Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models

Whole-cell models that explicitly represent all cellular components at the molecular level have the potential to predict phenotype from genotype. However, even for simple bacteria, whole-cell models will contain thousands of parameters, many of which are poorly characterized or unknown. New algorithms are needed to estimate these parameters and enable researchers to build increasingly comprehensive models. We organized the Dialogue for Reverse Engineering Assessments and Methods (DREAM) 8 Whole-Cell Parameter Estimation Challenge to develop new parameter estimation algorithms for whole-cell models. We asked participants to identify a subset of parameters of a whole-cell model given the model’s structure and in silico “experimental” data. Here we describe the challenge, the best performing methods, and new insights into the identifiability of whole-cell models. We also describe several valuable lessons we learned toward improving future challenges. Going forward, we believe that collaborative efforts supported by inexpensive cloud computing have the potential to solve whole-cell model parameter estimation.     

Preparation, Purification, and Stability of Tuberculin

The method used to produce “Connaught” tuberculin purified protein derivative (PPD) is described. The tuberculin PPD for the multiple-puncture method was shown to be stable for at least 24 months at 5 C; tuberculin PPD for the intracutaneous method was shown to be stable at 5 C and 24 C for a period of 18 months in the presence of Tween 80. Evans blue or brillant vital red was added to tuberculin PPD for improved testing by the multiple-puncture method. These tinted tuberculin preparations were found to be as stable as the Connaught tuberculin PPD preparations without dye at 5 C. Freeze-dried tuberculin PPD with Plasdone as an inert base was found to be remarkably stable for a period of at least 24 months at 5, 24, and 37 C.     

Cardiac Pressure-Volume Loop Analysis Using Conductance Catheters in Mice

Cardiac pressure-volume loop analysis is the “gold-standard” in the assessment of load-dependent and load-independent measures of ventricular systolic and diastolic function. Measures of ventricular contractility and compliance are obtained through examination of cardiac response to changes in afterload and preload. These techniques were originally developed nearly three decades ago to measure cardiac function in large mammals and humans. The application of these analyses to small mammals, such as mice, has been accomplished through the optimization of microsurgical techniques and creation of conductance catheters. Conductance catheters allow for estimation of the blood pool by exploiting the relationship between electrical conductance and volume. When properly performed, these techniques allow for testing of cardiac function in genetic mutant mouse models or in drug treatment studies. The accuracy and precision of these studies are dependent on careful attention to the calibration of instruments, systematic conduct of hemodynamic measurements and data analyses. We will review the methods of conducting pressure-volume loop experiments using a conductance catheter in mice.     

Analysis of collagen cyanogen bromide peptides using electrophoresis in continuous concave gradient polyacrylamide gels.

A rapid and simple spectrophotometric method is described for the estimation of microgram quantities of glycosaminoglycans following the formation of soluble complexes with alcian blue dye. The method is based on the different absorption spectra of the dye and dye-glycosaminoglycan complexes. No heating, centrifugation, lengthy equilibration, or sophisticated instrumentation which hamper other methods are required. Samples are mixed with freshly prepared dye solution and absorbance readings at 480 nm are compared to an appropriate standard curve. Albumin and individual monosaccharides do not interfere with the assay but high concentrations of chloride ion do. The method is suitable for the estimation of total glycosaminoglycan levels in biological fluids such as urine and blood.     

Development of a Compatible Taper Function and Stand-Level Merchantable Volume Model for Chinese Fir Plantations

