Pneumocystis carinii in corticosteroid-treated voles: a comparison of three different staining methods.

Pneumocystis carinii (PC) is an opportunistic pathogen which causes clinical disease in immunocompromised hosts. Three different staining protocols were employed to detect this organism in lung samples of corticosteroid treated voles in order to discover a suitable method for large-scale screening. The procedures employed were: Grocotts methenamine silver (GMS)-stained paraffin sections, toluidine blue O-stained impression smears, and methenamine-silver-stained frozen sections. GMS-stained paraffin sections were relatively easy to interpret and gave more positive results than the other methods. It seemed to be the satisfactory method for large-scale population analyses. An unexpected result was that methylprednisolone treatment did not induce in voles a similarly fatal pneumocystosis infection as occurred in rats. All infections found in voles were mild. This might be due to species-dependent differences in metabolizing methylprednisolone.     

Resource cost comparison of implant-based breast reconstruction versus TRAM flap breast reconstruction

Relatively little has been published to date comparing the resource costs of transverse rectus abdominis musculocutaneous (TRAM) flap and prosthetic breast reconstruction. The data that have been published reflect the experience at just one medical center with a previously known clear preference for autologous breast reconstruction. The goal of this study was to compare the resource costs of TRAM flap and prosthetic reconstruction in an institution where both procedures continue to be performed using modern techniques and at a relatively equivalent frequency. All available medical records were reviewed for patients who had completed their breast reconstruction between 1987 and 1997. Records of patients who had undergone TRAM flap or prosthetic reconstruction were reviewed to compare resource costs, including hospital stay, operating room time, anesthesia time, prosthetic devices, and physician's fees. Of 835 patients reviewed who had completed breast reconstruction, a total of 140 suitable patients were identified who had all the necessary financial information available. The patient population comprised 64 patients who received TRAM flaps and 76 patients who had undergone prosthetic reconstruction. The length of stay for the TRAM flap group, including all subsequent admissions for each patient, ranged from 2 to 24 days (mean, 6.25 days), and that for the prosthetic reconstruction group ranged from 0 to 20 days (mean, 4.36 days). Operating room time for the complete multistage reconstructive process for a TRAM flap ranged from 5 hours, 20 minutes to 12 hours, 25 minutes (mean, 7 hours, 34 minutes); with implant-based reconstruction, operating time ranged from 1 hour, 45 minutes to 8 hours, 56 minutes (mean, 4 hours, 6 minutes). With prostheses costing from $600 to $1200, a surgeon's fee of $160/hour, and an assistant's fee of $45/hour, the average cost of TRAM flap reconstructions was $19,607 (range, $11,948 to $49,402), compared with $15,497 for prosthetic reconstructions (range, $6422 to $40,015). The results were statistically significant (p < 0.001). Several factors weigh into the decision as to which reconstructive operation best suits the patient's needs. These factors include surgical risk, potential morbidity, and aesthetic results. On the basis of this review of autologous and prosthetic breast reconstruction in an institution where both are performed frequently, during a 10-year period with a mean time elapsed since reconstruction of 7.45 years, prosthetic reconstruction was significantly less expensive.     

Sampling demersal zooplankton: A comparison of field collections using three different emergence traps

Comparisons of demersal zooplankton collected in three structurally different emergence traps indicated that density and diversity estimates are affected by design features and sampling procedures. The smallest mesh netting (63 μm) in the walls of Hobson-Chess traps contained larger catches than traps with 202- or 333-μm mesh. Samples from Porter-Porter traps tethered 1 and 10 cm above the bottom had statistically more zooplankton than all other traps set on the substratum. A consistently greater total number of demersal zooplankton was captured in the Alldredge-King traps when all three trap types sampled at the same time and area. The abundance and rank order of all but the most numerous animals ( = harpacticoid copepods) differed between the traps. Alldredge-King traps caught more of the larger organisms (= polychaetes, cumaceans, and gammaridean amphipods), whereas, the Porter-Porter and Hobson-Chess traps contained larger densities of smaller zooplankton ( = copepod nauplii and gastropod veligers).     

