Estimation of FPAR and FPAR profile for maize canopies using airborne LiDAR

FPAR (fraction of photosynthetically active radiation) and FPAR profile (vertical FPAR distribution) are important parameters for characterizing the vegetation growth status and studying global climate change. Few studies have been carried out to estimate FPAR and FPAR profile using waveform LiDAR data. This research explored the potential of airborne small-footprint full-waveform LiDAR in the estimation of FPAR and FPAR profile of the maize canopy in Huailai County of Hebei Province, China. First, the maize growing area was identified by a simple decision tree model. Second, raw waveform data were processed to extract LiDAR-derived energy ratio and energy ratio profile. Third, FPAR and FPAR profile were estimated from LiDAR-derived metrics. Finally, we analyzed the FPAR and FPAR profile estimation results and assessed the model validity using the leave-one-out cross-validation (LOOCV) method. The comparative analyses found that the LiDAR-derived energy ratio profile and field-measured FPAR profile had the same trend and similar change rate for all maize layers. The accuracy assessments indicated that the FPAR and FPAR profile were estimated well by the LiDAR waveform data, with the high R² (0.90 for the whole canopy, and 0.95, 0.90, 0.93, 0.92, and 0.97 for layers 1–5) and low RMSEs (0.042 for the whole canopy, and 0.033, 0.035, 0.039, 0.043, and 0.044 for layers 1–5). The spatial distribution map of FPAR was produced to describe the maize growth status of the whole study area, and the map showed that the FPAR distributed relatively uniformly. This study suggested that airborne small-footprint full-waveform LiDAR was useful in accurately measuring FPAR and FPAR profile of the maize canopy and in effectively mapping the maize FPAR spatial distribution.     

Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities

The profile method, for detecting distantly related proteins by sequence comparison, has been extended to incorporate secondary structure information from known X-ray structures. The sequence of a known structure is aligned to sequences of other members of a given folding class. From the known structure, the secondary structure (alpha-helix, beta-strand or "other") is assigned to each position of the aligned sequences. As in the standard profile method, a position-dependent scoring table, termed a profile, is calculated from the aligned sequences. However, rather than using the standard Dayhoff mutation table in calculating the profile, we use distinct amino acid mutation tables for residues in alpha-helices, beta-strands or other secondary structures to calculate the profile. In addition, we also distinguish between internal and external residues. With this new secondary structure-based profile method, we created a profile for eight-stranded, antiparallel beta barrels of the insecticyanin folding class. It is based on the sequences of retinol-binding protein, insecticyanin and beta-lactoglobulin. Scanning the sequence database with this profile, it was possible to detect the sequence of avidin. The structure of streptavidin is known, and it appears to be distantly related to the antiparallel beta barrels. Also detected is the sequence of complement component C8, which we therefore predict to be a member of this folding class.     

Effects of pH profiles on nisin production in biofilm reactor

Apart from its widely accepted commercial applications as a food preservative, nisin emerges as a promising alternative in medical applications for bacterial infection in both humans and livestock. Improving nisin production through optimization of fermentation parameters would make nisin more cost-effective for various applications. Since nisin production by Lactococcus lactis NIZO 22186 was highly influenced by the pH profile employed during fermentation, three different pH profiles were evaluated in this study: (1) a constant pH profile at 6.8 (profile 1), (2) a constant pH profile with autoacidification at 4 h (profile 2), and (3) a stepwise pH profile with pH adjustment every 2 h (profile 3). The results demonstrated that the low-pH stress exerted during the first 4 h of fermentation in profile 3 detrimentally affected nisin production, resulting in a very low maximum nisin concentration (593 IU ml⁻¹). On the other hand, growth and lactic acid production were only slightly delayed, indicating that the loss in nisin production was not a result of lower growth or shifting of metabolic activity toward lactic acid production. Profile 2, in which pH was allowed to drop freely via autoacidification after 4 h of fermentation, was found to yield almost 1.9 times higher nisin (3,553 IU ml⁻¹) than profile 1 (1,898 IU ml⁻¹), possibly as a result of less adsorption of nisin onto producer cells. Therefore, a combination of constant pH and autoacidification period (profile 2) was recommended as the pH profile during nisin production in a biofilm reactor.     