Chinese fir (Cunninghamia lanceolata [Lamb.] Hook) is one of the most important plantation tree species in China with good timber quality and fast growth. It covers an area of 8.54 million hectare, which corresponds to 21% of the total plantation area and 32% of total plantation volume in China. With the increasing market demand, an accurate estimation and prediction of merchantable volume at tree- and stand-level is becoming important for plantation owners. Although there are many studies on the total tree volume estimation from allometric models, these allometric models cannot predict tree- and stand-level merchantable volume at any merchantable height, and the stand-level merchantable volume model was not seen yet in Chinese fir plantations. This study aimed to develop (1) a compatible taper function for tree-level merchantable volume estimation, and (2) a stand-level merchantable volume model for Chinese fir plantations. This “taper function system” consisted in a taper function, a merchantable volume equation and a total tree volume equation. 46 Chinese fir trees were felled to develop the taper function in Shitai County, Anhui province, China. A second-order continuous autoregressive error structure corrected the inherent serial autocorrelation of different observations in one tree. The taper function and volume equations were fitted simultaneously after autocorrelation correction. The compatible taper function fitted well to our data and had very good performances in diameter and total tree volume prediction. The stand-level merchantable volume equation based on the ratio approach was developed using basal area, dominant height, quadratic mean diameter and top diameter (ranging from 0 to 30 cm) as independent variables. At last, a total stand-level volume table using stand basal area and dominant height as variables was proposed for local forest managers to simplify the stand volume estimation.     

Errors of measurement for blood volume parameters: a meta-analysis.

The volume of red blood cells (V(RBC)) is used routinely in the diagnostic workup of polycythemia, in assessing the efficacy of erythropoietin administration, and to study factors affecting oxygen transport. However, errors of various methods of measurement of V(RBC) and related parameters are not well characterized. We meta-analyzed 346 estimates of error of measurement of V(RBC) for techniques based on Evans blue (V(RBC,Evans)), 51chromium-labeled red blood cells (V(RBC,51Cr)), and carbon monoxide (CO) rebreathing (V(RBC,CO)), as well as hemoglobin mass with the carbon-monoxide method (M(Hb,CO)), in athletes and active and inactive subjects undergoing various experimental and control treatments lasting minutes to months. Subject characteristics and experimental treatments had little effect on error of measurement, but measures with the smallest error showed some increase in error with increasing time between trials. Adjusted to 1 day between trials and expressed as coefficients of variation, mean errors for M(Hb,CO) (2.2%; 90% confidence interval 1.4-3.5%) and V(RBC,51Cr) (2.8%; 2.4-3.2%) were much less than those for V(RBC,Evans) (6.7%; 4.9-9.4%) and V(RBC,CO) (6.7%; 3.4-14%). Most of the error of V(RBC,Evans) was due to error in measurement of volume of plasma via Evans blue dye (6.0%; 4.5-7.8%), which is the basis of V(RBC,Evans). Most of the error in V(RBC,CO) was due to estimates from laboratories with a relatively large error in M(Hb,CO), the basis of V(RBC,CO). V(RBC,51Cr) and M(Hb,CO) are the best measures for research on blood-related changes in oxygen transport. With care, V(RBC,Evans) is suitable for clinical applications of blood-volume measurement.     

LOSS OF BLOOD AT OPERATION—A Method for Continuous Measurement

A method for continuous measurement of surgical blood loss has been devised and has been used clinically in some 400 cases. The method combines volumetric measure of the suction loss and gravimetric measure of the sponge loss. The volumetric device automatically deducts the volume of rinse water used and thus measures the amount of blood collected in a metering cylinder. The suction loss scale shows continuously the amount of blood in the metering cylinder. The gravimetric device requires counting sponges into the weighing pan, and turning a dial scale to deduct the initial weight of the sponges. The volume of blood in the sponges is then read directly on the dial scale. Use of the instrument, which is under the supervision of the anesthesiologist, adds about two minutes per hour to the time normally required for counting the sponges; and about three minutes per hour is required for tending the volumetric instrument.In clinical use, knowing constantly the amount of blood loss permits the starting of transfusion before serious deficit develops, and then maintaining the patient''s blood volume at a predetermined optimum level. In some 400 cases the continuous measurement of the blood loss served as a reliable guide for carrying out the loss-replacement plan within close limits of accuracy.     

