A novel method for early diagnosis of Alzheimer’s disease based on higher-order spectral estimation of spontaneous speech signals

One main challenge for medical investigators is the early diagnosis of Alzheimer’s disease (AD) because it provides greater opportunities for patients to be eligible for more clinical trials. In this study, higher order spectra of human speech signals during AD were explored to analyze and compare the quadratic phase coupling of spontaneous speech signals for healthy and AD subjects using bispectrum and bicoherence. The results showed that the quadratic phase couplings of spontaneous speech signal of persons with Alzheimer’s were reduced compared to healthy subject. However, the speech phase coupled harmonics shifted to the higher frequencies in Alzheimer’s than healthy subjects. In addition, it was shown not only are there significant differences between Alzheimer’s and control subjects in parameters estimated, but also the speech patterns appeared to have fluctuated in both types of spontaneous speech.     

Network genomics – A novel approach for the analysis of biological systems in the post-genomic era

Network Genomics studies genomics and proteomics foundations of cellular networks in biological systems. It complements systems biology in providing information on elements, their interaction and their functional interplay in cellular networks. The relationship between genomic and proteomic high-throughput technologies and computational methods are described, as well as several examples of specific network genomic application are presented.     

A middleware approach for pipelining communications in clusters

The Pipelining Communications Middleware (PCM) approach provides a flexible, simple, high-performance mechanism to connect parallel programs running on high performance computers or clusters. This approach enables parallel programs to communicate and coordinate with each other to address larger problems than a single program can solve. The motivation behind the PCM approach grew out of using files as an intermediate transfer stage between processing by different programs. Our approach supersedes this practice by using streaming data set transfers as an “online” communication channel between simultaneously active parallel programs. Thus, the PCM approach addresses the issue of sending data from a parallel program to another parallel program without exposing details such as number of nodes allocated to the program, specific node identifiers, etc. This paper outlines and analyzes our proposed computation and communication model to provide efficient and convenient communications between parallel programs running on high performance computing systems or clusters. We also discuss the PCM challenges as well as current PCM implementations. Our approach achieves scalability, transparency, coordination, synchronization and flow control, and efficient programming. We experimented with data parallel applications to evaluate the performance of the PCM approach. Our experiment results show that the PCM approach achieves nearly ideal throughput that scales linearly with the underlying network medium speed. PCM performs well with small and large data transfers. Furthermore, our experiments show that network infrastructure plays the most significant role in the PCM performance.

Shear-scaling-based approach for irreversible energy loss estimation in stenotic aortic flow – An in vitro study

Today, the functional and risk assessment of stenosed arteries is mostly based on ultrasound Doppler blood flow velocity measurements or catheter pressure measurements, which rely on several assumptions. Alternatively, blood velocity including turbulent kinetic energy (TKE) may be measured using MRI. The aim of the present study is to validate a TKE-based approach that relies on the fact that turbulence production is dominated by the flow’s shear to determine the total irreversible energy loss from MRI scans. Three-dimensional particle tracking velocimetry (3D-PTV) and phase-contrast magnetic resonance imaging (PC-MRI) simulations were performed in an anatomically accurate, compliant, silicon aortic phantom. We found that measuring only the laminar viscous losses does not reflect the true losses of stenotic flows since the contribution of the turbulent losses to the total loss become more dominant for more severe stenosis types (for example, the laminar loss is 0.0094 ± 0.0015 W and the turbulent loss is 0.0361 ± 0.0015 W for the Re_max = 13,800 case, where Re_max is the Reynolds number based on the velocity in the vena-contracta). We show that the commonly used simplified and modified Bernoulli’s approaches overestimate the total loss, while the new TKE-based method proposed here, referred to as “shear scaling” approach, results in a good agreement between 3D-PTV and simulated PC-MRI (mean error is around 10%). In addition, we validated the shear scaling approach on a geometry with post-stenotic dilatation using numerical data by Casas et al. (2016). The shear scaling-based method may hence be an interesting alternative for irreversible energy loss estimation to replace traditional approaches for clinical use. We expect that our results will evoke further research, in particular patient studies for clinical implementation of the new method.     

