ECG compression using the context modeling arithmetic coding with dynamic learning vector–scalar quantization

Electrocardiogram (ECG) compression can significantly reduce the storage and transmission burden for the long-term recording system and telemedicine applications. In this paper, an improved wavelet-based compression method is proposed. A discrete wavelet transform (DWT) is firstly applied to the mean removed ECG signal. DWT coefficients in a hierarchical tree order are taken as the component of a vector named tree vector (TV). Then, the TV is quantized with a vector–scalar quantizer (VSQ), which is composed of a dynamic learning vector quantizer and a uniform scalar dead-zone quantizer. The context modeling arithmetic coding is finally employed to encode those quantized coefficients from the VSQ. All tested records are selected from the Massachusetts Institute of Technology-Beth Israel Hospital arrhythmia database. Statistical results show that the compression performance of the proposed method outperforms several published compression algorithms.     

Lumbar–pelvic range and coordination during lifting tasks

Spine motion has been described to have two regions, a neutral zone where lumbar rotation can occur with little resistance and an elastic zone where structures such as ligaments, facet joints and intervertebral disks resist rotation. In vivo, the passive musculature can contribute to further limiting the functional neutral range of lumbar motion. Movement out of this functional neutral range could potentially put greater loads on these structures. In this study, the range of lumbar curvature rotation was examined in twelve healthy, untrained volunteers at four torso inclination angles. The lumbar curvature during straight-leg lifting tasks was then defined as a percentage of this range of possible lumbar curvatures. Subjects were found to remain neutrally oriented during the flexion phase of a lifting task. During the extension phase of the lifting task, however, subjects were found to assume a more kyphotic posture, approaching the edge of the functional range of motion. This was found to be most pronounced for heavy lifting tasks. By allowing the lumbar curvature to go into a highly kyphotic posture, subjects may be taking advantage of stretch-shortening behavior in extensor musculature and associated tendons to reduce the energy required to raise the torso. Such a kyphotic posture during extension, however, may put excessive loading on the elastic structures of the spine and torso musculature increasing the risk of injury.     

Quantitative analysis of trace gases of breath during exercise using the new SIFT–MS technique

Abstract

We show how the concentration of the breath gases ammonia, acetone, and isoprene vary with time during exercise using the new selected ion flow tube mass spectrometry (SIFT–MS) technique. The expired breath concentrations of ammonia, acetone and isoprene were observed within the range of 50–500, 100–1400 and 5–400 ppb, respectively. Increasing acetone levels were observed for most subjects during the exercise period. However, isoprene levels decreased with time during exercise. Older subjects showed higher levels of isoprene compared with younger subjects. The ammonia time profile with exercise showed both decreasing and increasing patterns for different subjects.     

Quantifying RNA–protein interactions in situ using modified-MTRIPs and proximity ligation

The stabilization, translation and degradation of RNA are regulated by interactions between trans-acting factors, such as microRNA and RNA-binding proteins (RBP). In order to investigate the relationships between these events and their significance, a method that detects the localization of these interactions within a single cell, as well as their variability across a cell population, is needed. To visualize and quantify RNA–protein interactions in situ, we developed a proximity ligation assay (PLA) that combined peptide-modified, multiply-labelled tetravalent RNA imaging probes (MTRIPs), targeted to sequences near RBP binding sites, with proximity ligation and rolling circle amplification (RCA). Using this method, we detected and quantified, with single-interaction sensitivity, the localization and frequency of interactions of the human respiratory syncytial virus (hRSV) nucleocapsid protein (N) with viral genomic RNA (gRNA). We also described the effects of actinomycin D (actD) on the interactions of HuR with β-actin mRNA and with poly(A)+ mRNA at both native and increased HuR expression levels.     

Is social coordination during escape flights a general phenomenon in birds?

Escape from predatory attack as a socially coordinated group is observed in many social animals, including birds, especially those in more open habitats where the group itself may be the only source of protection from an attacking predator. For many social birds, however, woody vegetative cover is the main refuge from attack, but such birds might nevertheless benefit from social coordination during escape flights to cover. Such benefits could reflect the confusion effect, selfish herd effect, or the simple dilution of risk. We examined this possibility of coordinated escape in mixed flocks of wintering passerellid sparrows (Passerellidae). These free-living birds fed in a patch of food flanked on opposite sides by two refuges composed of woody cover. Under such conditions, coordination in escape behavior should be expressed as a tendency to escape together as a group to the same cover location. Such behavior, however, was not the rule. During spontaneous flushes to cover, a group of escaping birds stayed together only when one cover location was clearly closer than the other. With cover equidistant from the food patch, escaping flocks tended to split about evenly between cover locations. Birds in close proximity prior to an escape flight did not show enhanced escape coordination, nor did those feeding at significant distances from protective cover. Evidence of escape coordination was observed in small groups (two–four birds), but even in such groups, flock splitting during escape was generally the rule. Flock splitting during attacks might reflect some sort of strategic decision-making process that lessens the risk of capture, but the most parsimonious explanation is that (all else equal) birds head for the nearest refuge, largely irrespective of the behavior of their flockmates. Our results thus provide little evidence of flock-wide social coordination during escape flights in cover-dependent birds.     