Loss of blood at operation; a method for continuous measurement

A method for continuous measurement of surgical blood loss has been devised and has been used clinically in some 400 cases. The method combines volumetric measure of the suction loss and gravimetric measure of the sponge loss. The volumetric device automatically deducts the volume of rinse water used and thus measures the amount of blood collected in a metering cylinder. The suction loss scale shows continuously the amount of blood in the metering cylinder. The gravimetric device requires counting sponges into the weighing pan, and turning a dial scale to deduct the initial weight of the sponges. The volume of blood in the sponges is then read directly on the dial scale. Use of the instrument, which is under the supervision of the anesthesiologist, adds about two minutes per hour to the time normally required for counting the sponges; and about three minutes per hour is required for tending the volumetric instrument.In clinical use, knowing constantly the amount of blood loss permits the starting of transfusion before serious deficit develops, and then maintaining the patient's blood volume at a predetermined optimum level. In some 400 cases the continuous measurement of the blood loss served as a reliable guide for carrying out the loss-replacement plan within close limits of accuracy.     

Special stereotactic radiotherapy techniques: procedures and equipment for treatment simulation and dose delivery

Stereotactic radiotherapy (SRT ) is a multi-step procedure with each step requiring extreme accuracy. Physician-dependent accuracy includes appropriate disease staging, multi-disciplinary discussion with shared decision-making, choice of morphological and functional imaging methods to identify and delineate the tumor target and organs at risk, an image-guided patient set-up, active or passive management of intra-fraction movement, clinical and instrumental follow-up. Medical physicist-dependent accuracy includes use of advanced software for treatment planning and more advanced Quality Assurance procedures than required for conventional radiotherapy. Consequently, all the professionals require appropriate training in skills for high-quality SRT.Thanks to the technological advances, SRT has moved from a “frame-based” technique, i.e. the use of stereotactic coordinates which are identified by means of rigid localization frames, to the modern “frame-less” SRT which localizes the target volume directly, or by means of anatomical surrogates or fiducial markers that have previously been placed within or near the target. This review describes all the SRT steps in depth, from target simulation and delineation procedures to treatment delivery and image-guided radiation therapy. Target movement assessment and management are also described.     

A modified whole blood partial thromboplastin test for the assessment of heparinization

Current methods of assessment of heparinization are either inconvenient as bedside procedures or lack correlation with the Lee-White whole blood clotting time over the therapeutic range. A new thromboplastin time (CAT time) has been developed to overcome these disadvantages by offering uniform contact activation. The test makes use of a partial thromboplastin activated by celite-adsorbed “contact factor”, thus eliminating the activation phase of the activated partial thromboplastin time. Preliminary experiments suggest that this modification will be helpful in the study of “contact factor” deficiencies.     

Blood Pressure: A Consideration of Terminology

Concepts of hypertension have changed and changes in terminology to reflect this state of affairs are suggested. Statistically, the best mortality experience is associated with blood pressure commonly regarded as subnormal, and increments of blood pressure above this level are associated with progressive increases in mortality. The terms “normal”, “benign” and “essential” in relation to blood pressure should be abandoned. “Optimal”, “acceptable” and “hypertensive” ranges of blood pressure are suggested. Hypertension is regarded as a symptom of disease, rather than as a disease in itself, and “hypertension”, when used as a diagnostic label, should be qualified always by the primary disease, if known, or by the modifying phrase, “of unknown cause”, if not known.     

Body Composition and Body Weight: Criteria of Overnutrition

The terms “body weight” and “body composition” are by no means synonymous, and attention is increasingly being focused on body composition. A measurement of relative fatness is a better criterion of caloric overnutrition than is body weight.The simple technique of skinfold measurement using established standard methods is the most practical for use in the field to obtain an estimate of fatness or caloric overnutrition. The current need is for the establishment of “norms” for skinfolds for population groups of all ages and both sexes. When these are established, excellent simple criteria for overnutrition will be available.Prior to the establishment of norms, more work is needed to indicate which skinfolds for each age group and for each sex best reflect total body fatness. Body fatness may then be studied in relation to body weight and both may be related to morbidity, mortality and longevity. Finally, the answer may be obtained to the question whether it is overweight per se or overfatness that is related to excess morbidity and mortality.     