A novel modeling approach for the “end-to-end” analysis of marine ecosystems

There is a growing demand for “end-to-end” models, which are modeling tools used to analyze and understand the fundamental complexities of marine ecosystems and processes emerging from the interaction of individuals from different trophic groups with respect to the physical environment and, even, human activity. These models are valuable quantitative tools for ecosystem-based management. To explore potential answers to complex questions regarding ecosystems using these models, it is necessary to incorporate classical ontogenic changes through the life cycle of target individuals, in addition to inherited behavioral strategies, as an additional differentiating aspect, particularly when the behavior has a direct impact on the ecosystem phenomena under study. However, it is difficult to combine different fine scale time and spatial granularities to infer animal behavior and ontogenic development. This complexity has kept these two levels of analysis separated, because most current tools do not have the required computational resources and advanced software architecture. To address this issue, we propose an individual-based modeling framework that is capable of handling and unifying the two experimental categories with a comprehensive biological and behavioral model that strictly adheres to the physiological functions of ingestion, growth, and metabolism of organisms. In addition, this model incorporates the exchange and transfer of mass and energy through local interactions at all trophic levels (lower to higher), the physical environment, and anthropogenic activity. For the framework to model short time events, such as classical predator–prey interactions, while also generating long-term ecosystem emergent properties, a special interleaving scheduling engine and physical space computer model was devised, which optimizes memory and processing resources. The framework was tested through several experiments with a three-population ecosystem containing up to 40 thousand organisms evolving inside a 200,000 m² simulation environment during 12,000 model-hours; yet, requiring only a few hours of program execution on a regular personal computer. The model included various environmental physical elements, such as several hundred shelters, the number of which can be easily modified in each experiment to simulate substrate degradation and its impact on populations. With the aid of the quantitative and qualitative tools provided by the model, it was possible to observe a coupling between prey and predator population dynamics. In conclusion, we confirmed that the end-to-end model developed here could successfully generate detailed specific hypotheses about fish behavior and quantify impacts on population dynamics.     

An improved selection method for λlacZ − phages based on galactose sensitivity

The determination of thelacZ mutant frequency in gt10lacZ phage vectors isolated from the transgenic mouse strain 40.6 (MutaMouse), requires the screening of large numbers of phages on -galactosidase activity. Existing methods rely on distinguishing a few white plaques on X-gal containing plates amongst a multide of blue ones which is both time-consuming and expensive. The new screening method described here employs the galactose sensitiveEscherichia coli C lacZ recA galE strain into which a multicopy plasmid has been introduced, which results in over-expression of thegalK andgalT genes. In the presence of phenyl--d-galactopyranoside, a substrate for -galactosidase, this leads to the suppression of lacZ ⁺ phage propagation without affecting the ability of lacZ ^– phages to form plaques. With this method it is possible to screen 1.5×10⁶ phages on a single 9-cm Petri dish. Furthermore, the need for blue/white screening has been eliminated.     

Index for estimation of muscle force from mechanomyography based on the Lempel–Ziv algorithm

The study of the amplitude of respiratory muscle mechanomyographic (MMG) signals could be useful in clinical practice as an alternative non-invasive technique to assess respiratory muscle strength. The MMG signal is stochastic in nature, and its amplitude is usually estimated by means of the average rectified value (ARV) or the root mean square (RMS) of the signal. Both parameters can be used to estimate MMG activity, as they correlate well with muscle force. These estimations are, however, greatly affected by the presence of structured impulsive noise that overlaps in frequency with the MMG signal. In this paper, we present a method for assessing muscle activity based on the Lempel–Ziv algorithm: the Multistate Lempel–Ziv (MLZ) index. The behaviour of the MLZ index was tested with synthesised signals, with various amplitude distributions and degrees of complexity, and with recorded diaphragm MMG signals. We found that this index, like the ARV and RMS parameters, is positively correlated with changes in amplitude of the diaphragm MMG components, but is less affected by components that have non-random behaviour (like structured impulsive noise). Therefore, the MLZ index could provide more information to assess the MMG–force relationship.     

