Multiple discriminant function analysis of sex and race in the postcranial skeleton

Terry Collection femora and innominates of 260 American Whites and Blacks (65 males and 65 females of each race) were analyzed by multiple discriminant function analysis. A stepwise procedure produced three optimal discriminant functions using 15 of our 32 measurements. These functions correctly identified 95% of the sample. The first two-one for sex and one for race-are statistically and biologically significant and form the basis of our analysis. The sexing function manifested both size and shape elements. Prominent among the former was joint size--acetabular diameter and epicondylar diameter of the femur. The shape elements included form of the greater sciatic notch and of the inferomedial aspect of the pubic body. The racing function highlighted a pattern of greater innominate dimensions, exclusive of the acetabular joint, in Whites. This was in contrast to the greater length of the Black femur. Overall, the function seems to express the established differences between the races in the ratio of lower limb length to torso length. While these functions have been applied successfully to forensic cases with confirmed identifications, questions regarding the breadth of applicability of discriminant functions make it desirable to validate our results on new material from the Terry and other collections.     

一个新的核酸序列比对算法及其在序列全局比对中的应用

目前在序列比对中所广泛使用的动态规划算法,虽然能达到最优比对结果,但却由于具有高计算复杂度O(N_2)而极大地降低了计算效率。将多阶段动态规划决策算法用于两两序列比对并用Visual BASIC编程实现,结果发现该新算法在将计算复杂度减小到O(N)的同时,也能够获得较为理想的计算精度,预期将在序列全局比对中起重要作用。     

Feature extraction in the analysis of proteomic mass spectra

Feature extraction or biomarker selection is a critical step in disease diagnosis and knowledge discovery based on protein MS. Many studies have discussed the classification methods applied in proteomics; however, few could be found to address feature extraction in detail. In this paper, we developed a systematic approach for the extraction of mass spectrum peak apex and peak area with special emphasis on noise filtration and peak calibration. Application to a head and neck cancer data generated at the Eastern Virginia Medical School [Wadsworth, J. T., Somers, K. D., Cazares, L. H., Malik, G. et al.., Clin. Cancer Res. 2004, 10, 1625-1632] revealed that the new feature extraction method would yield consistent and highly discriminatory biomarkers.     

Multi-conformational peptide dynamics derived from NMR data: A new search algorithm and its application to antamanide

Summary A search algorithm, called MEDUSA, is presented which allows the determination of multiple conformations of biomolecules in solution with exchange rate constants typically between 10³ and 10⁷ s^–1 on the basis of experimental high-resolution NMR data. Multiples of structures are generated which are consistent as ensembles with NMR cross-relaxation rates (NOESY, ROESY), scalar J-coupling constants, and T_1p measurements. The algorithm is applied to the cyclic decapeptide antamanide dissolved in chloroform. The characteristic radio-frequency field dependence of the T_1p relaxation rates found for the NH protons of Val¹ and Phe⁶ can be explained by a dynamical exchange between two structures.     

A new algorithm for 3D registration and its application in self-monitoring and early detection of lymphedema

Early detection and management of lymphedema (LE) can significantly reduce the potential of new symptoms and complications. In fact, effective diagnostic of LE can potentially affect the lives in the U.S. of nearly 500 000 current LE patients and over 2.4 million breast cancer survivors who are at-risk for developing this disease at some point in their lives. However, many cancer patients fail to seek medical assistance at the first sign of the disease in part due to the additional burden that constant monitoring imposes on patients. In that sense, a self-monitoring system could represent a major improvement in health-care management and delivery.The main challenges in self monitoring limb volume are in the design of a system that is at the same time inexpensive, easy to use, and accurate, despite being operated by a person without any training. In this paper, we present such a system. The proposed framework relies on off-the-shelf video gaming devices – the Kinect infrared device with a set of inertial sensors. In order to achieve high accuracy despite the typical low-texture and smoothness of the human skin, a new algorithm for 3D registration of clouds of points – Iterative Clustered Closest Points (ICCP) – is also proposed. The final result is a device that can be operated in the comfort of the patient's homes – i.e. it can be operated by professionals as well as non-professionals.In order to validate the system, we first tested its individual parts, more specifically the proposed ICCP algorithm for 3D registration and reconstruction of challenging objects. Then, we tested the complete system for the target application of limb-volume measurement by comparing our system against the gold standards: water displacement and perometer.     

