Single-beat estimation of right ventricular end-systolic pressure-volume relationship

Assessment of right ventricular (RV) contractility from end-systolic pressure-volume relationships (ESPVR) is difficult due to problems in measuring RV instantaneous volume and to effects of changes in RV preload or afterload. We therefore investigated in anesthetized dogs whether RV ESPVR and contractility can be determined without measuring RV volume and without changing RV preload or afterload. The maximal RV pressure of isovolumic beats (P(max)) was predicted from isovolumic portions of RV pressure during ejecting beats and compared with P(max) measured during the first beat after pulmonary artery clamping. In RV pressure-volume loops obtained from RV pressure and integrated pulmonary arterial flow, end-systolic elastance (E(es)) was assessed as the slope of P(max)-derived ESPVR, pulmonary artery effective elastance (E(a)) as the slope of end-diastolic to end-systolic relation, and coupling efficiency as the E(es)-to-E(a) ratio (E(es)/E(a)). Predicted P(max) correlated with observed P(max) (r = 0.98 +/- 0.02). Dobutamine increased E(es) from 1.07 to 2.00 mmHg/ml and E(es)/E(a) from 1.64 to 2.49, and propranolol decreased E(es)/E(a) from 1.64 to 0.91 (all P < 0.05). After adrenergic blockade, preload reduction did not affect E(es), whereas hypoxia and arterial constriction markedly increased E(a) and somewhat increased E(es) due to the Anrep effect. Low preload did not affect E(es)/E(a) and high afterload decreased E(es)/E(a). In conclusion, in the right ventricle 1) P(max) can be calculated from normal beats, 2) P(max) can be used to determine ESPVR without change in load, and 3) P(max)-derived ESPVR can be used to assess ventricular contractility and ventricular-arterial coupling efficiency.     

Left ventricular end-diastolic pressure-volume relationship in septic rats with open thorax

To estimate changes in compliance, we evaluated the effects of sepsis on the end-diastolic pressure-volume relationship (EDPVR) in the left ventricle of rats that had undergone an open thorax procedure. Sepsis was induced in male Wistar Hannover rats (n = 7; 240 to 270 g) by intraperitoneal administration of a slurry of cecal contents; control rats (n = 7) were given 5% dextrose only. On the third day after induction of sepsis, left ventricular (LV) pressure and LV dimensions were recorded simultaneously in animals of both groups. Using a micromanometer and ultrasonic crystals, measurements were obtained at baseline and during the increase of afterload. Blood samples were taken for determination of complete blood count, white blood cell differential count, and lactate concentration, and for bacteriologic examination. Septic rats lost weight, and developed changes in body temperature, ascites, and abscesses in the abdominal and thoracic cavities, gram-negative bacteremia, and increase in heart rate. On the third day after induction of sepsis, LV EDPVR decreased, compared with that in the control rats (regression coefficients: control group, 8.41 to 23.95; sepsis group, 3.94 to 7.92). Myocardial compliance in the left ventricle increased on the third day of sepsis in the open-thorax rat model, as evidenced by the downward shift of LV EDPVR in rats with sepsis, compared with controls.     

PREDICT: a method for inferring novel drug indications with application to personalized medicine

Inferring potential drug indications, for either novel or approved drugs, is a key step in drug development. Previous computational methods in this domain have focused on either drug repositioning or matching drug and disease gene expression profiles. Here, we present a novel method for the large‐scale prediction of drug indications (PREDICT) that can handle both approved drugs and novel molecules. Our method is based on the observation that similar drugs are indicated for similar diseases, and utilizes multiple drug–drug and disease–disease similarity measures for the prediction task. On cross‐validation, it obtains high specificity and sensitivity (AUC=0.9) in predicting drug indications, surpassing existing methods. We validate our predictions by their overlap with drug indications that are currently under clinical trials, and by their agreement with tissue‐specific expression information on the drug targets. We further show that disease‐specific genetic signatures can be used to accurately predict drug indications for new diseases (AUC=0.92). This lays the computational foundation for future personalized drug treatments, where gene expression signatures from individual patients would replace the disease‐specific signatures.     