Is the simple auger coring method reliable for below-ground standing biomass estimation in Eucalyptus forest plantations?

Background and Aims

Despite their importance for plant production, estimations of below-ground biomass and its distribution in the soil are still difficult and time consuming, and no single reliable methodology is available for different root types. To identify the best method for root biomass estimations, four different methods, with labour requirements, were tested at the same location.

Methods

The four methods, applied in a 6-year-old Eucalyptus plantation in Congo, were based on different soil sampling volumes: auger (8 cm in diameter), monolith (25 × 25 cm quadrate), half Voronoi trench (1·5 m³) and a full Voronoi trench (3 m³), chosen as the reference method.

Key Results

With the reference method (0–1m deep), fine-root biomass (FRB, diameter <2 mm) was estimated at 1·8 t ha⁻¹, medium-root biomass (MRB diameter 2–10 mm) at 2·0 t ha⁻¹, coarse-root biomass (CRB, diameter >10 mm) at 5·6 t ha⁻¹ and stump biomass at 6·8 t ha⁻¹. Total below-ground biomass was estimated at 16·2 t ha⁻¹ (root : shoot ratio equal to 0·23) for this 800 tree ha⁻¹ eucalypt plantation density. The density of FRB was very high (0·56 t ha⁻¹) in the top soil horizon (0–3 cm layer) and decreased greatly (0·3 t ha⁻¹) with depth (50–100 cm). Without labour requirement considerations, no significant differences were found between the four methods for FRB and MRB; however, CRB was better estimated by the half and full Voronoi trenches. When labour requirements were considered, the most effective method was auger coring for FRB, whereas the half and full Voronoi trenches were the most appropriate methods for MRB and CRB, respectively.

Conclusions

As CRB combined with stumps amounted to 78 % of total below-ground biomass, a full Voronoi trench is strongly recommended when estimating total standing root biomass. Conversely, for FRB estimation, auger coring is recommended with a design pattern accounting for the spatial variability of fine-root distribution.     

Establishing woody perennials on hostile soils in arid and semi-arid regions – A review

Background and aims

Woody perennials can be difficult to establish on harsh soils in arid and semi-arid regions. Historically, technological advances have focussed on methods to improve transplanting and direct-seeding but the available information on these advances remains fragmented and the edaphic factors have been largely ignored. This review explores the literature on plant establishment and identifies soil properties that limit plant response in harsh environments.

Conclusions

We reveal that some woody perennials are particularly well-adapted to dry conditions and can also help reclaim degraded landscapes. Furthermore, the environmental and phenological factors that limit the success of direct seeding are well understood but the edaphic factors are not. For example, seedbed preparation and subsoil amelioration before seeding have not been evaluated in dry regions. Seed-priming and seed-placement are also poorly understood, as is the tolerance of woody perennials to different salt types in waterlogged soils of extreme pH and high soil strength. The reason why woody perennials can penetrate strong, hard soils is not obvious from the literature. They apparently cannot exert root growth pressures of the same magnitude as domesticated plants, so they must be able to exploit soil biopores and cracks more efficiently. Other gaps in our understanding of the soil factors that limit woody perennial establishment on hostile soils are identified.     

A novel approach to identification of somatic retroelements’ insertions in human genome

The activity of retroelements is one of the factors leading to genetic variability of the modern humans. Insertions of retroelements may result in alteration of gene expression and functional diversity between cells. In recent years an increasing amount of data indicating an elevated level of retroelements’ mobilisation in some human and animal tissues has been reported. Therefore, the development of a system for the detection of somatic retroposition events is required. Here we describe a novel approach to the whole-genome identification of somatic retroelement insertions in human genome. The developed approach was applied for the comparisons of somatic mosaicism levels in two tissues of the investigated individual. A total of 3410 insertions of retroelements belonging to AluYa5 subfamily were identified.     

