'98 Escherichia coli SWISS-2DPAGE database update

The combination of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), computer image analysis and several protein identification techniques allowed the Escherichia coli SWISS-2DPAGE database to be established. This is part of the ExPASy molecular biology server accessible through the WWW at the URL address http://www.expasy.ch/ch2d/ch2d-top.html . Here we report recent progress in the development of the E. coli SWISS-2DPAGE database. Proteins were separated with immobilized pH gradients in the first dimension and sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the second dimension. To increase the resolution of the separation and thus the number of identified proteins, a variety of wide and narrow range immobilized pH gradients were used in the first dimension. Micropreparative gels were electroblotted onto polyvinylidene difluoride membranes and spots were visualized by amido black staining. Protein identification techniques such as amino acid composition analysis, gel comparison and microsequencing were used, as well as a recently described Edman "sequence tag" approach. Some of the above identification techniques were coupled with database searching tools. Currently 231 polypeptides are identified on the E. coli SWISS-2DPAGE map: 64 have been identified by N-terminal microsequencing, 39 by amino acid composition, and 82 by sequence tag. Of 153 proteins putatively identified by gel comparison, 65 have been confirmed. Many proteins have been identified using more than one technique. Faster progress in the E. coli proteome project will now be possible with advances in biochemical methodology and with the completion of the entire E. coli genome.     

Addressing the tertiary structure of human parathyroid hormone-(1-34)

Parathyroid hormone (PTH) regulates mineral metabolism and bone turnover by activating specific receptors located on osteoblastic and renal tubular cells and is fully functional as the N-terminal 1-34 fragment, PTH-(1-34). Previously, a "U-shaped" conformation with N- and C-terminal helices brought in close proximity by a turn has been postulated. The general acceptance of this hypothesis, despite limited experimental evidence, has altered the direction of the design of PTH-analogs. Examining the structure of human PTH-(1-34) under conditions that encompass the different environments the hormone may experience in the approach to and interaction with the G-protein-coupled receptor (including benign aqueous and saline solutions and in the presence of dodecylphosphocholine), we observe no evidence for a U-shape conformation or any tertiary structure. Instead, the N- and C-terminal helical domains, which vary in length and stability depending on the conditions, are separated by a highly flexible region of undefined conformation. These observations are in complete accord with recent conformational studies of PTH-related protein analogs containing lactams (Mierke, D. F., Maretto, S., Schievano, E. , DeLuca, D., Bisello, A., Mammi, S., Rosenblatt, M., Peggion, E., and Chorev, M. (1997) Biochemistry 36, 10372-10383) or a model amphiphilic alpha-helix (Pellegrini, M., Bisello, A., Rosenblatt, M., Chorev, M., and Mierke, D. F. (1997) J. Med. Chem. 40, 3025-3031). Reliable structural data from different environmental conditions are absolutely requisite for the next step in the design of non-peptide PTH analogs.     

Accuracy and efficacy of chest radiography in the intensive care unit

264 patients with cancer of larynx, 21 female and 234 male, had a testosterone and sex hormone binding globulin (SHBG) before the treatment in serum estimated. Because of dependence of levels of hormones the group of patients was divided into three following groups: "lower than standard", "standard", "higher than standard". The correlation between these groups and sex, age, localization of tumor, organs' advances, stage of morphological malignancy and type of cancer was reported. Anomalous values of testosterone were in male group more frequently reported. Anomalous values of SHBG were similar in male and female groups, but in the female group there was a significant majority of "lower than standard" values reported. The majority of abnormal values of testosterone and SHBG was described in groups of age higher than 50 years. There were no differences in testosterone and SHBG levels in different localization of tumors in larynx. In advanced stage T3 and T4 there were more frequent lower mean values of testosterone levels and higher values of SHBG levels in comparison to T2 stages. In tumors in G1 and G2 stages of histological malignancy higher levels of SHBG and higher mean levels of testosterone. The tumors in stage G3 the hormone levels were lowers were observed. The levels of SHBG in groups of carcinoma planoepitheliale keratodes were in 66% higher than in a group of carcinoma planoepitheliale akeratodes but in both groups the levels of testosterone were nearing the same. In group of patients with larynx cancer the negative correlation between the levels of testosterone and SHBG was not observed. Higher SHBG levels were not always accompanied by lower testosterone levels.     

