Identical Threshold Research Articles

Detecting depression in Chinese adults with mild dementia: Findings with two versions of the Center for Epidemiologic Studies Depression Scale

This study investigates the extent to which the diagnostic performance of the Center for Epidemiologic Studies Depression Scale (CES-D; both 20- and 10-item versions) varies with cognitive status, and whether the same threshold can be applied regardless of cognitive status. Three hundred and ninety-six persons aged 60+ referred for psychiatric assessment were broken down into four groups depending on age (< 70 and ≥ 70) and dementia status (mild vs. none). All were independently interviewed using the CES-D before their first evaluation by a psychiatrist. Receiver operating characteristic curves showed that both versions of the CES-D produced essentially identical results, regardless of age and dementia status. Both versions were more or less robust to the effect of mild dementia but were vulnerable to the effect of age itself. Furthermore, the optimal threshold for the 20-item version varied somewhat across the different age–dementia groups, and no clear-cut threshold existed in old-old persons with dementia. On the contrary, the same threshold of 12 can be adopted for the 10-item version, regardless of age and dementia status. Compared with the full 20-item scale, the 10-item version has the added advantage of an identical threshold across age and cognitive status.

Geminivirus strain demarcation and nomenclature

Geminivirus taxonomy and nomenclature is growing in complexity with the number of genomic sequences deposited in sequence databases. Taxonomic and nomenclatural updates are published at regular intervals (Fauquet et al. in Arch Virol 145:1743-1761, 2000, Arch Virol 148:405-421, 2003). A system to standardize virus names, and corresponding guidelines, has been proposed (Fauquet et al. in Arch Virol 145:1743-1761, 2000). This system is now followed by a large number of geminivirologists in the world, making geminivirus nomenclature more transparent and useful. In 2003, due to difficulties inherent in species identification, the ICTV Geminiviridae Study Group proposed new species demarcation criteria, the most important of which being an 89% nucleotide (nt) identity threshold between full-length DNA-A component nucleotide sequences for begomovirus species. This threshold has been utilised since with general satisfaction. More recently, an article has been published to clarify the terminology used to describe virus entities below the species level [5]. The present publication is proposing demarcation criteria and guidelines to classify and name geminiviruses below the species level. Using the Clustal V algorithm (DNAStar MegAlign software), the distribution of pairwise sequence comparisons, for pairs of sequences below the species taxonomic level, identified two peaks: one at 85-94% nt identity that is proposed to correspond to "strain" comparisons and one at 92-100% identity that corresponds to "variant" comparisons. Guidelines for descriptors for each of these levels are proposed to standardize nomenclature under the species level. In this publication we review the status of geminivirus species and strain demarcation as well as providing updated isolate descriptors for a total of 672 begomovirus isolates. As a consequence, we have revised the status of some virus isolates to classify them as "strains", whereas several others previously classified as "strains" have been upgraded to "species". In all other respects, the classification system has remained robust, and we therefore propose to continue using it. An updated list of all geminivirus isolates and a phylogenetic tree with one representative isolate per species are provided.

Effect of electron irradiation on carrier removal rate in silicon and silicon carbide with 4H modification

Comparative study of the effect of successive (up to fluences of 3 × 1016 cm−2) irradiation with 900 keV electrons of samples made of FZ-Si and 4H-SiC (CVD) has been performed for the first time. Measurements on initial and irradiated samples were made using the van der Pauw method for silicon and the capacitance-voltage technique at a frequency of 1 kHz for silicon carbide. In addition, the spectrum of the defect levels introduced was monitored by the DLTS method for SiC. The carrier removal and defect introduction rates were determined for the two materials. It was found that the rates of defect introduction into FZ-Si and 4 H-SiC (CVD) are close to eachy other (∼0.1 cm−1), which is largely due to the almost identical threshold energies of defect generation.