Parameter estimation with a novel gradient-based optimization method for biological lattice-gas cellular automaton models

Lattice-gas cellular automata (LGCAs) can serve as stochastic mathematical models for collective behavior (e.g. pattern formation) emerging in populations of interacting cells. In this paper, a two-phase optimization algorithm for global parameter estimation in LGCA models is presented. In the first phase, local minima are identified through gradient-based optimization. Algorithmic differentiation is adopted to calculate the necessary gradient information. In the second phase, for global optimization of the parameter set, a multi-level single-linkage method is used. As an example, the parameter estimation algorithm is applied to a LGCA model for early in vitro angiogenic pattern formation.     

A novel noninvasive method for assessing glutathione-conjugate efflux systems in the brain

Brain efflux systems export such conjugated metabolites as glutathione (GSH) and glucuronate conjugates, generated by the detoxification process, from the brain and serve to protect the brain from harmful metabolites. The intracerebral injection of a radiolabeled conjugate is a useful technique to assess brain efflux systems; however, this technique is not applicable to humans. Hence, we devised a novel noninvasive approach for assessing GSH-conjugate efflux systems using positron emission tomography. Here, we investigated whether or not a designed proprobe can deliver its GSH conjugate into the brain. Radiolabeled 6-chloro-7-methylpurine (7m6CP) was designed as the proprobe, and [(14)C]7m6CP was prepared by the reaction of 6-chloropurine with [(14)C]CH(3)I as a model of [(11)C]CH(3)I. The radiochemical yield and purity of [(14)C]7m6CP were 10-20% and greater than 99%, respectively. High brain uptake (0.8% ID/g) at 1 min was observed, followed by gradual radioactivity clearance from the brain for 5-60 min after the injection of [(14)C]7m6CP into rats. Analysis of metabolites confirmed that the presence of [(14)C]7m6CP was hardly observed, and 80% of the radioactivity was identical to its GSH conjugate for 15-60 min. The brain radioactivity was single-exponentially decreased during the period of 15-60 min post-injection of [(14)C]7m6CP, and the first-order efflux rate constant of the conjugate, estimated from the slope, was 0.0253 min(-1). These results showed that (1) [(14)C]7m6CP readily entered the brain, (2) it efficiently and specifically transformed to the GSH conjugate within the brain, and (3) after [(14)C]7m6CP disappearance, the clearance of radioactivity represented the only efflux of GSH conjugate. We conclude that 7m6CP can deliver the GSH conjugate into the brain and would be useful for assessing GSH-conjugate efflux systems noninvasively.     

A method for automated pathogenic content estimation with application to rheumatoid arthritis

Background

Sequencing technologies applied to mammals’ microbiomes have revolutionized our understanding of health and disease. Hence, to assess diseases’ progression as well as therapies longterm effects, the impact of maladies and drugs on the gut-intestinal (GI) microbiome has to be evaluated. Typical metagenomic analyses are run to associate to a condition (disease, therapy, diet) a pool of bacteria, whose eubiotic/dysbiotic potential is assessed either by α-diversity, a measure of the varieties populating the microbiome, or by Firmicutes to Bacteroides ratio, associated to systemic inflammation, and finally by manual and direct inspection of bacteria’s biological functions, when known. These approaches lead to results sometimes difficult to interpret in terms of the evolution towards a specific microbial composition, harmed by large areas of unknown.

Results

We propose to additionally evaluate a microbiome based on its global composition, by automatic annotation of pathogenic genera and statistical assessment of the net varied frequency of harmless versus harmful organisms. This application is intuitive, quantitative and computationally efficient and designed to cope with the currently incomplete species’ functional knowledge. Our results, applied to human GI-microbiome data exemplify how this layer of information provides additional insights into treatments’ impact on the GI microbiome, allowing to characterize a more physiologic effects of Prednisone versus Methotrexate, two treatments for rheumatoid arthritis (RA) a complex autoimmune systemic disease.

Conclusions

Our quantitative analysis integrates with previous approaches offering an additional systemic level of interpretation here applied, for its potential to translate into clinically relevant information, to the therapies for RA.

