterial pressure (MAP) response to fluid infusion following prolonged hypotension, anti-C5 treatment led to an estimated 4.7- and 4.1-fold increase in mean arterial pressure response per unit Hextend and lactated Ringer's infused, respectively. We observed no significant postresuscitation metabolic differences between the anti-C5 groups and controls. Whether anti-C5 could serve as a volume-sparing adjunct that improves responsiveness to fluid administration in humans deserves further study.