Robust discriminant analysis and its application to identify protein coding regions of rice genes

Identification of protein coding regions is fundamentally a statistical pattern recognition problem. Discriminant analysis is a statistical technique for classifying a set of observations into predefined classes and it is useful to solve such problems. It is well known that outliers are present in virtually every data set in any application domain, and classical discriminant analysis methods (including linear discriminant analysis (LDA) and quadratic discriminant analysis (QDA)) do not work well if the data set has outliers. In order to overcome the difficulty, the robust statistical method is used in this paper. We choose four different coding characters as discriminant variables and an approving result is presented by the method of robust discriminant analysis.     

Sulfonation of polyvinylidene difluoride resin and its application in extraction of restriction enzymes from DNA digestion solutions

Sulfonation of polyvinylidene difluoride (PVDF) resin was achieved by incubation of the resin with sulfuric acid at a moderately high temperature. The sulfonated PVDF (SPVDF) resin was studied for its ability to extract restriction enzymes from DNA digestion solutions. The SPVDF resin was effective in adsorbing restriction enzymes such as EcoRI and BamHI and the extraction procedure was easy and simple to perform. The adsorption depended upon the amount of the resin added. We found that 1 mg of the SPVDF resin could completely remove all restriction enzyme activity routinely used in DNA digestion within 2 min after its addition. Treatment of a digestion solution with the SPVDF resin did not change the reaction solution and the same digestion buffer could be used for another digestion of the same DNA with other enzymes. We also found that, in comparison with normal PVDF, the SPVDF resin adsorbed less DNA, resulting in less loss of DNA in the extraction step. The potential application of the SPVDF resin in other procedures of molecular cloning and enzyme purification is discussed.     

A new approach to the measurement of phospholipase A2 in tissue homogenates and its application to human skin

We describe a new approach to the quantification of tissue phospholipase A2 based on the observation that the Vmax is increased by several orders of magnitude in the presence of high concentrations of dimethyl sulphoxide. The enzyme from human skin showed optimal activity at 30% dimethyl sulphoxide and pH 6-7.5, and had an absolute dependence on Ca2+ (apparent Km = 1.4 mmol/l). The relationship between reaction velocity and substrate concentration did not follow Michaelis-Menten kinetics. The enzyme was inhibited by p-bromophenacyl bromide, half-maximal inhibition occurring at 2.4 mumol/l. Surprisingly, assay of specimens of various human tissues indicated that, with the exception of pancreas, skin contained higher levels of phospholipase A2 activity than any other tissue investigated. Equally surprising was that primate skin (in particular human) seems considerably more active than that of other mammals. Speculatively, these findings may be related to the high levels of free fatty acids occurring on the skin surface.     

A new type porous carrier and its application to culture of suspension cells

A new type porous carrier was fabricated from a mixture of sodium alginate, bovine serum albumin and sodium bicarbonate. The porous space of the carrier is an assembly of void spaces. The carrier was successfully applied to the cultivation of suspension animal cells. In the culture, while both cells and carriers were held in suspension, the cells were entrapped hydrodynamically into the void spaces in the carriers. A culture of hybridoma cells using this carrier resulted in a cell density up to 5.7×10⁷ cells per ml-carrier.     

Alkaline butanol extraction of bile salt and steroid sulfate esters: application to the assay of sulfotransferases

A butan-1-ol solvent-extraction procedure has been evaluated for the assay of 3'-phosphoadenosine-5'-phosphosulfate:sulfotransferase activity with various bile salt and steroid substrates. Although butanol extracted the sulfate esters of steroids and bile salts from aqueous solution at neutral pH, extraction at basic pH gave optimum recovery which was independent of protein in the sample. Greater than 99.9% of unreacted 3'-phosphoadenosine-5'-phospho[35S]sulfate remained in the aqueous phase. The data for sulfotransferase activities obtained with this solvent-extraction assay were not significantly different from those obtained with a standard thin-layer chromatography method. Solvent extraction has enabled multiple, rapid assays of several steroid and bile salt sulfotransferases during chromatographic purification of these enzymes from tissue fractions.     

A new method of quantitative affinity chromatography and its application to the study of myosin.

A new method of quantifying the interactions between two or three components of an interacting system, one of which is insoluble, is described. The method differs from those previously applied to affinity chromatography systems in that it does not require that elution volumes be measured, but is instead dependent on measurements of the quantity of affinity-bound material. Theoretical expressions are derived for systems in which the acceptor is immobilized. Examples presented to illustrate the validity of the theory are of the latter type and are from studies on the myosin-adenosine nucleotide-PPi system. With Sepharose-myosin columns (myosin covalently coupled to CNBr-activated Sepharose) a dissociation constant of 1.8 muM for ATP4- was found. Data were also obtained under conditions that closely approximate to those found in vivo, i.e. on columns packed with a slurry of Sephadex G-50 and precipitated myosin filaments formed at low ionic strength. The binding of MgATP2-, MgADP-, ATP4- and MgPPi2- to "filamentous" myosin in both two- (myosin and nucleotide) and three- (myosin, nucleotide and PPi) component systems at different temperatures was studied and the dissociation constants obtained agreed well with previously published values. Except for the binding of ATP4- to filamentous myosin at 4 degrees when 85% of the protein was interacting with the nucleotide, much lower values for the number of available sites occupied by the nucleotides were as a routine found in this system. Although this apparent discrepancy is difficult to explain, it is not an anomaly of the theoretical approach and may reflect the present state of understanding of the myosin system.     

