Treating the nestedness temperature calculator as a "black box" can lead to false conclusions

We used the nestedness temperature calculator to examine patterns of nestedness in two datasets on birds in fragmented landscapes in southeastern Australia. During our initial analyses, we found that the nestedness calculator was susceptible to detect nestedness as an artifact of passive sampling. To examine this problem in more detail, we created random matrices that simulated a situation where nestedness did not occur, and we re-analysed two previously published datasets. Our results showed that the nestedness calculator may (1) overestimate the degree of nestedness and its statistical significance, and (2) consider some datasets which include both ubiquitous and rare species to be significantly nested although they are not. Our results highlight the danger of blindly relying on the p -values generated by analytical packages such as the nestedness calculator. We suggest that users of analytical packages (often field ecologists) will need to be more critical in future and familiarise themselves in more detail with the packages they use. In addition, the developers of analytical packages (often theoretical ecologists) will need to communicate more clearly the limitations and assumptions underlying analytical tools such as the nestedness calculator.     

A calculator program for least-squares parameter estimation according to the one-compartment kinetic model with zero-order input

A calculator program that performs a nonlinear least-squares fit to data conforming to the one-compartment model with zero-order input is described. The program, which is designed for the Hewlett-Packard HP-41 CV calculator, is based on the Gauss-Newton iterative algorithm as modified by Hartley. A subroutine for calculation of initial parameter estimates is incorporated into the program. Plasma concentration data relative to a single oral dose of a sustained-release theophylline formulation are used to demonstrate the practical application of the program.     

NP-Sticky: A Web Server for Optimizing DNA Ligation with Non-Palindromic Sticky Ends

High-efficiency DNA ligation is vital for many molecular biology experiments, and it is best achieved using reactants with non-palindromic sticky ends to maximize specificity. However, optimizing such multi-parametric ligation reactions often involves extensive trial and error. We have developed a freely available Web-based ligation calculator, NP-Sticky (http://sarkarlab.umn.edu/npsticky/), that predicts product distribution for given reactant concentrations, thus enabling straightforward computational optimization of these reactions. Built-in schemes include two-piece and three-piece linear ligation, as well as insert-vector circular ligation. The only parameters needed for the underlying thermodynamic model are the free energies of ligation for each sticky end, which can be estimated by the calculator from the overhang sequences or provided by the user from direct experimental measurement. Free energies of sticky-end mismatches are also calculated for determining the extent of byproduct formation. This ligation calculator allows rapid identification of the optimal conditions for maximizing incorporation, efficiency, and/or accuracy, based on specific needs.     

Multi RS-232 C channel scanner operated by a desktop calculator

This paper describes a scanner developed to link analytical instruments to a desktop calculator in a laboratory for clinical chemistry. The analytical instruments connected to the scanner use the RS-232 C standard for information exchange. This scanner permits the connection of an almost unlimited number of analytical instruments with a simple desktop calculator having a restricted number of possible interface slots.     

SPCalc: A web-based calculator for sample size and power calculations in micro-array studies

Calculation of the appropriate sample size in planning microarray studies is important because sample collection can be expensive and time-consuming. Sample-size calculation is also a challenging issue for microarray studies because the number of genes is far larger than the number of samples so that traditional methods of sample-size calculation cannot be directly applied. To help investigators answer the question of how many samples are needed in their microarray studies, we developed a user-friendly web-based calculator, SPCalc, for calculating sample size and power for a variety of commonly used experimental designs, including completely randomized treatmentcontrol design, matched-pairs design, multiple-treatment design having an isolated treatment effect, and randomized block design. AVAILABILITY: The web-based calculator SPCalc is publicly available at http://www.biostat.harvard.edu /people/faculty/mltlee/webfront-r.html.     

The use of a pocket-size, programmable calculator for phenotype tallying of a three-point cross.

A program is presented which permits use of a pocket-size programmable calculator, the HP-65, to tally phenotypes resulting from a three-point cross. For practical purposes the total number recorded for any of the eight possibel phenotypic combinations is unlimited. Although programmed operation of the calculator for tallying purposes is slower than a single purpose instrument designed for tallying, this deficiency is componensated by the computational capability of this instrument.     

An online calculator for marine phytoplankton iron culturing experiments

Laboratory experiments with iron offer important insight into the physiology of marine phytoplankton and the biogeochemical cycles they influence. These experiments often rely on chelators to buffer the concentration of available iron, but the buffer can fail when cell density increases, causing the concentration of that iron to drop rapidly. To more easily determine the point when the iron concentration falls, we developed an online calculator to estimate the maximum phytoplankton density that a growth medium can support. The results of the calculator were compared to the numerical simulations of a Fe‐limited culture of the diatom Thalassiosira weissflogii (Grunow) Fryxell and Hasle. Modeling reveals that the assumptions behind thermodynamic estimates of unchelated Fe concentration can fail before easily perceptible changes in growth rate, potentially causing physiological changes that could alter the conclusions of culture experiments. The calculator is available at http://www.marsci.uga.edu/fidoplankter .     