Properties of a ribosome-inactivating protein, gelonin, purified using three different methods.

Ribosome-inactivating protein, gelonin, isolated from an Indian plant Gelonium multiflorum of Euphorbiaceae family has been used to design and synthesize immunotoxins and hormonotoxins for selective targeting purposes. Since gelonin isolated by aqueous extraction, cation-exchange chromatography and gel-filtration chromatography (Method I), contains non-proteinous material absorbing at 280 nm, the ammonium sulphate precipitation method (Method II) and Cibacron blue affinity chromatography method. (Method III) have been used to purify gelonin from the dry seeds. Three batches of gelonin purified by each method were prepared and subjected to extensive physico-chemical and immunochemical characterization. The molecular weight was determined by gel-filtration chromatography on a pre-calibrated Sephadex G-100, TSK-G4000 TW on HPLC or Superose-12 on fast protein liquid chromatography. In all cases, the molecular weight was approximately 30,000Da. The SDS-PAGE also revealed a homogeneous protein of 30kDa molecular weight. In Method II, the non-proteinous material which binds to CMC-gel in association of gelonin was substantially removed during ammonium sulphate fractionation. A careful analysis clearly revealed that Method II, although yielded low protein, gave gelonin devoid of the non-proteinous material. The SPDP modification of epsilon-NH2 groups of gelonin obtained from Methods I, II, and III was also carried out and its effect on immunoreactivity was studied.     

A comparison of different methods of half-diallel analysis

Summary A comparison among various forms of half-diallel analysis was made. The different half-diallel techniques used were: Griffing's model I, method 2 and 4, Morley-Jones' model; Walters and Morton's model, and Gardner and Eberhart's model. All these methods of diallel analysis were found to be interrelated. However, as the Gardner and Eberhart's model partitioned heterosis into different components as well as gave information about combining ability, this method had certainly some advantages over the others. The results further indicated the possibility of dominance variance being confounded with the additive variance of general combining ability.     

The preservation of lactobacilli: A comparison of three methods

Lyophilization, desiccation on pumice stone and storage in dilute glycerol at-20C were compared for the preservation of Lactobacillus cultures. After storage for two years, 73% of the lyophilized cultures were viable. Desiccation on pumice stone gave erratic results and is not recommended. Storage in 20% (v/v) glycerol at-20C is simple and convenient and after 24 months, 75% of the cultures were viable. It is a useful method of maintaining routinely accessed cultures.     

A comparison of three methods of hydrolysis for estrogen conjugates

The efficiencies for estrogen conjugate hydrolysis were compared between enzyme hydrolysis, acid solvolysis and a new method, ammonolysis. Samples included: 1) crystalline 1,3,5(10)-estratriene-3, 17 beta-diol disulfate (estradiol 3,17-disulfate), 2) squirrel monkey urine collected following an intravenous injection of [2,4,6,7-H] 1,3,5(10)-estratriene-3,17 beta-diol (estradiol) and 3) a pool of human pregnancy urine. Ammonolysis demonstrated a significant increase over the other techniques in "free" estrogen yields, specifically, from estradiol 3,17-disulfate.     

A comparison of three methods of glycogen measurement in tissues

Three methods have been used for analysis of glycogen in tissue homogenates: hydrolysis of the tissue in acid and followed by enzymic analysis of the resulting glucose; enzymic hydrolysis with amylo-α-1,4-α-1,6-glucosidase, again followed by enzymic measurement of glucose; and degradation of the glycogen with phosphorylase and debrancher complex coupled to measurement of the resulting glucose-1-P. The two enzymic procedures yielded equivalent results with all tissues examined (brain, liver, muscle and polymorphonuclear leucocytes). Acid hydrolysis of the tissues resulted in higher values for brain tissue only, presumably due to the hydrolysis of the gangliosides and cerebrosides present in brain.     