     

Toward a noninvasive subject-specific estimation of abdominal aortic pressure

A method for estimation of central arterial pressure based on linear one-dimensional wave propagation theory is presented in this paper. The equations are applied to a distributed model of the arterial tree, truncated by three-element windkessels. To reflect individual differences in the properties of the arterial trees, we pose a minimization problem from which individual parameters are identified. The idea is to take a measured waveform in a peripheral artery and use it as input to the model. The model subsequently predicts the corresponding waveform in another peripheral artery in which a measurement has also been made, and the arterial tree model is then calibrated in such a way that the computed waveform matches its measured counterpart. For the purpose of validation, invasively recorded abdominal aortic, brachial, and femoral pressures in nine healthy subjects are used. The results show that the proposed method estimates the abdominal aortic pressure wave with good accuracy. The root mean square error (RMSE) of the estimated waveforms was 1.61 +/- 0.73 mmHg, whereas the errors in systolic and pulse pressure were 2.32 +/- 1.74 and 3.73 +/- 2.04 mmHg, respectively. These results are compared with another recently proposed method based on a signal processing technique, and it is shown that our method yields a significantly (P < 0.01) lower RMSE. With more extensive validation, the method may eventually be used in clinical practice to provide detailed, almost individual, specific information as a valuable basis for decision making.     

An alternative method for analysing pressure-volume curves produced with the pressure chamber

Abstract. An equation is derived relating tissue water potential to relative water content. This equation may be used to lit a single curve to a set of data such as the standard pressure volume measurements made with a pressure chamber. From such a single curve fitting operation, estimates of the parameters involved may be found, and this allows calculation of such quantities as bulk modulus of elasticity, osmotic potential at full turgor and at the turgor loss point, pressure potential, and the weight of symplastic water. The method of analysis has several advantages, which are illustrated using pressure chamber data obtained from leaves of Lombardy poplar, Populus nigra L. 'italica'.     

A secreted form of the asialoglycoprotein receptor, sH2a, as a novel potential noninvasive marker for liver fibrosis

Background and Aim

The human asialoglycoprotein receptor is a membrane heterooligomer expressed exclusively in hepatocytes. A soluble secreted form, sH2a, arises, not by shedding at the cell surface, but by intracellular cleavage of its membrane-bound precursor, which is encoded by an alternatively spliced form of the receptor H2 subunit. Here we determined and report that sH2a, present at constant levels in serum from healthy individuals is altered upon liver fibrosis, reflecting the status of hepatocyte function.

Methods

We measured sH2a levels in serum using a monoclonal antibody and an ELISA assay that we developed, comparing with routine liver function markers. We compared blindly pretreatment serum samples from a cohort of 44 hepatitis C patients, which had METAVIR-scored biopsies, with 28 healthy individuals.

Results

sH2a levels varied minimally for the healthy individuals (150±21 ng/ml), whereas the levels deviated from this normal range increasingly in correlation with fibrosis stage. A simple algorithm combining sH2a levels with those of alanine aminotransferase allowed prediction of fibrosis stage, with a very high area under the ROC curve of 0.86.

Conclusions

sH2a has the potential to be a uniquely sensitive and specific novel marker for liver fibrosis and function.     

Rare actinomycetes: a potential storehouse for novel antibiotics

New antimicrobial agents are desperately needed to combat the increasing number of antibiotic resistant strains of pathogenic microorganisms. Natural products remain the most propitious source of novel antibiotics. It is widely accepted that actinobacteria are prolific producers of natural bioactive compounds. We argue that the likelihood of discovering a new compound having a novel chemical structure can be increased with intensive efforts in isolating and screening rare genera of microorganisms. Screening rare actinomycetes and their previously under-represented genera from unexplored environments in natural product screening collections is one way of achieving this. Rare actinomycetes are usually regarded as the actinomycete strains whose isolation frequency is much lower than that of the streptomycete strains isolated by conventional methods. Many natural environments are still either unexplored or under-explored and thus, can be considered as a prolific resource for the isolation of less exploited microorganisms. More and different ecological niches need to be studied as sources of a greater diversity of novel microorganisms. In this review, we wish to update our understanding of the potential of the rare actinomycetes by focusing on the ways and means of enhancing their bio-discovery potential.     