Tracking in a Dense Crowd Using Multiple Cameras

Tracking people in a dense crowd is a challenging problem for a single camera tracker due to occlusions and extensive motion that make human segmentation difficult. In this paper we suggest a method for simultaneously tracking all the people in a densely crowded scene using a set of cameras with overlapping fields of view. To overcome occlusions, the cameras are placed at a high elevation and only people’s heads are tracked. Head detection is still difficult since each foreground region may consist of multiple subjects. By combining data from several views, height information is extracted and used for head segmentation. The head tops, which are regarded as 2D patches at various heights, are detected by applying intensity correlation to aligned frames from the different cameras. The detected head tops are then tracked using common assumptions on motion direction and velocity. The method was tested on sequences in indoor and outdoor environments under challenging illumination conditions. It was successful in tracking up to 21 people walking in a small area (2.5 people per m²), in spite of severe and persistent occlusions.     

3D Shape Recovery of Smooth Surfaces: Dropping the Fixed-Viewpoint Assumption

We present a new method for recovering the 3D shape of a featureless smooth surface from three or more calibrated images illuminated by different light sources (three of them are independent). This method is unique in its ability to handle images taken from unconstrained perspective viewpoints and unconstrained illumination directions. The correspondence between such images is hard to compute and no other known method can handle this problem locally from a small number of images. Our method combines geometric and photometric information in order to recover dense correspondence between the images and accurately computes the 3D shape. Only a single pass starting at one point and local computation are used. This is in contrast to methods that use the occluding contours recovered from many images to initialize and constrain an optimization process. The output of our method can be used to initialize such processes. In the special case of fixed viewpoint, the proposed method becomes a new perspective photometric stereo algorithm. Nevertheless, the introduction of the multiview setup, self-occlusions, and regions close to the occluding boundaries are better handled, and the method is more robust to noise than photometric stereo. Experimental results are presented for simulated and real images.     

Should we try to measure software quality attributes directly?

Most external software quality attributes are conceptually subjective. For example, maintainability is an external software quality attribute, and it is subjective because interpersonally agreed definitions for the attribute include the phrase ‘the ease with which maintenance tasks can be performed’. Subjectivity clearly makes measurement of the attributes and validation of prediction systems for the attributes problematic. In fact, in spite of the definitions, few statistically valid attempts at determining the predictive capability of prediction systems for external quality attributes have been published. When validations have been attempted, one approach used is to ask experts to indicate if the values provided by the prediction system informally agree with the experts’ intuition. These attempts are undertaken without determining, independently of the prediction system, whether the experts are capable of direct consistent measurement of the attribute. Hence, a statistically valid and unbiased estimate of the predictive capability of the prediction system cannot be obtained (because the experts’ measurement process is not independent of the prediction system’s values). In this paper, it is argued that the problem of subjective measurement of quality attributes should not be ignored if quality is to be introduced into software in a controlled way. Further, it is argued that direct measurement of quality attributes should be encouraged and that in fact such measurement can be quantified to establish consistency using an existing approach. However, the approach needs to be made more accessible to promote its use. In so doing, it would be possible to decide whether consistent independent estimates of the true values of software quality attributes can be assigned and prediction systems for quality attributes developed.

Comparison of functional performance of a soldier in full chemical and biological protection versus battle dress

The comparison of functional performance between a soldier wearing a chemical and biological (CB) protective equipment and an ordinary battle dress (BD) was conducted at Protechnik's facilities and Jozini–South Africa. The basis of the comparison was that CB protective equipment causes compatibility problems such as mobility and clearance, and that these factors would affect the soldier when performing various activities. Sixteen obstacle courses were erected to simulate a range of functions normally performed by an infantry soldier. Time taken by each soldier to complete a variety of motions and obstacle clearance activities was recorded. It was found that the CB protective equipment interfered with the soldier's performance. The soldier's movements were observed to be restricted and abnormal. The time taken to complete similar activities was longer when wearing the CB protective equipment than ordinary BD.

Relevance to industry

To determine the effect of protective equipment on functional performance.     

Optimal structural topologies with transmissible loads

In optimal topological design of structures one obtains the configuration of optimal structures when the design domain, the displacement boundary conditions and the applied loads are specified. In the optimal structure one often notices a marked difference between the main bearing structure and the load transfer zones. The latter are composed of relatively light elements the exact nature of which is not always very distinct. The main purpose of this paper is to allow the main bearing part of the structure to emerge. Moreover the actual location of the load along its line of action is not always a design requirement. In order to include this relaxed condition regarding the loading position the concept of transmissible or sliding forces is introduced in topological design of structures. A transmissible force is a force of given magnitude and direction which can be applied at any point along the line of action of the force. The optimization formulation is similar to standard topological design procedure in addition to the condition of transmissability of the forces. It is shown that this condition reduces to an equal displacement constraint along the line of action of the forces. The method is illustrated by typical structural examples. It is observed that this numerical method produces indeed crisp images of the main structural components, unblurred by the secondary load transfer elements. It is also indicated that many results are often replicas of Prager structures which were previously obtained by analytical methods. Received March 3, 1999