Distantly related lipocalins share two conserved clusters of hydrophobic residues: use in homology modeling

BackgroundLipocalins are widely distributed in nature and are found in bacteria, plants, arthropoda and vertebra. In hematophagous arthropods, they are implicated in the successful accomplishment of the blood meal, interfering with platelet aggregation, blood coagulation and inflammation and in the transmission of disease parasites such as Trypanosoma cruzi and Borrelia burgdorferi.The pairwise sequence identity is low among this family, often below 30%, despite a well conserved tertiary structure. Under the 30% identity threshold, alignment methods do not correctly assign and align proteins. The only safe way to assign a sequence to that family is by experimental determination. However, these procedures are long and costly and cannot always be applied. A way to circumvent the experimental approach is sequence and structure analyze. To further help in that task, the residues implicated in the stabilisation of the lipocalin fold were determined. This was done by analyzing the conserved interactions for ten lipocalins having a maximum pairwise identity of 28% and various functions.ResultsIt was determined that two hydrophobic clusters of residues are conserved by analysing the ten lipocalin structures and sequences. One cluster is internal to the barrel, involving all strands and the 310 helix. The other is external, involving four strands and the helix lying parallel to the barrel surface. These clusters are also present in RaHBP2, a unusual "outlier" lipocalin from tick Rhipicephalus appendiculatus. This information was used to assess assignment of LIR2 a protein from Ixodes ricinus and to build a 3D model that helps to predict function. FTIR data support the lipocalin fold for this protein.ConclusionBy sequence and structural analyzes, two conserved clusters of hydrophobic residues in interactions have been identified in lipocalins. Since the residues implicated are not conserved for function, they should provide the minimal subset necessary to confer the lipocalin fold. This information has been used to assign LIR2 to lipocalins and to investigate its structure/function relationship. This study could be applied to other protein families with low pairwise similarity, such as the structurally related fatty acid binding proteins or avidins.

Diversity of the Bacterial Community Found in Sammanarezushi (Saury Narezushi Revealed by the 16S rRNA Gene Clone Library

Narezushi is one of Japanese traditional foods and is made by fermenting salted fish meat and cooked rice together. In this study, the microbial diversity of samma-narezushi (narezushi using saury, Cobolabis saira) was analyzed by the 16S ribosomal RNA gene (rDNA) clone library. Randomly selected 89 clones were sequenced and phylogenetically analyzed. The sequences were classified into 12 operational taxonomy units (OTUs) at the 97% identity threshold. Most of the clones (89%) were lactic acid bacteria (LAB) and included Lactobacillus sakei, Leuconostoc gelidum, Lactococcus lactis subsp. lactis and L. pisium. The most predominant clone was L. sakei at 72% of the clones. The second most abundant clone was L. gelidum. These results suggest that L. sakei mainly contributes to the lactic acid fermentation process, taste and flavor of samma-narezushi. The present study showed that the culture independent method is useful for the microbial diversity analysis of narezushi.

Unassigned MURF1 of kinetoplastids codes for NADH dehydrogenase subunit 2

BackgroundIn a previous study, we conducted a large-scale similarity-free function prediction of mitochondrion-encoded hypothetical proteins, by which the hypothetical gene murf1 (maxicircle unidentified reading frame 1) was assigned as nad2, encoding subunit 2 of NADH dehydrogenase (Complex I of the respiratory chain). This hypothetical gene occurs in the mitochondrial genome of kinetoplastids, a group of unicellular eukaryotes including the causative agents of African sleeping sickness and leishmaniasis. In the present study, we test this assignment by using bioinformatics methods that are highly sensitive in identifying remote homologs and confront the prediction with available biological knowledge.ResultsComparison of MURF1 profile Hidden Markov Model (HMM) against function-known profile HMMs in Pfam, Panther and TIGR shows that MURF1 is a Complex I protein, but without specifying the exact subunit. Therefore, we constructed profile HMMs for each individual subunit, using all available sequences clustered at various identity thresholds. HMM-HMM comparison of these individual NADH subunits against MURF1 clearly identifies this hypothetical protein as NAD2. Further, we collected the relevant experimental information about kinetoplastids, which provides additional evidence in support of this prediction.ConclusionOur in silico analyses provide convincing evidence for MURF1 being a highly divergent member of NAD2.