A method for the estimation of χ1 torsion angles in proteins

Summary A method for estimating CH-CH coupling constants from the shape and fine structure of NH-CH fingerprint-region cross peaks of COSY spectra is presented. Spectral simulations have been used to analyse the effect of variations in ³J_NH-CH, ³J_CH-CH, linewidths and digital resolution on the appearance of NH-CH COSY cross peaks. On the basis of these simulations a set of rules for broadly categorising experimental NH-CH cross peaks according to CH-CH coupling constants has been devised. The method has been applied to the analysis of NH-CH cross peaks of hen lysozyme. The results are compared to previous measurements of CH-CH coupling constants using E.COSY techniques.     

Did food resource shortage cause Ryukyu-ayu extinction on Okinawa-jima Island? A clue based on morphological approach

Ichthyological Research - The Ryukyu-ayu population on Okinawa-jima Island went extinct suddenly in the late 1970s, but the cause remains unclear. Reports say that genetic diversity was not...     

A novel spectrofluorimetric method based on a reaction with an azoisoxazoles–benzenesulfonamide derivative for determination of uranium (VI) ions in water samples

Selective fluorometric detection and determination of uranium ions is provided here using a novel fluorescent reagent, namely (E)-4-([4-hydroxynaphthalen-1-yl]diazenyl)-N-(5-methyleisoxazol-3-yl) benzenesulfonamide (U^VI reagent). The U^VI reagent offers a selective fluorescence enhancement behaviour at emission wavelength = 557 nm. The parameters affecting fluorometric detection of uranium ions, such as the pH, solvent type, ligand concentration, interaction time, and interfering ions, were investigated and adjusted. The proposed U^VI reagent can detect and determine uranium ions even at low concentrations, for which the obtained limit of detection was 0.1 ppm. Additionally, this proposed determination protocol was successfully used to detect, monitor, and determine uranium ions in actual water samples.     

A novel technique based on a PNA hybridization probe and FRET principle for quantification of mutant genotype in fibrous dysplasia/McCune–Albright syndrome

Somatic mutations are present in various proportions in numerous developmental pathologies. Somatic activating missense mutations of the GNAS gene encoding the Gs_α protein have previously been shown to be the cause of fibrous dysplasia of bone (FD)/McCune-Albright syndrome (MAS). Because in MAS patients, tissues as diverse as melanocytes, gonads and bone are affected, it is generally accepted that the GNAS mutation in this disease must have occurred early in development. Interestingly, it has been shown that the development of an active FD lesion may require both normal and mutant cells. Studies of the somatic mosaic states of FD/MAS and many other somatic diseases need an accurate method to determine the ratio of mutant to normal cells in a given tissue. A new method for quantification of the mutant:normal ratio of cells using a PNA hybridization probe-based FRET technique was developed. This novel technique, with a linear sensitivity of 2.5% mutant alleles, was used to detect the percentage mutant cells in a number of tissue and cell culture samples derived from FD/MAS lesions and could easily be adapted for the quantification of mutations in a large spectrum of diseases including cancer.     

A novel two-step synthesis of α-linked mannobioses based on an acid-assisted reverse hydrolysis reaction

Instead of an enzyme-assisted reverse hydrolysis reaction for the synthesis of manno-oligosaccharides, we propose here a versatile new approach. By Fischer type glycosylation, a D-mannose solution of extremely high concentration (approximately 83% (w/w)) was incubated at 60°C for 65 h in 0.5 M HCl. After dilution and neutralization, the small amount of formed β-linked oligosaccharides was hydrolyzed by β-mannosidase. The yields of α-D-Manp-(1→2)-D-Manp (7.9%), α-D-Manp-(1→3)-D-Manp (7.9%), and α-D-Manp-(1→6)-D-Manp (29.1%) isolated by an activated carbon column chromatography were almost identical to those of the enzymatic reaction, but the yield of α-D-Manp-(1→3)-D-Manp increased enormously by the present method.     