系统发育谱构建方法研究

随着后基因组时代的到来,系统发育谱方法作为一种非同源性的功能注释方法,已经被成功的应用到基因组功能预测、蛋白质相互作用预测等一些重要领域的研究中去。本文阐述了系统发育谱法的基本原理,详细地介绍了现有的几种系统发育谱的构建方法,并提出了利用ortholog来构建基因的系统发育谱的思想。     

Location of high-affinity metal binding sites in the profile structure of the Ca+2-ATPase in the sarcoplasmic reticulum by resonance x-ray diffraction.

Resonance x-ray diffraction measurements on the lamellar diffraction from oriented multilayers of isolated sarcoplasmic reticulum (SR) membranes containing a small concentration of lanthanide (III) ions (lanthanide/protein molar ratio approximately 4) have allowed us to calculate both the electron density profile of the SR membrane and the separate electron density profile of the resonant lanthanide atoms bound to the membrane to a relatively low spatial resolution of approximately 40 A. Analysis of the membrane electron density profile and modeling of the separate low resolution lanthanide atom profile, using step-function electron density models based on the assumption that metal binding sites in the membrane profile are discrete and localized, resulted in the identification of a minimum of three such binding sites in the membrane profile. Two of these sites are low-affinity, low-occupancy sites identified with the two phospholipid polar headgroup regions of the lipid bilayer within the membrane profile. Up to 20% of the total lanthanide (III) ions bind to these low-affinity sites. The third site has relatively high affinity for lanthanide ion binding; its Ka is roughly an order of magnitude larger than that for the lower affinity polar headgroup sites. Approximately 80% of the total lanthanide ions present in the sample are bound to this high-affinity site, which is located in the "stalk" portion of the "headpiece" within the profile structure of the Ca+2 ATPase protein, approximately 12 A outside of the phospholipid polar headgroups on the extravesicular side of the membrane profile. Based on the nature of our results and on previous reports in the literature concerning the ability of lanthanide (III) ions to function as Ca+2 analogues for the Ca+2 ATPase we suggest that we have located a high-affinity metal binding site in the membrane profile which is involved in the active transport of Ca+2 ions across the SR membrane by the Ca+2 ATPase.     

Effects of fed-batch fermentation and pH profiles on nisin production in suspended-cell and biofilm reactors

A biofilm reactor not only shortens the lag phase of nisin production, but also enhances nisin production when combined with an appropriate pH profile. Due to the substrate inhibition that takes place at high levels of carbon source, fed-batch fermentation was proposed as a better alternative for nisin production. In this study, the combined effects of fed-batch fermentation and various pH profiles on nisin production in a biofilm reactor were evaluated. The tested pH profiles include 1) a constant pH profile at 6.8 (profile 1), 2) a constant pH profile with an autoacidification after 4 h (profile 2), and 3) a step-wise pH profile with pH adjustment every 2 h (profile 3). When profile 1 was applied, fed-batch fermentation enhanced nisin production for both suspended-cell (4,188 IU ml⁻¹) and biofilm (4,314 IU ml⁻¹) reactors, yielded 1.8- and 2.3-fold higher nisin titer than their respective batch fermentation. On the other hand, pH profiles that include periods of autoacidification (profiles 2 and 3) resulted in a significantly lower nisin production in fed-batch fermentation (2,494 and 1,861 IU ml⁻¹ for biofilm reactor using profile 2 and 3, respectively) due to toxicity of excess lactic acid produced during the fermentation. Overall, this study suggested that fed-batch fermentation can be successfully used to enhance nisin production for both suspended-cell and biofilm reactors.     