Sub-terahertz testing of silicon MOSFET

The difference in the terahertz response of Si MOSFETs with identical above threshold characteristics but different values of the leakage current in the below threshold regime is demonstrated. The results show that the terahertz response test can be used as a complementary testing technique of a Si MOS VLSI under bias.

Distributed Detection in Wireless Sensor Networks Using Dynamic Sensor Thresholds

This paper presents a new approach for distributed target detection in wireless sensor networks (WSNs). Contrary to the conventional practice where every sensor uses an identical threshold for decision-making, an unequal and dynamic local sensor threshold selection scheme is proposed. This threshold selection scheme is based on a recently proposed statistical metric for multiple testing problems called the False Discovery Rate (FDR). Assuming a signal attenuation model, where the received signal power decays as the distance from the target increases, various performance indices like the system level probability of detection and the probability of false alarm are studied. Simulation results are provided to demonstrate the effectiveness of this approach.

Effect of the grain size on the macroscopic response of aluminum to shock loading

Shock tests of two lots of a 1420 aluminum-lithium alloy are performed. The mean grain size is 24 µm in the first lot and 1.6 µm in the second lot obtained by the method of equal-channel angular pressing. Two characteristics of dynamic strength of the material were determined in experiments on the high-velocity impact of flat samples: threshold of dynamic stability with respect to compression on the fore front of the compression pulse and spall strength of the material. The materials of both types have an identical threshold of dynamic stability with respect to compression, whereas the spall strength of the microcrystalline alloy is 20% greater than the spall strength of the polycrystalline alloy. The reason is the consumption of energy on structure formation in the coarse-grain material in passing to a larger-scale structural level (in the case with a fine-grain material, such a structure is available in the initial state). The experiments reveal the presence of a second plastic front whose amplitude is approximately 10% of the first plastic front.

Evolutionary Networks in the Formatted Protein Sequence Space

In our recent work, a new approach to establish sequence relatedness, by walking through the protein sequence space, was introduced. The sequence space is built from 20 amino acid long fragments of proteins from a very large collection of fully sequenced prokaryotic genomes. The fragments, points in the space, are connected, if they are closely related (high sequence identity). The connected fragments form variety of networks of sequence kinship. In this research the networks in the formatted sequence space and their topology are analyzed. For lower identity thresholds a huge network of complex structure is formed, involving up to 10% points of the space. When the threshold is increased, the major network splits into a set of smaller clusters with a wide diversity of sizes and topologies. Such "evolutionary networks" may serve as a powerful sequence annotation tool that allows one to reveal fine details in the evolutionary history of proteins.

Does chemotherapy influence the quantification of SUV when contrast-enhanced CT is used in PET/CT in lymphoma?