Quantitative structure–activity relationship analysis using deep learning based on a novel molecular image input technique

Quantitative structure–activity relationship (QSAR) analysis uses structural, quantum chemical, and physicochemical features calculated from molecular geometry as explanatory variables predicting physiological activity. Recently, deep learning based on advanced artificial neural networks has demonstrated excellent performance in the discipline of QSAR research. While it has properties of feature representation learning that directly calculate feature values from molecular structure, the use of this potential function is limited in QSAR modeling. The present study applied this function of feature representation learning to QSAR analysis by incorporating 360° images of molecular conformations into deep learning. Accordingly, I successfully constructed a highly versatile identification model for chemical compounds that induce mitochondrial membrane potential disruption with the external validation area under the receiver operating characteristic curve of ≥0.9.     

Influence of COD/NH3–N ratio on organic removal and nitrification using a modified RBC

Synthetic wastewaters were prepared with different influent concentrations of ammonia nitrogen (NH₃–N) and COD and the treatment studies were conducted using a rotating biological contactor (RBC). If organic removal and nitrification can be simultaneously effected in one process, it will be an ideal solution to water pollution control. The RBC used in the present study was a four stage laboratory model and the discs were modified by attaching porous netlon sheets to enhance biofilm area. The COD loads (S ₀) used were about 1000 and 1500?mg/l whereas NH₃–N concentrations used were in the range of 20 to 185?mg/l. Hydraulic load (q) of 0.03?m³?.?m^-2?.?d^-1 and ammonia nitrogen loadings in the range of 0.66 to 5.5?g NH₃–N?.?m^-2?.?d^-1 were used. The RBC was operated at two different rotating speeds of 6 and 12?rpm. The results showed that the nitrification and percentage of COD removal were not affected up to the value of the COD/NH₃–N in the range from 47 to 23 at w=6?rpm and for an average influent COD of 1003?mg/l. Beyond that range only the nitrification rate decreased much whereas the percentage of COD removal was not affected. Similarly, at an influent COD load of 1557?mg/l, the nitrification and percentage COD removal were not affected for the value of the COD/NH₃–N in the range from 44 to 23 but beyond that range only the nitrification rate decreased while the percentage of COD removal was approximately constant and still high. A correlation plot between the NH₃–N removed and NH₃–N applied was presented at a rotating speed of 6?rpm and it was found that the nitrification rate of 3.93?g NH₃–N?.?m^-2?.?d^-1 was achieved at ammonia loading of 5.55?g NH₃–N?.?m^-2?.?d^-1. Also the results at w=12?rpm showed improvement of nitrification rate over those at 6?rpm.     

Quantitative evaluation of refolding conditions for a disulfide-bond-containing protein using a concise ¹⁸O-labeling technique

A concise method was developed for quantifying native disulfide‐bond formation in proteins using isotopically labeled internal standards, which were easily prepared with proteolytic ¹⁸O‐labeling. As the method has much higher throughput to estimate the amounts of fragments possessing native disulfide arrangements by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF‐MS) than the conventional high performance liquid chromatography (HPLC) analyses, it allows many different experimental conditions to be assessed in a short time. The method was applied to refolding experiments of a recombinant neuregulin 1‐β1 EGF‐like motif (NRG1‐β1), and the optimum conditions for preparing native NRG1‐β1 were obtained by quantitative comparisons. Protein disulfide isomerase (PDI) was most effective at the reduced/oxidized glutathione ratio of 2:1 for refolding the denatured sample NRG1‐β1 with the native disulfide bonds.     

Influence of urea–calcium mixtures as rumen slow-release feed on in vitro fermentation using a gas production technique

