Comparison of systematic search and database methods for constructing segments of protein structure

Two principal methods of determining the conformation of shortpieces of polypeptide backbone in proteins have been developed:using a database of known structures and systematicallygeneratingall conformations. In this paper, we compare the effectivenessof these two techniques. The completeness of the database forsegments of different lengths is examined and it is found tocontain most conformations for segments seven residues long,but to deteriorate rapidly for longer regions. When the databasesegment is to be incorporated into the rest of a structure,at least seven residues are required to build four new residues,because of the need to positionthe segment relative to the restof the structure.It is found that such positioning using flankingresidues results in large errors in the inserted region. Weconclude that the database method is currently not effectivefor comparative modeling, even for short segments. The systematicsearchprocedure is found to generate almost all structures of shortsegments found in proteinsIn contrast to the database method,low root mean square error structures are obtained for a setof trial segments embedded in the rest of a protein structure.Thus, it should be considered the method of choice.     

Treatment of pathologic fractures of the humerus with Seidel nailing

A retrospective study is presented of 14 patients with pathologic fractures of the humerus (12 established, two impending) treated with Seidel nailing from 1988 through 1995 in the authors' institution. There were nine women and five men whose average age was 59.5 years. Breast, prostate, and kidney hypernephroma accounted for the majority of the primary lesions. All but one lesion were located in the middle shaft of the humerus. Ten lesions were considered large (> 5 cm long). In five cases an open curettage and allografting were done. Early pain relief was successful in 85% of the patients. The worst complication found was definite nerve palsy in two (14.28%) patients. Ten fractures healed and two failed to heal. Two thirds of the patients had good functional results. The average survival was 12 months. Intramedullary fixation of pathologic fractures improves the quality of life by controlling pain for most patients.     

Towards a functional neuroanatomy of conscious perception and its modulation by volition: implications of human auditory neuroimaging studies

Conscious sensory perception and its modulation by volition are integral to human mental life. Functional neuroimaging techniques provide a direct means of identifying and characterizing in vivo the systems-level patterns of brain activity associated with such mental functions. In a series of positron emission tomography activation experiments, we and our colleagues have examined a range of normal and abnormal auditory states that, when contrasted, provide dissociations relevant to the question of the neural substrates of sensory awareness. These dissociations include sensory awareness in the presence and absence of external sensory stimuli, the transition from sensory unawareness to awareness (or vice versa) in the presence of sensory stimuli, and sensory awareness with and without volition. The auditory states studied include hallucinations, mental imagery, cortical deafness modulated by attention, and hearing modulated by sedation. The results of these studies highlight the distributed nature of the functional neuroanatomy that is sufficient, if not necessary, for sensory awareness. The probable roles of unimodal association (as compared with primary) cortices, heteromodal cortices, limbic/paralimbic regions and subcortical structures (such as the thalamus) are discussed. In addition, interactions between pre- and post-rolandic regions are examined in the context of top-down, volitional modulation of sensory awareness.     

Coordinated induction of plasminogen activator inhibitor-1 (PAI-1) and inhibition of plasminogen activator gene expression by hypoxia promotes pulmonary vascular fibrin deposition

PURPOSE: In a rabbit model, transposition of a muscle pedicle flap to an ischemic hind limb has been shown to result in the development of new blood vessels that connect the arterial circulation of the flap to the circulation of the limb. The hypothesis that exogenous recombinant basic fibroblast growth factor (bFGF) would enhance the development of this new blood supply was examined and the regulation of bFGF in this process was investigated. METHODS: The right common iliac artery was ligated in 12 male New Zealand white rabbits. An abdominal wall muscle flap based on the left inferior epigastric artery was transposed to the right thigh. bFGF in phosphate-buffered saline (PBS) at 3 ng/h (n = 6), or PBS alone (n = 6), was infused for 7 days via mini-osmotic pumps with an infusion catheter positioned at the flap-muscle interface. The flap-muscle interface was immunostained with anti-alpha-actin antibody to determine blood vessel density (number of vessels/mm) and with anti-bFGF antibody to evaluate bFGF distribution. RNA was isolated from these sections, and polymerase chain reaction (PCR) was used to examine endogenous bFGF messenger RNA (mRNA) expression. RESULTS: Blood vessel density was significantly increased in animals receiving exogenous bFGF (22. 0 +/- 10.6 vessels/mm vs. 10.7 +/- 8.8 vessels/mm, P =.009). In the controls, neovessels were arranged in clusters with endogenous bFGF concentrated around these clusters. In bFGF-treated animals, vessels were diffusely scattered throughout the flap-limb interface, corresponding to the distribution pattern of infused bFGF. There was no difference in bFGF mRNA expression between the control and the bFGF-treated groups. CONCLUSION: Exogenous bFGF infusion significantly augmented new blood vessel development at the flap-limb interface. Endogenous bFGF was up-regulated around the newly developed microvessels in control animals, and vessel growth correlated with the diffuse distribution of exogenous bFGF, implicating bFGF as an important factor in angiogenesis. Exogenous bFGF did not affect bFGF mRNA expression, suggesting that the regulation of bFGF is not under autocrine control.     