In patients with lymphoma, we investigated the impact of contrast-enhanced CT on PET attenuation correction in lesions and normal tissues, particularly when PET/CT was performed after chemotherapy. Fifty patients (51+/-18 years) with Hodgkin's disease (n=17) or non-Hodgkin lymphomas (n=33) were studied before and after chemotherapy. PET/CT scans were performed 60 min after injection of FDG. Iopamiron 300 (iopamidol, 1.5 cc/kg) was injected immediately afterwards, followed 50 s later by a second craniocaudal CT (CT+). PET images were successively reconstructed using the unenhanced CT (PET-) and the CT+ (PET+) for attenuation correction, using iterative reconstruction (4 iterations, 8 subsets, 5 mm post-filtering). HU(mean), SUV(max) and SUV(mean) were measured before and after chemotherapy in ten non-tumoural ROIs [aorta, femur, kidney, lung, iliopsoas muscle, occipital cortex, T12 vertebra, liver, spleen and inferior vena cava (IVC)] and in tumoural lymphadenopathies or malignant tissues (n=397 and 51 VOIs respectively before and after chemotherapy) using a 3D-thresholding method (identical threshold for PET- and PET+). ROIs were defined on the PET- and automatically applied on the unenhanced CT (CT-), the CT+ and the PET+. In the non-tumoural tissues, HU(mean) increased significantly in the CT+ compared with the CT- in the vessels and the highly vascularised organs, and slight increases were observed in the occipital cortex (+11%), the iliopsoas muscle (+6%) and the femur (+3%). SUV(max) increased significantly in the PET+ compared with the PET- in the aorta (+14%), the liver (+10%), the spleen (+10%) and the IVC (+12%). SUV(mean) increased significantly in the PET+ compared with the PET- in the aorta (+15%), the kidney (+13%), the liver (+11%), the spleen (10%) and the IVC (+12%). In the lesions, HU(mean) was not significantly different before and after chemotherapy, whatever the normal region considered. SUV(max) increased significantly after treatment in the T12 vertebra (+12%). SUV(mean) increased significantly after treatment in the T12 vertebra (+13%) and in the liver (+12%). HU(mean) increased significantly in the CT+ compared with the CT- in the lesions (+55%) before chemotherapy. SUV(max) and SUV(mean) increased significantly in the PET+ compared with the PET- in the lesions (+4%) only before chemotherapy. No significant difference was seen in measurements (HU(mean), SUV(max) and SUV(mean)) after chemotherapy. Our study demonstrates that use of enhanced CT for attenuation correction has a negligible effect on quantification at staging and after chemotherapy. A "single-shot" enhanced PET/CT may thus be performed in the evaluation of patients with lymphoma at staging, during treatment and at follow-up.

Enhanced coding for exponentially distributed signals using suprathreshold stochastic resonance

Our previous work on stochastic resonance (SR) in threshold based systems proved that the SR effect is dependent on the nature of the input signal distribution; more specifically, for certain types of signal distribution SR is not observed [Das A, Stocks NG, Nikitin A, Hines EL. Quantifying stochastic resonance in a single threshold detector for random aperiodic signals. Fluctuation Noise Lett 2004;4:L247–65]. Here we show that suprathreshold stochastic resonance (SSR) – a novel and distinct form of SR – removes this limitation and hence leads to the conclusion that SSR can probably enhance the transmission of signals of any distribution and amplitude. SSR effects are studied in a parallel array of identical nonlinear threshold based devices. A double exponential signal distribution is chosen because this distribution did not demonstrate conventional SR effects in a single threshold device [Das A, Stocks NG, Nikitin A., Hines EL. Quantifying Stochastic resonance in a single threshold detector for random aperiodic signals. Fluctuation and Noise Letters 2004;4:L247-L265.]. SSR as a possible mechanism for enhancing transmission of speech signals in the human ear is also discussed.

Optimal stimulus and noise distributions for information transmission via suprathreshold stochastic resonance

Suprathreshold stochastic resonance (SSR) is a form of noise-enhanced signal transmission that occurs in a parallel array of independently noisy identical threshold nonlinearities, including model neurons. Unlike most forms of stochastic resonance, the output response to suprathreshold random input signals of arbitrary magnitude is improved by the presence of even small amounts of noise. In this paper, the information transmission performance of SSR in the limit of a large array size is considered. Using a relationship between Shannon's mutual information and Fisher information, a sufficient condition for optimality, i.e., channel capacity, is derived. It is shown that capacity is achieved when the signal distribution is Jeffrey's prior, as formed from the noise distribution, or when the noise distribution depends on the signal distribution via a cosine relationship. These results provide theoretical verification and justification for previous work in both computational neuroscience and electronics.