A new derivative of vitamin C and its application to the synthesis of labelled ascorbic acid

1. The preparation of a mono-O-cyclohexylidene derivative of l-ascorbic acid is described. 2. The new compound is shielded by the cyclohexanone group at C-5 and C-6 of the ascorbic acid molecule, while the double bond between C-2 and C-3 is kept intact. 3. The double bond of the new derivative is more resistant to oxidation than its parent compound. 4. Ascorbic acid is easily regenerated by mild acid hydrolysis. 5. The new derivative facilitates the synthesis of (14)C-labelled vitamin C.     

Sex determination using discriminant function analysis in Indigenous (Kurubas) children and adolescents of Coorg,Karnataka, India: A lateral cephalometric study

Aim: To test the validity of sex discrimination using lateral cephalometric radiograph and discriminant function analysis in Indigenous (Kuruba) children and adolescents of Coorg, Karnataka, India. Methods and materials: Six hundred and sixteen lateral cephalograms of 380 male and 236 females of age ranging from 6.5 to 18 years of Indigenous population of Coorg, Karnataka, India called Kurubas having a normal occlusion were included in the study. Lateral cephalograms were obtained in a standard position with teeth in centric occlusion and lips relaxed. Each radiograph was traced and cephalometric landmarks were measured using digital calliper. Calculations of 24 cephalometric measurements were performed. Results: Males exhibited significantly greater mean angular and linear cephalometric measurements as compared to females (p < 0.05) (Table 5). Also, significant differences (p < 0.05) were observed in all the variables according to age (Table 6). Out of 24 variables, only ULTc predicts the gender. The reliability of the derived discriminant function was assessed among study subjects; 100% of males and females were recognized correctly. Conclusion: The final outcome of this study validates the existence of sexual dimorphism in the skeleton as early as 6.5 years of age. There is a need for further research to determine other landmarks that can help in sex determination and norms for Indigenous (Kuruba) population and also other Indigenous population of Coorg, Karnataka, India.     

A model-based parallel origin and orientation refinement algorithm for cryoTEM and its application to the study of virus structures

We present a model-based parallel algorithm for origin and orientation refinement for 3D reconstruction in cryoTEM. The algorithm is based upon the Projection Theorem of the Fourier Transform. Rather than projecting the current 3D model and searching for the best match between an experimental view and the calculated projections, the algorithm computes the Discrete Fourier Transform (DFT) of each projection and searches for the central section ("cut") of the 3D DFT that best matches the DFT of the projection. Factors that affect the efficiency of a parallel program are first reviewed and then the performance and limitations of the proposed algorithm are discussed. The parallel program that implements this algorithm, called PO(2)R, has been used for the refinement of several virus structures, including those of the 500 Angstroms diameter dengue virus (to 9.5 Angstroms resolution), the 850 Angstroms mammalian reovirus (to better than 7A), and the 1800 Angstroms paramecium bursaria chlorella virus (to 15 Angstroms).     

Adaptations to new environments in humans: the role of subtle allele frequency shifts

Humans show tremendous phenotypic diversity across geographically distributed populations, and much of this diversity undoubtedly results from genetic adaptations to different environmental pressures. The availability of genome-wide genetic variation data from densely sampled populations offers unprecedented opportunities for identifying the loci responsible for these adaptations and for elucidating the genetic architecture of human adaptive traits. Several approaches have been used to detect signals of selection in human populations, and these approaches differ in the assumptions they make about the underlying mode of selection. We contrast the results of approaches based on haplotype structure and differentiation of allele frequencies to those from a method for identifying single nucleotide polymorphisms strongly correlated with environmental variables. Although the first group of approaches tends to detect new beneficial alleles that were driven to high frequencies by selection, the environmental correlation approach has power to identify alleles that experienced small shifts in frequency owing to selection. We suggest that the first group of approaches tends to identify only variants with relatively strong phenotypic effects, whereas the environmental correlation methods can detect variants that make smaller contributions to an adaptive trait.