Measurement and analysis of gas exchange during exercise using a programmable calculator

Although exercise testing is useful in the diagnosis and management of cardiovascular and pulmonary diseases, a rapid comprehensive method for measurement of ventilation and gas exchange has been limited to expensive complex computer-based systems. We devised a relatively inexpensive, technically simple, and clinically oriented exercise system built around a desktop calculator. This system automatically collects and analyzes data on a breath-by-breath basis. Our calculator system overcomes the potential inaccuracies of gas exchange measurement due to water vapor dilution and mismatching of expired flow and gas concentrations. We found no difference between the calculator-derived minute ventilation, CO2 production, O2 consumption, and respiratory exchange ratio and the values determined from simultaneous mixed expired gas collections in 30 constant-work-rate exercise studies. Both tabular and graphic displays of minute ventilation, CO2 production, O2 consumption, respiratory exchange ratio, heart rate, end-tidal O2 tension, end-tidal CO2 tension, and arterial blood gas value are included for aid in the interpretation of clinical exercise tests.     

Analysis of variance and Westlake's test of bioavailability data using a programmable minicalculator

A program for the HP-41 CV calculator with adapted printer is described for the analysis of variance of bioavailability data based upon the areas under the curve measured during a two-way cross-over pharmacokinetic study of two different drug formulations. The program can also perform the test of Westlake to compute the 95% confidence interval and determine if both formulations are bioequivalent.     

Prediction of centrifugation times for equilibrium and velocity sedimentation on various gradients

Computer and calculator programs have been prepared which can predict sedimentation times for a significant fraction of the kinds of density gradient centrifugation experiments currently being carried out in biochemistry. Gradients of sucrose, glycerol, or CsCl were accommodated for linear or several forms of convex or concave gradient profiles. Times of sedimentation to various uniformly spaced points between the meniscus and the bottom of the tube, or to a point near the isopycnic density, are predicted.     

Fractionation of unlabeled and radioactive nucleotides by ionophoresis in two dimensions on a flat plate

Difficulties in determining the initial velocities of enzyme reactions during which the enzyme is itself inactivated have been considered. The problems are increased in pH-stat assays where the progress curves do not, in general, pass through the origin.Several methods of fitting such data are given. The most general solution requires fitting the results of the assays to an exponential. Simpler solutions, which can be handled on a small computer or even on a desk calculator are valid under certain conditions.     

Strategies to Avoid Wrongly Labelled Genomes Using as Example the Detected Wrong Taxonomic Affiliation for Aeromonas Genomes in the GenBank Database

Around 27,000 prokaryote genomes are presently deposited in the Genome database of GenBank at the National Center for Biotechnology Information (NCBI) and this number is exponentially growing. However, it is not known how many of these genomes correspond correctly to their designated taxon. The taxonomic affiliation of 44 Aeromonas genomes (only five of these are type strains) deposited at the NCBI was determined by a multilocus phylogenetic analysis (MLPA) and by pairwise average nucleotide identity (ANI). Discordant results in relation to taxa assignation were found for 14 (35.9%) of the 39 non-type strain genomes on the basis of both the MLPA and ANI results. Data presented in this study also demonstrated that if the genome of the type strain is not available, a genome of the same species correctly identified can be used as a reference for ANI calculations. Of the three ANI calculating tools compared (ANI calculator, EzGenome and JSpecies), EzGenome and JSpecies provided very similar results. However, the ANI calculator provided higher intra- and inter-species values than the other two tools (differences within the ranges 0.06–0.82% and 0.92–3.38%, respectively). Nevertheless each of these tools produced the same species classification for the studied Aeromonas genomes. To avoid possible misinterpretations with the ANI calculator, particularly when values are at the borderline of the 95% cutoff, one of the other calculation tools (EzGenome or JSpecies) should be used in combination. It is recommended that once a genome sequence is obtained the correct taxonomic affiliation is verified using ANI or a MLPA before it is submitted to the NCBI and that researchers should amend the existing taxonomic errors present in databases.     

How to analyze binding,enzyme and uptake data: The simplest case,a single phase

The results of many biochemical, pharmacological and physiological experiments fit a rectangular hyperbola. Several methods for analysis of this curve have been developed but these techniques have not been readily available to researchers who are not interested in becoming mathematical statisticians. We have reviewed these analytical methods and concluded that, the Eadie-Hofstee technique is the best choice. We explain how to use this method and include sample calculations and calculator programs. We are especially interested in showing scientists who are not particularly mathematically inclined how to use these methods effectively and thus save a great deal of time and expense.     

The structural simplification of an epidemiological compartment model

It is shown how a multicompartmental infectious disease model can be systematically examined for reduction of structural complexity. For steadystate situations, four basic rules are proposed for eliminating components of flow-lines, whole flow-lines, and compartments, plus combining compartments. An application to a typhoid fever model allows calculations to be done on a pocket calculator. The approach could be particularly important in developing countries.     