The CC-NBS-LRR Subfamily in Pinus monticola: Targeted Identification, Gene Expression, and Genetic Linkage with Resistance to Cronartium ribicola

ABSTRACT To investigate disease resistance gene analogs (RGAs) encoding coiled-coil-nucelotide-binding site-leucine-rich repeats (CC-NBS-LRR) proteins in western white pine, degenerate primers targeting the conserved motifs in the NBS domain were designed to amplify RGAs from genomic DNA and cDNA. Sixty-one distinct RGAs were identified with identities to well-known R proteins of the CC-NBS-LRR subfamily. These RGAs exhibited variation of putative amino acid sequences from 13% to 98%, representing a complex CC-NBS-LRR subfamily. A phylogenetic tree constructed from the amino acid sequence alignment revealed that these 61 RGAs were grouped with other CC-NBS-LRR members from angiosperms, and could be further divided into six classes with an identity threshold of 68%. To map RGAs, RGA polymorphisms and a modified amplified fragment length polymorphism (AFLP) method with incorporated sequences from the NBS domain were used to reveal NBS or NBS-AFLP markers. RGA polymorphism study revealed that three off the identified RGAs were not linked to the Cr2 gene imparting resistance to white pine blister rust. However, the AFLP strategy, using bulk segregant analysis (BSA) and haploid segregation analysis, identified 11 NBS-AFLP markers localized in the Cr2 linkage, the closest two to the gene being 0.41 cM and 1.22 cM away at either side. Eight of these markers showed significant amino acid sequence homologies with RGAs.

Water Clustering and Percolation in Low Hydration DNA Shells

The hydrogen-bonded networks of water at the surface of a model DNA molecule are analyzed. At low hydrations, only small water clusters are attached to the DNA surface, whereas, at high hydrations, it is homogeneously covered by a spanning water network. The spanning water network is formed via a percolation transition at an intermediate hydration number of about 15 water molecules per nucleotide, which is very close to the midpoint of polymorphic transitions between A- and B-forms of the double helix. The percolation transition can occur in both A- and B-DNA hydration shells with nearly identical percolation thresholds. However, the mechanism of the percolation transition in A- and B-DNA is qualitatively different in regard to the roles played by the two opposite grooves of the double helix. Free ions can shift the percolation threshold by preventing some water molecules from hydrogen bond networking. The results corroborate the suggested relationship between water percolation and the low hydration polymorphism in DNA.

A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining

The major aim of tertiary structure prediction is to obtain protein models with the highest possible accuracy. Fold recognition, homology modeling, and de novo prediction methods typically use predicted secondary structures as input, and all of these methods may significantly benefit from more accurate secondary structure predictions. Although there are many different secondary structure prediction methods available in the literature, their cross-validated prediction accuracy is generally <80%. In order to increase the prediction accuracy, we developed a novel hybrid algorithm called Consensus Data Mining (CDM) that combines our two previous successful methods: (1) Fragment Database Mining (FDM), which exploits the Protein Data Bank structures, and (2) GOR V, which is based on information theory, Bayesian statistics, and multiple sequence alignments (MSA). In CDM, the target sequence is dissected into smaller fragments that are compared with fragments obtained from related sequences in the PDB. For fragments with a sequence identity above a certain sequence identity threshold, the FDM method is applied for the prediction. The remainder of the fragments are predicted by GOR V. The results of the CDM are provided as a function of the upper sequence identities of aligned fragments and the sequence identity threshold. We observe that the value 50% is the optimum sequence identity threshold, and that the accuracy of the CDM method measured by Q(3) ranges from 67.5% to 93.2%, depending on the availability of known structural fragments with sufficiently high sequence identity. As the Protein Data Bank grows, it is anticipated that this consensus method will improve because it will rely more upon the structural fragments.

Walking through protein sequence space

Following the original idea of Maynard Smith on evolution of the protein sequence space, a novel tool is developed that allows the “space walk”, from one sequence to its likely evolutionary relative and further on. At a given threshold of identity between consecutive steps, the walks of many steps are possible. The sequences at the ends of the walks may substantially differ from one another. In a sequence space of randomized (shuffled) sequences the walks are very short. The approach opens new perspectives for protein evolutionary studies and sequence annotation.