Blood volume measurement in baboons: simultaneous estimation of red cell volume and plasma volume

A method is described for frequent sequential blood volume estimation in baboons using 32P for red cell volume measurements and 125I-albumin for simultaneous plasma volume measurements. Values for red cell, plasma, and total blood volumes are reported. Close correlations of the volumes to bodyweight were demonstrated. Circulatory half-lives of the isotopes, determined from disappearance curves, confirmed their suitability for serial measurements in these baboons.     

Use of Malachite Green-Loop Mediated Isothermal Amplification for Detection of Plasmodium spp. Parasites

Malaria elimination efforts are hampered by the lack of sensitive tools to detect infections with low-level parasitemia, usually below the threshold of standard diagnostic methods, microscopy and rapid diagnostic tests. Isothermal nucleic acid amplification assays such as the loop-mediated isothermal amplification (LAMP), are well suited for field use as they do not require thermal cyclers to run the test. However, the use of specialized equipment, as described by many groups, reduces the versatility of the LAMP technique as a simple tool for use in endemic countries. In this study, the use of the malachite green (MG) dye, as a visual endpoint readout, together with a simple mini heat block was evaluated for the detection of malaria parasites. The assay was performed for 1 hour at 63°C and the results scored by 3 independent human readers. The limit of detection of the assay was determined using well-quantified Plasmodium spp. infected reference samples and its utility in testing clinical samples was determined using 190 pre-treatment specimens submitted for reference diagnosis of imported malaria in the United States. Use of a simplified boil and spin methods of DNA extraction from whole blood and filter paper was also investigated. We demonstrate the accurate and sensitive detection of malaria parasites using this assay with a detection limit ranging between 1–8 parasites/μL, supporting its applicability for the detection of infections with low parasite burden. This assay is compatible with the use of a simple boil and spin sample preparation method from both whole blood and filter papers without a loss of sensitivity. The MG-LAMP assay described here has great potential to extend the reach of molecular tools to settings where they are needed.     

Evans Blue as a Simple Method to Discriminate Mosquitoes’ Feeding Choice on Small Laboratory Animals

Background

Temperature, humidity, vision, and particularly odor, are external cues that play essential roles to mosquito blood feeding and oviposition. Entomological and behavioral studies employ well-established methods to evaluate mosquito attraction or repellency and to identify the source of the blood meal. Despite the efficacy of such methods, the costs involved in the production or acquisition of all parts, components and the chemical reagents involved are unaffordable for most researchers from poor countries. Thus, a simple and relatively low-cost method capable of evaluating mosquito preferences and the blood volume ingested is desirable.

Principal Findings

By using Evans blue (EB) vital dye and few standard laboratory supplies, we developed and validated a system capable of evaluating mosquito’s choice between two different host sources of blood. EB-injected and PBS-injected mice submitted to a number of situations were placed side by side on the top of a rounded recipient covered with tulle fabric and containing Aedes aegypti mosquitoes. Homogenates from engorged mosquitoes clearly revealed the blood source (EB- or PBS-injected host), either visually or spectrometrically. This method was able to estimate the number of engorded mosquitoes, the volume of blood ingested, the efficacy of a commercial repellent and the attractant effects of black color and human sweat.

Significance

Despite the obvious limitations due to its simplicity and to the dependence of a live source of blood, the present method can be used to assess a number of host variables (diet, aging, immunity, etc) and optimized for several aspects of mosquito blood feeding and vector-host interactions. Thus, it is proposed as an alternative to field studies, and it could be used for initial screenings of chemical compound candidates for repellents or attractants, since it replicates natural conditions of exposure to mosquitoes in a laboratory environment.     