Classification of Spectral Patterns Obtained from Eustachian Tube Sonometry

Spectral patterns of sound transmission through the Eustachian tube (ET) have been obtained in a series of experiments designed to identify ET dysfunction. Previous studies of ET function using sonometry have relied on heuristic and somewhat arbitrary methods in interpreting the data. In this study, an automated classification algorithm was developed to separate these sonograms into three distinct groups. From a total of 150 sample spectra, 75 were used in the formation of learning sets. The remaining spectra were classified into these three groups using standard Bayesian techniques. Both parametric and nonparametric methods were applied in estimating conditional probability density functions. Results of classification are compared with an independent test of ET function. Agreement between our classifier and the results of the independent test was as good as 97.3 percent. The results of this study indicate that an automated classification procedure can effectively distinguish among the three major types of sonograms obtained from ET sonometry.     

RSA-OAEP Is Secure under the RSA Assumption

Recently Victor Shoup noted that there is a gap in the widely believed security result of OAEP against adaptive chosen-ciphertext attacks. Moreover, he showed that, presumably, OAEP cannot be proven secure from the one-wayness of the underlying trapdoor permutation. This paper establishes another result on the security of OAEP. It proves that OAEP offers semantic security against adaptive chosen-ciphertext attacks, in the random oracle model, under the partial-domain one-wayness of the underlying permutation. Therefore, this uses a formally stronger assumption. Nevertheless, since partial-domain one-wayness of the RSA function is equivalent to its (full-domain) onewayness, it follows that the security of RSA-OAEP can actually be proven under the sole RSA assumption, although the reduction is not tight.     

Shannon number and information capacity of three-dimensional integral imaging

Integral imaging systems performance has been previously investigated with regard to different parameters such as lateral resolution, field of view, and depth of view. Those parameters are linked to one another, and, since the information capacity of an integral imaging system is finite, there are always trade-offs among them. We use the Shannon number and information capacity limit as figures of merit of integral imaging systems. The Shannon number and information capacity provide compact assessments of the system and are useful for analysis and design. The limitations on the Shannon number and the information capacity of an integral imaging system are determined by the recording and display media.     

Semivolatile organic compounds in window films from lower Manhattan after the September 11th World Trade Center attacks

The September 11th World Trade Center (WTC) terrorist attacks resulted in the large-scale release of contaminants that were deposited on the environment of New York City (NYC). Six weeks after the attacks, samples of an organic film on window surfaces were collected and analyzed for polybrominated diphenyl ethers (PBDE), polychlorinated biphenyls (PCB), polychlorinated naphthalenes (PCN), polycyclic aromatic hydrocarbons (PAH), and organochlorine pesticides (OCPs). Concentrations dropped by an order of magnitude within 1 km of the WTC and reached background concentrations by 3.5 km. Concentrations within 1 km of the WTC averaged 3280 ng/m2 for sigmaPBDE, 900 ng/m2 for sigmaPCB, 33 ng/m2 for sigmaPCN, and 77100 ng/m2 for sigmaPAH. Congener profiles of the sites nearest the WTC suggested a combination of combustion and evaporative sources of all compounds, whereas the background sites exhibited profiles consistent with evaporative sources. PBDE profiles showed enrichment in lower molecular weight congeners near the WTC, suggesting that these congeners were formed as a result of the combustion conditions. Homologue fractions of PCN combustion markers were approximately 2-9 times greater at near WTC sites compared to background NYC. Gas-phase air concentrations were back-calculated from measured film concentrations using the film-air partition coefficient (KFA), and calculated air concentrations followed spatial trends observed in films.     

Using VNIR and SWIR field imaging spectroscopy for drought stress monitoring of beech seedlings

Drought stress is expected to become a recurrent problem for central European forests due to regional climate change. In order to study the effects on one of the most common tree species in Germany, the European beech (Fagus sylvatica), young potted beech trees were exposed to drought stress in a controlled experiment and their reaction was observed using visible/near-infrared (VNIR) and shortwave infrared (SWIR) field imaging spectroscopy cameras mounted on a platform. Equivalent water thickness (EWT) and leaf chlorophyll content (LCC) were measured and partial least squares (PLS) regression models were trained using these reference measurements and reflectance spectra of the trees. The models were applied to create maps of these properties with a spatial resolution in the millimetre range. These maps can be used to study the spatial distribution of EWT and LCC for single leaves or even for intra-leaf variability. Both properties can be estimated using only the VNIR sensor, but EWT estimation improves considerably by also incorporating SWIR data. LCC estimations with SWIR data alone do not work satisfactorily.