Role of sterol type on lateral pressure profiles of lipid membranes affecting membrane protein functionality: Comparison between cholesterol, desmosterol, 7-dehydrocholesterol and ketosterol

Lateral pressure profiles have been suggested to play a significant role in many cellular membrane processes by affecting, for example, the activation of membrane proteins through changes in their conformational state. This may be the case if the lateral pressure profile is altered due to changes in molecular composition surrounding the protein. In this work, we elucidate the effect of varying sterol type on the lateral pressure profile, an issue of topical interest due to lipid rafts and their putative role for membrane protein functionality. We find that the lateral pressure profile is altered when cholesterol is replaced by either desmosterol, 7-dehydrocholesterol, or ketosterol. The observed changes in the lateral pressure profile are notable and important since desmosterol and 7-dehydrocholesterol are the immediate precursors of cholesterol along its biosynthetic pathway. The results show that the lateral pressure profile and the resulting elastic behavior of lipid membranes are sensitive to the sterol type, and support a mechanism where changes in protein conformational state are facilitated by changes in the lateral pressure profile. From a structural point of view, the results provide compelling evidence that despite seemingly minor differences, sterols are characterized by structural specificity.     

Computational investigation of pressure profiles in lipid bilayers with embedded proteins

The distribution of surface tension within a lipid bilayer, also referred to as the lateral pressure profile, has been the subject of theoretical scrutiny recently due to its potential to radically alter the function of biomedically important membrane proteins. Experimental measurements of the pressure profile are still hard to come by, leaving first-principles all-atom calculations of the profile as an important investigative tool. We describe and validate an efficient implementation of pressure profile calculations in the molecular dynamics package NAMD, capable of distinguishing between internal, bonded and nonbonded contributions as well as those of selected atom groups. The new implementation can also be used in conjunction with Ewald summation for long-range electrostatics, improving the accuracy and reproducibility of the calculated profiles. We then describe results of the calculation of a pressure profile for a simple protein–lipid system consisting of melittin embedded in a DMPC bilayer. While the lateral pressure in the protein–lipid system is nearly the same as that of the bilayer alone, partitioning of the lateral pressure by atom type revealed substantial perturbation of the pressure profile and surface tension in an asymmetric manner.     

A numerical calculation of flow in a curved tube model of the left main coronary artery

The flow pattern in the left main coronary artery has been calculated using an idealized geometry and by numerically solving the full Navier-Stokes equations for a Newtonian fluid. Two different forms for the entrance velocity profile were used, one a time-varying, flat profile and the other a time-varying, less flat velocity profile. The results obtained demonstrate the presence of secondary motions for conditions simulating flow in the left main coronary artery, with maximum secondary flow velocities being on the order of three to four percent of the maximum axial velocity. This secondary flow phenomenon has an important influence on the wall shear stress distribution, in spite of the fact that there is virtually no alteration in the axial velocity profile. The maximum ratio of the outer wall shear stress to that on the inner wall is 1.4 at a Reynolds number of Re = 270, and it increases with increasing Reynolds number, reaching a value of 1.7 at Re = 810. Although there are significant differences in the results in the immediate vicinity of the inlet for the two different forms of the entrance velocity profile used, this difference does not persist far into the tube. Independent of the choice of the entrance velocity profile, it appears that there will be significant secondary flow effects on the wall shear stress.     

Experimental Study of the Flexural and Compression Performance of an Innovative Pultruded Glass-Fiber-Reinforced Polymer-Wood Composite Profile