Forecasting Helicoverpa populations in Australia： A comparison of regression based models and a bioclimatic based modelling approach

Abstract Long-term forecasts of pest pressure are central to the effective management of many agricultural insect pests. In the eastern cropping regions of Australia, serious infestations of Helicoverpa punctigera (Wallengren) and H. armigera (Hübner)(Lepidoptera: Noctuidae) are experienced annually. Regression analyses of a long series of light-trap catches of adult moths were used to describe the seasonal dynamics of both species. The size of the spring generation in eastern cropping zones could be related to rainfall in putative source areas in inland Australia. Subsequent generations could be related to the abundance of various crops in agricultural areas, rainfall and the magnitude of the spring population peak. As rainfall figured prominently as a predictor variable, and can itself be predicted using the Southern Oscillation Index (SOI), trap catches were also related to this variable. The geographic distribution of each species was modelled in relation to climate and CLIMEX was used to predict temporal variation in abundance at given putative source sites in inland Australia using historical meteorological data. These predictions were then correlated with subsequent pest abundance data in a major cropping region. The regression-based and bioclimatic-based approaches to predicting pest abundance are compared and their utility in predicting and interpreting pest dynamics are discussed.     

A mobility index for Canadian butterfly species based on naturalists’ knowledge

Mobility is a key component of species’ biology. Research on mobility is inherently difficult, however, resulting in studies of narrow taxonomic, spatial, and temporal scope with results that are difficult to compare between studies. We had three goals for our research: (1) construct a data set of mobility estimates for the butterfly species of Canada based on naturalists’ knowledge; (2) develop methods to evaluate aspects of accuracy and precision for knowledge-based ecological research such as ours; and (3) using our data set, test mobility-related hypotheses of species-level relationships. We distributed a questionnaire to amateur and professional lepidopterists in Canada and northern USA, asking them to estimate the mobility of Canadian butterfly species based on their field experience. Based on responses from 51 lepidopterists with approximately 800 years of combined field experience, we received mobility estimates for almost all (291 out of 307) of Canada’s butterfly taxa. Mobility estimates were consistent among respondents and were not affected by respondent expertise. Mobility carries a strong phylogenetic signal and is positively related to wingspan (albeit weakly), range size, and host plant breadth, and negatively related to conservation risk. Reliance upon naturalists’ experience was essential to the feasibility of our project, and provides a promising method for many types of ecological research.     

Hedgehog pathway activation in chronic myeloid leukemia: A promise for a novel combination therapeutic approach?

Chronic Myeloid Leukemia (CML) is a hematopoietic stem cell malignancy that is driven by the oncogenic BCR-ABL fusion protein, and for which treatment with ABL tyrosine kinase inhibitors (TKI) has yielded great success. While this is the case, BCR-ABL leukemic stem cells can persist despite TKI therapy, and efforts have intensified towards determining the molecular pathways that are critical for the maintenance of such cells. Recent studies indicate that aberrant Hedgehog (Hh) signaling plays a crucial role in the survival of the leukemic stem cell population. The Hh pathway displays crucial roles during embryonic development, tissue regeneration and repair in adults. Several mechanisms that lead to the aberrant activation of the Hh pathway have been identified in various cancers. Here we review in detail the discovery that Hh signaling governs the maintenance of the critical leukemia initiating cells or leukemic stem cells (LSCs) in BCR-ABL-induced CML as well as discuss investigations on the role of Hh signaling in normal hematopoeisis. As inhibitors that directly target the positive Hh signal transducer Smoothened (SMO) have entered clinical trials, these findings offer a unique opportunity to potentially target the LSC population that is not eliminated with ABL tyrosine kinase inhibition therapy in CML.