In this experiment the effects of different urea products (urea [U] and urea–calcium mixtures [UCM]) on rumen fermentation were investigated in dependence of different energy sources by using in vitro techniques. The 7 × 2 factorial arrangement followed a completely randomised design using seven urea products (U100, U40CaCl₂, U50CaCl₂, U60CaCl₂, U40CaSO₄, U50CaSO₄ and U60CaSO₄) in combination with cassava chips (CC) or corn meal (CM). Compared with other treatments, the cumulative gas production (96 h) was significantly increased for U60CaCl₂ + CC and U60CaSO₄ + CC (p < 0.01), which was combined with a higher in vitro true digestibility (p < 0.01). In addition, the concentration of volatile fatty acids in the fluid of U60CaCl₂ + CC and U60CaSO₄ + CC was significantly higher than in other treatments. Urea treatments (U100 + CC and U100 + CM) caused the highest concentration of ruminal ammonia nitrogen (p < 0.01), which was significantly decreased by all UCM products in combination with CC, but not with CM. The highest levels of total bacteria, Fibrobacter succinogenes and anaerobic fungi were found for treatment U60CaCl₂ + CC and U60CaSO₄ + CC (p < 0.05). The findings revealed that the utilisation of U60CaCl₂ and U60CaSO₄ in combination with cassava chips improved the ruminal fluid fermentation in terms of NH₃-N and volatile fatty acid concentration, digestibility of energy and increased the fibrobacter concentrations.     

Expression and purification of coronavirus envelope proteins using a modified β-barrel construct

Coronavirus envelope (E) proteins are short (～100 residues) polypeptides that contain at least one transmembrane (TM) domain and a cluster of 2-3 juxtamembrane cysteines. These proteins are involved in viral morphogenesis and tropism, and their absence leads in some cases to aberrant virions, or to viral attenuation. In common to other viroporins, coronavirus envelope proteins increase membrane permeability to ions. Although an NMR-based model for the TM domain of the E protein in the severe acute respiratory syndrome virus (SARS-CoV E) has been reported, structural data and biophysical studies of full length E proteins are not available because efficient expression and purification methods for these proteins are lacking. Herein we have used a novel fusion protein consisting of a modified β-barrel to purify both wild type and cysteine-less mutants of two representatives of coronavirus E proteins: the shortest (76 residues), from SARS-CoV E, and one of the longest (109 residues), from the infectious bronchitis virus (IBV E). The fusion construct was subsequently cleaved with cyanogen bromide and all polypeptides were obtained with high purity. This is an approach that can be used in other difficult hydrophobic peptides.     

Estimation of photosynthesis parameters for a modified Farquhar–von Caemmerer–Berry model using simultaneous estimation method and nonlinear mixed effects model

The aims of this paper was to modify the photosynthesis model of Farquhar, von Caemmerer and Berry (FvCB) to be able to predict light dependency of the carboxylation capacity (V_c) and to improve the prediction of temperature dependency of the maximum carboxylation capacity (V_cmax) and the maximum electron transport rate (J_max). The FvCB model was modified by adding a sub-model for Ribulose-1,5-bisphosphate carboxylase (Rubisco) activation and validating the parameters for temperature dependency of V_cmax and J_max. Values of parameters for temperature dependency of V_cmax and J_max were validated and adjusted based on data of the photosynthesis response to temperature. Parameter estimation was based on measurements under a wide range of environmental conditions, providing parameters with broad validity. The simultaneous estimation method and the nonlinear mixed effects model were applied to ensure the accuracy of the parameter estimation. The FvCB parameters, V_cmax, J_max, α (the efficiency of light energy conversion), θ (the curvature of light response of electron transport), and R_d (the non-photorespiratory CO₂ release) were estimated and validated on a dataset from two other years. Observations and predictions matched well (R² = 0.94). We conclude that incorporating a sub-model of Rubisco activation improved the FvCB model through predicting light dependency of carboxylation rate; and that estimating V_cmax, J_max, α, θ, and R_d requires data sets of both CO₂ and light response curves.     

Thermodynamics of protein folding using a modified Wako-Sait?-Mu?oz-Eaton model

Herein, we propose a modified version of the Wako-Saitô-Muñoz-Eaton (WSME) model. The proposed model introduces an empirical temperature parameter for the hypothetical structural units (i.e., foldons) in proteins to include site-dependent thermodynamic behavior. The thermodynamics for both our proposed model and the original WSME model were investigated. For a system with beta-hairpin topology, a mathematical treatment (contact-pair treatment) to facilitate the calculation of its partition function was developed. The results show that the proposed model provides better insight into the site-dependent thermodynamic behavior of the system, compared with the original WSME model. From this site-dependent point of view, the relationship between probe-dependent experimental results and model’s thermodynamic predictions can be explained. The model allows for suggesting a general principle to identify foldon behavior. We also find that the backbone hydrogen bonds may play a role of structural constraints in modulating the cooperative system. Thus, our study may contribute to the understanding of the fundamental principles for the thermodynamics of protein folding.     

Quantifying threats in a Mediterranean wetland: are there any changes in their evaluation during a training course?