Improved method for estimation of inorganic phosphate: implications for its application in enzyme assays

The conventional method of Fiske and Subba Row for the estimation of inorganic phosphate (Pi) is although rapid, but suffers from the disadvantage that the color is unstable and hence the optical density (OD) measurements have to be carried out within a short time span of 8-12 min. This poses a restriction on the number of samples, which can be handled in a batch. Although, modified procedures involving use of alternate reducing agents/or increasing the concentration of H2SO4 in conventional method have been subsequently developed, but the problem of color stability could not be solved. In addition, the use of higher concentrations H2SO4 has rendered the methods unsuitable in enzyme assays, especially if the acid labile phosphate containing substrates have been used. In the present study, attempts have been made to suitably modify the method to improve the stability of the color and sensitivity and also for its applicability in enzyme assays, especially when acid labile phosphate containing substrates such as ATP is used. We used the higher concentrations (0.625, 0.8 and 1.0 N) of H2SO4 rather than 0.5 N used in the conventional assay procedures. Under these conditions, the reagent blanks do not develop color for up to 24 h, whereas the intensity of the molybdenum blue color in the standard and/or experimental tubes increased with time reaching optimum value at 24 h. Simultaneously, the absorption maximum shifts from 660 nm to 820 nm. The highest concentration of H2SO4 (1.0 N) is found to be the most effective in the process of color development. The sensitivity of the method is from 1.7 to 2.1 times higher, as compared to the conventional Fiske and Subba Row method for the measurements carried out at the end of 15 min at 820 nm and with the highest concentration of H2SO4 (1.0 N); the sensitivity increased 4.8-fold at the end of 24 h. Presence of glucose and sucrose (1-10 mM), NaCl and KCI (5-100 mM), MgCl2 (1-10 mM) and BSA (10 to 500 microg per assay tube) do not interfere either with color development or with OD measurements. The extent of ATP hydrolysis is 1.6 to 3.4% for up to 1 hi, depending upon the concentration of H2SO4 used. Only negligible hydrolysis of G6P is observed under these conditions. These results suggest that the presently modified method is suitable for Pi analysis in the enzyme assays, in the presence of labile phosphate containing substrates.     

Rare actinomycetes: a potential storehouse for novel antibiotics

New antimicrobial agents are desperately needed to combat the increasing number of antibiotic resistant strains of pathogenic microorganisms. Natural products remain the most propitious source of novel antibiotics. It is widely accepted that actinobacteria are prolific producers of natural bioactive compounds. We argue that the likelihood of discovering a new compound having a novel chemical structure can be increased with intensive efforts in isolating and screening rare genera of microorganisms. Screening rare actinomycetes and their previously under-represented genera from unexplored environments in natural product screening collections is one way of achieving this. Rare actinomycetes are usually regarded as the actinomycete strains whose isolation frequency is much lower than that of the streptomycete strains isolated by conventional methods. Many natural environments are still either unexplored or under-explored and thus, can be considered as a prolific resource for the isolation of less exploited microorganisms. More and different ecological niches need to be studied as sources of a greater diversity of novel microorganisms. In this review, we wish to update our understanding of the potential of the rare actinomycetes by focusing on the ways and means of enhancing their bio-discovery potential.     

Postnatal gestational age estimation via newborn screening analysis: application and potential

ABSTRACT

Introduction: Preterm birth is a major global health concern, contributing to 35% of all neonatal deaths in 2016. Given the importance of accurately ascertaining estimates of preterm birth and in light of current limitations in postnatal gestational age (GA) estimation, novel methods of estimating GA postnatally in the absence of prenatal ultrasound are needed. Previous work has demonstrated the potential for metabolomics to estimate GA by analyzing data captured through routine newborn screening.