Repeated Blood Collection for Blood Tests in Adult Zebrafish

Repeated blood collection is one of the most common techniques performed on laboratory animals. However, a non-lethal protocol for blood collection from zebrafish has not been established. The previous methods for blood collection from zebrafish are lethal, such as lateral incision, decapitation and tail ablation. Thus we have developed a novel “repeated” blood collection method, and present here a detailed protocol outlining this procedure. This method is minimally invasive and results in a very low mortality rate (2.3%) for zebrafish, thus enabling repeated blood sampling from the same individual. The maximum volume of blood sampling is dependent on body weight of the fish. The volume for repeated blood sampling at intervals should be ≤0.4% of body weight every week or ≤1% every 2 weeks, which were evaluated by measurements of blood hemoglobin. Additionally, hemoglobin, fasting blood glucose, plasma triacylglycerol (TG) and total cholesterol levels in male and female adult zebrafish were measured. We also applied this method to investigate the dysregulation of glucose metabolism in diet-induced obesity. This blood collection method will allow many applications, including glucose and lipid metabolism and hematological studies, which will increase the use of zebrafish as a human disease model organism.     

Quirks of dye nomenclature. 1. Evans blue

The history, origin, identity, chemistry and use of Evans blue dye are described along with the first application to staining by Herbert McLean Evans in 1914. In the 1930s, the dye was marketed under the name, Evans blue dye, which was profoundly more acceptable than the ponderous chemical name.     

Discriminating Different Classes of Biological Networks by Analyzing the Graphs Spectra Distribution

The brain''s structural and functional systems, protein-protein interaction, and gene networks are examples of biological systems that share some features of complex networks, such as highly connected nodes, modularity, and small-world topology. Recent studies indicate that some pathologies present topological network alterations relative to norms seen in the general population. Therefore, methods to discriminate the processes that generate the different classes of networks (e.g., normal and disease) might be crucial for the diagnosis, prognosis, and treatment of the disease. It is known that several topological properties of a network (graph) can be described by the distribution of the spectrum of its adjacency matrix. Moreover, large networks generated by the same random process have the same spectrum distribution, allowing us to use it as a “fingerprint”. Based on this relationship, we introduce and propose the entropy of a graph spectrum to measure the “uncertainty” of a random graph and the Kullback-Leibler and Jensen-Shannon divergences between graph spectra to compare networks. We also introduce general methods for model selection and network model parameter estimation, as well as a statistical procedure to test the nullity of divergence between two classes of complex networks. Finally, we demonstrate the usefulness of the proposed methods by applying them to (1) protein-protein interaction networks of different species and (2) on networks derived from children diagnosed with Attention Deficit Hyperactivity Disorder (ADHD) and typically developing children. We conclude that scale-free networks best describe all the protein-protein interactions. Also, we show that our proposed measures succeeded in the identification of topological changes in the network while other commonly used measures (number of edges, clustering coefficient, average path length) failed.     

Improving the Network Scale-Up Estimator: Incorporating Means of Sums,Recursive Back Estimation,and Sampling Weights

Researchers interested in studying populations that are difficult to reach through traditional survey methods can now draw on a range of methods to access these populations. Yet many of these methods are more expensive and difficult to implement than studies using conventional sampling frames and trusted sampling methods. The network scale-up method (NSUM) provides a middle ground for researchers who wish to estimate the size of a hidden population, but lack the resources to conduct a more specialized hidden population study. Through this method it is possible to generate population estimates for a wide variety of groups that are perhaps unwilling to self-identify as such (for example, users of illegal drugs or other stigmatized populations) via traditional survey tools such as telephone or mail surveys—by asking a representative sample to estimate the number of people they know who are members of such a “hidden” subpopulation. The original estimator is formulated to minimize the weight a single scaling variable can exert upon the estimates. We argue that this introduces hidden and difficult to predict biases, and instead propose a series of methodological advances on the traditional scale-up estimation procedure, including a new estimator. Additionally, we formalize the incorporation of sample weights into the network scale-up estimation process, and propose a recursive process of back estimation “trimming” to identify and remove poorly performing predictors from the estimation process. To demonstrate these suggestions we use data from a network scale-up mail survey conducted in Nebraska during 2014. We find that using the new estimator and recursive trimming process provides more accurate estimates, especially when used in conjunction with sampling weights.