The plate of a pultruded fiber-reinforced polymer or fiber-reinforced plastic (FRP) profile produced via a pultrusion process is likely to undergo local buckling and cracking along the fiber direction under an external load. In this study, we constructed a pultruded glass-fiber-reinforced polymer-light wood composite (PGWC) profile to explore its mechanical performance. A rectangular cross-sectional PGWC profile was fabricated with a paulownia wood core, alkali-free glass fiber filaments, and unsaturated phthalate resin. Three-point bending and short column axial compression tests were conducted. Then, the stress calculation for the PGWC profile in the bending and axial compression tests was performed using the Timoshenko beam theory and the composite component analysis method to derive the flexural and axial compression rigidity of the profile during the elastic stress stage. The flexural capacity for this type of PGWC profile is 3.3-fold the sum of the flexural capacities of the wood core and the glass-fiber-reinforced polymer (GFRP) shell. The equivalent flexural rigidity is 1.5-fold the summed flexural rigidity of the wood core and GFRP shell. The maximum axial compressive bearing capacity for this type of PGWC profile can reach 1.79-fold the sum of those of the wood core and GFRP shell, and its elastic flexural rigidity is 1.2-fold the sum of their rigidities. These results indicate that in PGWC profiles, GFRP and wood materials have a positive combined effect. This study produced a pultruded composite material product with excellent mechanical performance for application in structures that require a large bearing capacity.     

Diversity within Serogroups of Rhizobium leguminosarum biovar viceae in the Palouse Region of Eastern Washington as Indicated by Plasmid Profiles, Intrinsic Antibiotic Resistance, and Topography

Serology, plasmid profiles, and intrinsic antibiotic resistance (IAR) were determined for 192 isolates of Rhizobium leguminosarum biovar viceae from nodules of peas (Pisum sativum L.) grown on the south slope and bottomland topographic positions in eastern Washington State. A total of 3 serogroups and 18 plasmid profile groups were identified. Nearly all isolates within each plasmid profile group were specific for one of the three serogroups. Cluster analysis of IAR data showed that individual clusters were dominated by one serogroup and by one or two plasmid profile groups. Plasmid profile analysis and IAR analysis grouped 72% of the isolates similarly. Most plasmid profile groups and several IAR clusters favored either the south slope or the bottomland topographic position. These findings show that certain intraserogroup strains possess a greater competitiveness for nodulation and/or possess a greater ability to survive in adjacent soil environments.     

Fourier harmonic analysis of the sagittal profile of the Plesianthropus transvaalensis (STS5) skull

An analytical morphometrical investigation of fronto facial profile of Plesianthropus transvaalensis was carried out by means of Fourier spectral series. Amplitude of contributors was evaluated in comparison with harmonic sets of a modern skull and two "mosaics" obtained by a convenient merging of segments of modern and hominid skull profiles. Patterns are distinctly different in Plesianthropus and modern profile because amplitude of second harmonic is greater than first in the former and viceversa in the latter; moreover while in Plesianthropus first and second harmonic give the same phase, it does not occur for modern skull. Fourier series of "mosaic" obtained by frontal profile of Plesianthropus and facial profile of modern resembles the set of modern skull while "mosaic" of modern frontal profile and hominid facial one resembles closely pattern of Plesianthropus.     

弥漫大B 淋巴瘤12 号染色体基因表达的研究

目的:研究弥漫大B淋巴瘤(Diffuse Large B-Cell Lymphoma,DLBCL)12号染色体基因表达情况。方法:收取临床DLBCL病人淋巴结标本液氮速冻,快速冷冻切片,采用激光显微切割技术分离单纯淋巴瘤细胞,提取淋巴瘤细胞中的mRNA与表达谱芯片杂交,通过信号扫描、处理后获得表达基因杂交信号强度。每基因设11-20对探针。杂交信号与错配探针对比,扣除背景值后,使用Wilcoxon符号秩和检验选取与错配杂交信号有显著差异的基因作为分析结果(P=0.05)。随机选取两个检测到的基因,使用PCR方法检验基因芯片结果的可靠性。结果:成功地从快速冷冻保存的DLBCL标本中提取了RNA。使用表达谱芯片进行研究,发现了共164条12号染色体编码的基因在淋巴瘤细胞中表达。并根据胞内定位,基因功能和基因所属的代谢通路三种分类方法对所得基因进行分类分析。基因表达密度分析显示12号染色体上的基因表达情况与编码基因分布情况比较一致。结论:使用表达谱芯片研究了12号染色体上的基因表达情况,为研究DLBCL提供了依据。     

Profile matching and profile subtraction: application of computer-based image analysis system for two-dimensional electrophoresis gels

The microcomputer-based image analysis system IB-1000 (developed by Indiana Biotech, Highland, IN) for two-dimensional electrophoresis gels has been described previously (9). It allows the user to compare protein spots between two profiles and identify those spots that are commonly shared in both profiles. This report describes two applications of the system's global comparison routine-profile matching and profile subtraction. This application is able to subtract commonly shared spots from one profile, creating a new profile made up by the unmatched spots in the other profile. These applications can be employed in a large variety of research projects.     