“Threats analysis” is a conservation discipline directed to identify, quantify, rank, map the human-induced threats occurring in a specific study area, assessing their spatial-temporal regime (e.g., the extension and intensity on specific targets of conservation concern). This approach may be particularly useful in order to define the priorities in the management strategies to be adopted by nature reserves, especially those that are situated in human-altered multi-disturbed contexts. In a remnant Mediterranean wetland of central Italy, where 15 human-induced threats were identified, we compared the assessment given for two regime parameters (scope and severity) of each threat by a panels of not-expert students (n = 13) during different phases of a training academic course, thus evaluating perception modifications during three steps. We applied an experience-based method, then comparing the assessments obtained during the training course with the values obtained previously from a panel of experts (n = 10). Two direct threats (pollution and alien species) significantly changed their mean values in scope during the three steps, and three threats (habitat conversion, garbage, and aircraft) significantly changed as for severity. Students tended to significantly correct their responses in such a way to progressively match with the experts’ responses for a set of threats either for scope (habitat conversion, linear infrastructures, grazing, garbage, fires on reed-beds) or severity (pollution, garbage, fires on reed-beds). Despite the responses were not clear for some threats (aircraft), we suppose that students could assign a initial emphasis towards more charismatic threats as pollution, garbage, fires that instead locally did not appear of priority concern, while threats being uneasily detected (as alien species) were underestimated. Our study showed that a training course with field surveys allows to better define and contextualize the threats affecting a given area, reducing the perception effect that each student had prior to the beginning of the course, when their education information was mainly mass-media based.     

Simultaneous assay of muscarinic and β-adrenergic receptors using a double isotope technique

Muscarinic receptor and β-adrenergic receptor binding were measured simultaneously in a membrane fraction of bovine tracheal smooth muscle using [³H]-L-quinuclidinyl benzilate and [¹²⁵I]-(?)iodocyanopindolol. The binding characteristics, affinity and receptor density, obtained in the double receptor assay and in the control experiments were the same within experimental error. Moreover, there appears to be neither a significant influence of an excess of d,l-propranolol on [³H]-L-quinuclidinyl benzilate binding nor a significant influence of an excess of l-quinuclidinyl benzilate on [¹²⁵I]-(?)iodocyanopindolol binding. The method is advantageous where both receptors have to be assayed and where limited amounts of biological material, like in biopsy specimen, are available.     

Expression ofEscherichia coli recA andada genes inSaccharomyces cerevisiœ using a vector with geneticin resistance

Construction ofE. coli-yeast shuttle plasmids containing theneo selection gene is described. The protein-coding regions of theE. coli ada orrecA genes under the control of theADH1 promoter and terminator were ligated into theSphI unique site of pNF2 to produce pMSada and pMSrecA, respectively. The plasmids were used for transformation of the haploid and diploidpso4-1 strains ofS. cerevisiœ and their corresponding wild types. Transformants were obtained by selection for geneticin (G418) resistance. Crude protein samples were extracted from the individual transformants. Both the RecA and Ada proteins were present in all strains containing therecA andada genes on plasmids, respectively. Thus the geneticin selection system was successfully used for the preparation of model, yeast strains.     

A new 10-min ligation method using a modified buffer system with a very low amount of T4 DNA ligase: the “Coffee Break Ligation” technique

The ligation reaction is widely used in molecular biology. There are several kits available that complete the ligation reaction very rapidly but they are rather expensive. In this study, we successfully modified the ligation buffer with much lower cost than existing kits. The ligation reaction can be completed in 10 min using very low activities such as 0.01 U T4 DNA ligase, and costs only $1 for 100 reactions of 20 μl scale. We name this ligation system the “Coffee Break Ligation” system; one can complete ligation reaction while drinking a cup of coffee, and perform 100 reactions by spending money equivalent to a cup of coffee.     

Biodegradation of ketoprofen using a microalgal–bacterial consortium

Objective

To test the toxicity of ketoprofen (a commonly-used NSAIDs) using two microalgal strains and Artemia sp. following the isolation of bacterial and microalgal strains and testing their ability to biodegrade and tolerate ketoprofen.

Results

Chlorella sp. was the most resistant to ketoprofen. A defined bacterial consortium (K₂) degraded 5 mM ketoprofen as a sole carbon source both in the dark or continuous illumination. Ketoprofen did not undergo photodegradation. In the dark, biodegradation was faster with a lag phase of 10 h, 41% COD removal and 82 % reduction in toxicity. The consortium degraded up to 16 mM ketoprofen. The consortium was composed of four bacterial isolates that were identified. MS/MS analysis suggested a ketoprofen biodegradation pathway that has not been previously reported. Combining Chlorella sp. and the K₂ consortium, ketoprofen was degraded within 7 days under a diurnal cycle of 12 h light/12 h dark.

Conclusion

The feasibility of using a microalgal–bacterial system to treat pharmaceutical wastewater is promising for the reduction of the process cost and providing a safer technology for pharmaceutical wastewater treatment.