Application of a programmable calculator in data fitting according to one and two compartment open models in clinical pharmacokinetics

The plasma or blood concentration profiles are fitted by single or two compartment open models using log-linear regression analyses. For two compartment models, “feathering” is performed at 95% equilibration time obtained from raw pharmacokinetic data. The equations have been programmed onto a Texas Instrument SR 52 pocket calculator and recorded on 8.5 × 1.7 cm magnetic strips, facilitating drug dosage regimen calculations through individual patient titrations in a clinical setting.     

Novel artificial intelligence machine learning approaches to precisely predict survival and site-specific recurrence in cervical cancer: A multi-institutional study

BackgroundMachine learning (ML) has been gradually integrated into oncologic research but seldom applied to predict cervical cancer (CC), and no model has been reported to predict survival and site-specific recurrence simultaneously. Thus, we aimed to develop ML models to predict survival and site-specific recurrence in CC and to guide individual surveillance.MethodsWe retrospectively collected data on CC patients from 2006 to 2017 in four hospitals. The survival or recurrence predictive value of the variables was analyzed using multivariate Cox, principal component, and K-means clustering analyses. The predictive performances of eight ML models were compared with logistic or Cox models. A novel web-based predictive calculator was developed based on the ML algorithms.ResultsThis study included 5112 women for analysis (268 deaths, 343 recurrences): (1) For site-specific recurrence, larger tumor size was associated with local recurrence, while positive lymph nodes were associated with distant recurrence. (2) The ML models exhibited better prognostic predictive performance than traditional models. (3) The ML models were superior to traditional models when multiple variables were used. (4) A novel predictive web-based calculator was developed and externally validated to predict survival and site-specific recurrence.ConclusionML models might be a better analytic approach in CC prognostic prediction than traditional models as they can predict survival and site-specific recurrence simultaneously, especially when using multiple variables. Moreover, our novel web-based calculator may provide clinicians with useful information and help them make individual postoperative follow-up plans and further treatment strategies.     

A Paleolatitude Calculator for Paleoclimate Studies

Realistic appraisal of paleoclimatic information obtained from a particular location requires accurate knowledge of its paleolatitude defined relative to the Earth’s spin-axis. This is crucial to, among others, correctly assess the amount of solar energy received at a location at the moment of sediment deposition. The paleolatitude of an arbitrary location can in principle be reconstructed from tectonic plate reconstructions that (1) restore the relative motions between plates based on (marine) magnetic anomalies, and (2) reconstruct all plates relative to the spin axis using a paleomagnetic reference frame based on a global apparent polar wander path. Whereas many studies do employ high-quality relative plate reconstructions, the necessity of using a paleomagnetic reference frame for climate studies rather than a mantle reference frame appears under-appreciated. In this paper, we briefly summarize the theory of plate tectonic reconstructions and their reference frames tailored towards applications of paleoclimate reconstruction, and show that using a mantle reference frame, which defines plate positions relative to the mantle, instead of a paleomagnetic reference frame may introduce errors in paleolatitude of more than 15° (>1500 km). This is because mantle reference frames cannot constrain, or are specifically corrected for the effects of true polar wander. We used the latest, state-of-the-art plate reconstructions to build a global plate circuit, and developed an online, user-friendly paleolatitude calculator for the last 200 million years by placing this plate circuit in three widely used global apparent polar wander paths. As a novelty, this calculator adds error bars to paleolatitude estimates that can be incorporated in climate modeling. The calculator is available at www.paleolatitude.org. We illustrate the use of the paleolatitude calculator by showing how an apparent wide spread in Eocene sea surface temperatures of southern high latitudes may be in part explained by a much wider paleolatitudinal distribution of sites than previously assumed.     

Calculator-assisted measurements of photosynthetic,respiration and photorespiration rates in a closed gas exchange system

A closed gas exchange system has been designed for connection to the Hewlett-Packard programmable calculator controlled data acquisition system to provide a complete process of measuring and control. The system enables routine measurements of photosynthetic and dark respiration rates at different irradiances and different carbon dioxide and oxygen concentrations and leaf temperatures, and also a simple and rapid automatic control of irradiance according to the actual photosynthetic rate.     

Estimation of the most probable number with a programable pocket calculator.

The most-probable-number method has many potential applications, particularly if many tubes per dilution and many dilution levels are used. Increasing the number of cultures is possible with modern automatic and semiautomatic equipment. However, available tables are not sufficiently detailed to handle data from a large number of culture tubes used in an assay. This paper provides a computer program capable of handling the necessary arithmetic and written for a hand-held, advanced programable calculator.     

菌物分子系统学研究进展

分子生物学技术的发展以及计算机的广泛使用给菌物系统学在分子水平上带来了革命性变化,本文简要回顾了菌物分子系统学研究现状与分析方法,并就目前菌物分子系统学中存在的问题以及该研究的发展方向提出了一些看法。