SU-FF-J-42: Cone Beam CT Based Treatment Planning

Purpose: To evaluate treatment planning based on cone beam CT (CBCT) using latest software on a LINAC 21IX CBCT imaging system. Method and Materials: An anthropomorphic chest phantom having bone, soft tissue, and lung components was used to create and evaluate treatment plans based on conventional CT and CBCT images. Conventional CT images of 2.5 mm slice thickness were taken with a GE discovery LS CT/PET system. CBCT images slices were also reconstructed from flat panel system on a Varian LINAC 21IX. Eclipse treatment planning system was used to compare treatment plans from the conventional CT and CBCT images. The AAA algorithm was used in the treatment planning system for inhomogeneity correction. Regions of interest around the bone, soft tissue, and lung in both CT and CBCT images using identical HU threshold values were drawn. Identical targets located in the lung were used in each treatment plan. Analysis of the treatment plans was performed by comparison of geometrical dimensions, total volumes and dose volume histograms of the target and regions of interest. Results: Geometric comparison of actual external spatial dimensions and others in lung and bone were found to be within 1 mm. Volumetric comparison of the regions of interest resulted in a 2.8% difference of the vertebrae, 3.3% of the right lung, and 3.7% of the total external volume. Dosimetric results show similar dose distributions. Dose volume histograms are also comparable. Conclusion: Results demonstrate that treatment planning based on CBCT is feasible. Plans created from CBCT images are comparable to plans created with conventional CT systems. Conflict of Interest: Partly funded by Prostate Cancer Foundation grant UW 133-HR30.

Operant methods for mouse psychoacoustics

Tone detection thresholds for a 10-kHz tone in NMRI mice were determined in psychoacoustic experiments using both a constant-stimuli procedure and a two-down/one-up adaptive-tracking procedure in the same subjects and applying identical threshold criteria (70.7% response probability). Constant-stimuli thresholds were on average 24 dB lower than adaptive-tracking thresholds, and there was a trend indicating that constant-stimuli thresholds were less variable than adaptive-tracking thresholds. Furthermore, in the constant-stimuli procedure the number of trials constituting the psychometric function could be reduced from 100 to 50 trials without a large loss of accuracy of threshold determination. In the constant-stimuli procedure, the threshold value was affected by the threshold criteria. The lowest and least variable constant-stimuli thresholds were obtained by applying signal detection theory and a criterion of d' = 1. Thus, the constant-stimuli procedure in combination with signal detection theory appears to be better suited than the adaptive-tracking procedure to determine auditory sensory thresholds.

In vivo enhancement of sensory perception recovery in a tissue-engineered skin enriched with laminin

The use of autologous reconstructed skin appears to be a promising treatment for the permanent coverage of deep and extensive burns. However, the capability of reconstructed skin transplanted on wounds to promote recovery of sensory perception is a major concern. Our aim was to assess the effect of laminin on cutaneous nerve regeneration. We prepared collagen-chitosan sponges enriched with 0, 1, 10 or 50 μg of laminin/sponge to produce tissue-engineered reconstructed skins by culture of human fibroblasts and keratinocytes, then grafted on the back of athymic mice for 120 days. Immunohistochemical studies demonstrated that there were 7 times more neurofilament 150 kD-positive nerve fibers migrating in the graft in the samples enriched with 10 μg laminin/sponge, compared to reconstructed skin without laminin, 120 days after graft. A significant improvement in the current perception threshold of the A β and A δ nerve fibers was measured using a Neurometer ® in all grafts enriched with laminin. In addition, the type C nerve fibers reached an identical current perception threshold than mouse skin, in all reconstructed skins enriched or not with laminin. We conclude that the use of a tissue-engineered autologous skin graft enriched with laminin has the potential to efficiently optimize cutaneous sensory nerve regeneration in vivo.