Effect of inlet velocity profiles on patient-specific computational fluid dynamics simulations of the carotid bifurcation

Patient-specific computational fluid dynamics (CFD) is a powerful tool for researching the role of blood flow in disease processes. Modern clinical imaging technology such as MRI and CT can provide high resolution information about vessel geometry, but in many situations, patient-specific inlet velocity information is not available. In these situations, a simplified velocity profile must be selected. We studied how idealized inlet velocity profiles (blunt, parabolic, and Womersley flow) affect patient-specific CFD results when compared to simulations employing a "reference standard" of the patient's own measured velocity profile in the carotid bifurcation. To place the magnitude of these effects in context, we also investigated the effect of geometry and the use of subject-specific flow waveform on the CFD results. We quantified these differences by examining the pointwise percent error of the mean wall shear stress (WSS) and the oscillatory shear index (OSI) and by computing the intra-class correlation coefficient (ICC) between axial profiles of the mean WSS and OSI in the internal carotid artery bulb. The parabolic inlet velocity profile produced the most similar mean WSS and OSI to simulations employing the real patient-specific inlet velocity profile. However, anatomic variation in vessel geometry and the use of a nonpatient-specific flow waveform both affected the WSS and OSI results more than did the choice of inlet velocity profile. Although careful selection of boundary conditions is essential for all CFD analysis, accurate patient-specific geometry reconstruction and measurement of vessel flow rate waveform are more important than the choice of velocity profile. A parabolic velocity profile provided results most similar to the patient-specific velocity profile.     

Optimization of feeding profile for a fed-batch bioreactor by an evolutionary algorithm

The optimal feeding profile of a fed batch process was designed by means of an evolutionary algorithm. The algorithm chromosomes include the real-valued parameters of a profile function, defined by previous knowledge. Each chromosome is composed of the parameters that define the feeding profile: the feed rates, the singular arc parameters and the switching times between the profile states. The feed profile design was tested on a fed-batch process simulation. The accepted profiles were smooth and similar to those derived analytically in other studies. Two selection functions, roulette wheel and geometric ranking, were compared. In order to overcome the problem of model mismatches, a novel optimization scheme was carried out. During its operation the process was sampled, the model was updated and the optimization procedure was applied. The on-line optimization showed improvement in the objective function for relatively low sample times. Choosing the sampling frequencies depends on the process dynamics and the time required for the measurements and optimization. Further study on experiments of fed-batch process demonstrated the use of complex, non-differentiable model and produced improved process performances using the optimal feeding profile.     

Gene profiling for determining pluripotent genes in a time course microarray experiment

In microarray experiments, it is often of interest to identifygenes which have a prespecified gene expression profile withrespect to time. Methods available in the literature are, however,typically not stringent enough in identifying such genes, particularlywhen the profile requires equivalence of gene expression levelsat certain time points. In this paper, the authors introducea new methodology, called gene profiling, that uses simultaneousdifferential and equivalent gene expression level testing torank genes according to a prespecified gene expression profile.Gene profiling treats the vector of true gene expression levelsas a linear combination of appropriate vectors, for example,vectors that give the required criteria for the profile. Thisgene profile model is fitted to the data, and the resultingparameter estimates are summarized in a single test statisticthat is then used to rank the genes. The theoretical underpinningsof gene profiling (equivalence testing, intersection–uniontests) are discussed in this paper, and the gene profiling methodologyis applied to our motivating stem-cell experiment.