The human microbiota composition is associated with a number of diseases including obesity, inflammatory bowel disease, and bacterial vaginosis. Thus, microbiome research has the potential to reshape clinical and therapeutic approaches. However, raw microbiome count data require careful pre-processing steps that take into account both the sparsity of counts and the large number of taxa that are being measured. Filtering is defined as removing taxa that are present in a small number of samples and have small counts in the samples where they are observed. Despite progress in the number and quality of filtering approaches, there is no consensus on filtering standards and quality assessment. This can adversely affect downstream analyses and reproducibility of results across platforms and software. We introduce PERFect, a novel permutation filtering approach designed to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering. Methods are assessed on three "mock experiment" data sets, where the true taxa compositions are known, and are applied to two publicly available real microbiome data sets. The method correctly removes contaminant taxa in "mock" data sets, quantifies and visualizes the corresponding filtering loss, providing a uniform data-driven filtering criteria for real microbiome data sets. In real data analyses PERFect tends to remove more taxa than existing approaches; this likely happens because the method is based on an explicit loss function, uses statistically principled testing, and takes into account correlation between taxa. The PERFect software is freely available at https://github.com/katiasmirn/PERFect.

No abstract

No abstract

Development of methods to design optimal Gough-Stewart platform geometries capable of meeting desired specifications is of high interest. Computationally intensive methods have been used to treat this problem in various settings. This paper uses analytic methods to characterize all orthogonal Gough-Stewart platforms (OGSPs) and to study their properties over a small workspace. This characterization is used to design optimal OGSPs for precision applications that achieve a desired hyperellipsoid of velocities. Some examples demonstrating the versatility of this theory are discussed.

No abstract

A simple, green and efficient solventless procedure for the synthesis of 3,4-dihydropyrimidin-2-(1H)-ones (and -thiones) from aldehydes, β-ketoesters and urea or thiourea in the presence of catalytic amount of silica-supported P2O5(P2O5/SiO2) at 85 °C is described. Using this method, the title compounds were produced in high yields.

BackgroundProliferation and expansion of security risks necessitates new measures to ensure authenticity and validation of GMOs. Watermarking and other cryptographic methods are available which conceal and recover the original signature, but in the process reveal the authentication information. In many scenarios watermarking and standard cryptographic methods are necessary but not sufficient and new, more advanced, cryptographic protocols are necessary.ResultsHerein, we present a new crypto protocol, that is applicable in broader settings, and embeds the authentication string indistinguishably from a random element in the signature space and the string is verified or denied without disclosing the actual signature. Results show that in a nucleotide string of 1000, the algorithm gives a correlation of 0.98 or higher between the distribution of the codon and that of E. coli, making the signature virtually invisible.ConclusionsThis algorithm may be used to securely authenticate and validate GMOs without disclosing the actual signature. While this protocol uses watermarking, its novelty is in use of more complex cryptographic techniques based on zero knowledge proofs to encode information.

Abstract-Parallel mechanisms frequently possess an unstable type of singularity that has no counterpart in serial mechanisms. When the mechanism is at or near this type of singularity, it loses the ability to counteract external forces in certain directions. The determination of unstable singular configurations in parallel robots is challenging, and in the past, has been tackled by exhaustive numerical searches of the mechanism workspace using an accurate analytical model of the mechanism kinematics. This paper considers the singularity-determination problem from a geometric perspective for -legged spatial parallel mechanisms. By using the constraints on the passive joint velocities, a necessary condition for an unstable singularity is derived.