Areas covered: Circulating analytes found in newborn blood samples vary by GA. Leveraging newborn screening and demographic data, our group developed an algorithm capable of estimating GA postnatally to within approximately 1 week of ultrasound-validated GA. Since then, we have built on the model by including additional analytes and validating the model’s performance through internal and external validation studies, and through implementation of the model internationally.

Expert opinion: Currently, using metabolomics to estimate GA postnatally holds considerable promise but is limited by issues of cost-effectiveness and resource access in low-income settings. Future work will focus on enhancing the precision of this approach while prioritizing point-of-care testing that is both accessible and acceptable to individuals in low-resource settings.     

Confocal optical system: a novel noninvasive sensor to study mixing

A novel confocal optical system to study mixing time in small-scale bioreactors is presented. The system is designed to monitor fluorescence upon tracer addition from a localized confocal volume of 0.21 mL within a glass vessel. The key elements of the fluorescence-based confocal system are a pinhole, a lens, an APD (Avalanche photodiode) detector, and light filters. The optical technique was validated by comparison with a pH-based technique. Finally, the optical sensor was tested and a real cultivation media (i.e., spent mammalian cell media) was used to measure mixing time in a 12.5-mL stirred transparent vessel. High accuracy, easy results interpretation, and low costs are the three most attractive characteristics of the sensor. Because of its noninvasive nature and versatility, the results suggest that the confocal system is a promising tool to perform mixing time studies in stirred vessels.     

Improved noninvasive genotyping method: application to brown bear (Ursus arctos) faeces

We redesigned new microsatellite primers and one sex‐specific primer for amplification of faecal DNA from brown bears (Ursus arctos). We also combined a semi‐nested polymerase chain reaction (PCR) with a newly developed multiplex preamplification method in order to increase the quality of the amplified DNA fragments. In comparison with a conventional PCR approach, the genotyping error rate was substantially reduced and the amplification rate was increased. This new approach could be transposed to other species where conventional PCR methods experience low success due to limited DNA concentration and/or quality.     

REVCOM: a robust Bayesian method for evolutionary rate estimation

MOTIVATION: Evolutionary conservation estimated from a multiple sequence alignment is a powerful indicator of the functional significance of a residue and helps to predict active sites, ligand binding sites, and protein interaction interfaces. Many algorithms that calculate conservation work well, provided an accurate and balanced alignment is used. However, such a strong dependence on the alignment makes the results highly variable. We attempted to improve the conservation prediction algorithm by making it more robust and less sensitive to (1) local alignment errors, (2) overrepresentation of sequences in some branches and (3) occasional presence of unrelated sequences. RESULTS: A novel method is presented for robust constrained Bayesian estimation of evolutionary rates that avoids overfitting independent rates and satisfies the above requirements. The method is evaluated and compared with an entropy-based conservation measure on a set of 1494 protein interfaces. We demonstrated that approximately 62% of the analyzed protein interfaces are more conserved than the remaining surface at the 5% significance level. A consistent method to incorporate alignment reliability is proposed and demonstrated to reduce arbitrary variation of calculated rates upon inclusion of distantly related or unrelated sequences into the alignment.     

A novel method for the estimation of soybean chlorophyll content using a smartphone and image analysis

The development of smartphones, specifically their cameras, and imaging technologies has enabled their use as sensors/measurement tools. Here we aimed to evaluate the applicability of a fast and noninvasive method for the estimation of total chlorophyll (Chl), Chl a, Chl b, and carotenoids (Car) content of soybean plants using a smartphone camera. Single leaf disc images were obtained using a smartphone camera. Subsequently, for the same leaf discs, a Chl meter was used to obtain the relative index of Chl and the photosynthetic pigments were then determined using a classic method. The RGB, HSB and CIELab color models were extracted from the smartphone images and correlated to Chl values obtained using a Chl meter and by a standard laboratory protocol. The smartphone camera was sensitive enough to capture successfully a broad range of Chl and Car contents seen in soybean leaves. Although there was a variation between color models, some of the proposed regressions (e.g., the S and b index from HSB and Lab color models and NRI [RGB model]) were very close to the Chl meter values. Based on our findings, smartphones can be used for rapid and accurate estimation of soybean and Car contents in soybean leaves.