Comparing three different methods to detect selective loci using dominant markers

We carried out a simulation study to compare the efficiency of three alternative programs (dfdist , detseld and bayescan ) to detect loci under directional selection from genome‐wide scans using dominant markers. We also evaluated the efficiency of correcting for multiple testing those methods that use a classical probability approach. Under a wide range of scenarios, we conclude that bayescan appears to be more efficient than the other methods, detecting a usually high percentage of true selective loci as well as less than 1% of outliers (false positives) under a fully neutral model. In addition, the percentage of outliers detected by this software is always correlated with the true percentage of selective loci in the genome. Our results show, nevertheless, that false positives are common even with a combination of methods and multitest correction, suggesting that conclusions obtained from this approach should be taken with extreme caution.     

Estimating mass change of migrant songbirds during stopover: comparison of three different methods

ABSTRACT Stopover‐site quality has often been assessed using changes in the body mass of migrants estimated from individuals recaptured on subsequent days or using regression methods. We compared estimates of mass change using these two techniques to estimates of mass change determined from birds recaptured on the same day. Using spring and fall banding data collected on Appledore Island, Maine, from 1990–2007, we examined body mass changes of the five most common species. Over this period, 18,954 individuals of these five species were captured and banded, with 11.6% of birds recaptured at least 1 d after initial capture and 3.1% recaptured on the same day. Using both regression and same‐day recapture methods, all five species had positive hourly mass gains during fall migration; results were mixed for the subsequent‐day analysis method. Trends were less consistent during spring migration. Using all three methods of estimating mass change, Red‐eyed Vireos (Vireo olivaceus) lost mass, American Redstarts (Setophaga ruticilla) and Northern Waterthrushes (Parkesia noveboracensis) gained mass, and results for Yellow‐bellied Flycatchers (Empidonax flaviventris), and Black‐and‐white Warblers (Mniotilta varia) varied with method. We found similar trends in mass change using the same‐day recapture and regression methods. However, we found lower mean mass gain for most species using the same‐day recapture method, suggesting that there may be a short‐term capture and handling effect. Our results provide additional support for the use of regression models to compare changes in mass of migrating songbirds at stopover sites.     

Graph reconstruction using covariance-based methods

Methods based on correlation and partial correlation are today employed in the reconstruction of a statistical interaction graph from high-throughput omics data. These dedicated methods work well even for the case when the number of variables exceeds the number of samples. In this study, we investigate how the graphs extracted from covariance and concentration matrix estimates are related by using Neumann series and transitive closure and through discussing concrete small examples. Considering the ideal case where the true graph is available, we also compare correlation and partial correlation methods for large realistic graphs. In particular, we perform the comparisons with optimally selected parameters based on the true underlying graph and with data-driven approaches where the parameters are directly estimated from the data.     

High-resolution two-dimensional electrophoresis of nuclear proteins: a comparison of HeLa nuclei prepared by three different methods.

A comparative analysis of HeLa cell nuclear proteins is presented using Iso-Dalt methods of protein resolution in two dimensions. The nuclear proteins were prepared by (1) spin through glycerol cushion, (2) spin through sucrose cushion, or (3) Triton wash. Improved resolution of total nuclear proteins in the range of pH 4.5-6.0 was achieved by substituting longer isotubes in combination with broad-range ampholines during the isoelectric focusing step. An attempt to indicate silver stainable protein spots common to total cellular extracts and nuclear preparations has been made. Also, proteins that appear to be well represented in all three nuclear preparations and remain undetectable in the total cellular protein pattern have been marked as probably being enriched nuclear proteins. Such a comparative analysis of whole nuclear protein preparations made it possible to document that the different preparations preserved the same set of proteins. The Triton-wash method of obtaining nuclei was identified as the preferred choice. Coomassie-stained gels and blots of these nuclear proteins could serve as a guide for accessing relevant protein spots for further biochemical analysis such as immunoblotting.