Learning sparse log-ratios for high-throughput sequencing data.

MOTIVATION: The automatic discovery of sparse biomarkers that are associated with an outcome of interest is a central goal of bioinformatics. In the context of high-throughput sequencing (HTS) data, and compositional data (CoDa) more generally, an important class of biomarkers are the log-ratios between the input variables. However, identifying predictive log-ratio biomarkers from HTS data is a combinatorial optimization problem, which is computationally challenging. Existing methods are slow to run and scale poorly with the dimension of the input, which has limited their application to low- and moderate-dimensional metagenomic datasets. RESULTS: Building on recent advances from the field of deep learning, we present CoDaCoRe, a novel learning algorithm that identifies sparse, interpretable and predictive log-ratio biomarkers. Our algorithm exploits a continuous relaxation to approximate the underlying combinatorial optimization problem. This relaxation can then be optimized efficiently using the modern ML toolbox, in particular, gradient descent. As a result, CoDaCoRe runs several orders of magnitude faster than competing methods, all while achieving state-of-the-art performance in terms of predictive accuracy and sparsity. We verify the outperformance of CoDaCoRe across a wide range of microbiome, metabolite and microRNA benchmark datasets, as well as a particularly high-dimensional dataset that is outright computationally intractable for existing sparse log-ratio selection methods. AVAILABILITY AND IMPLEMENTATION: The CoDaCoRe package is available at https://github.com/egr95/R-codacore. Code and instructions for reproducing our results are available at https://github.com/cunningham-lab/codacore. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Estudio de indicadores bioquímicos en la orina de atletas juveniles de sable femenino en entrenamiento / Estudo de indicadores bioquímicos na urina de jovens atletas do sexo feminino sabre em treino / Study of biochemical indicators in the urine of juvenile female sabre athletes in training

RESUMEN El presente estudio tiene como objetivo determinar el comportamiento de algunos indicadores bioquímicos en la orina de atletas femeninas de sable, de edad juvenil, después de una sesión de entrenamiento, entre los que se destacan el pH (reacción), la glucosa, la albúmina y uno de los tres cuerpos cetónicos (la acetona). La muestra estuvo representada por siete atletas de sable femenino, pertenecientes a La Academia provincial de esgrima, categoría juvenil, con una edad promedio de 16 años y dos de experiencia. El estadígrafo utilizado para las comparaciones fue la media. La determinación del pH, cuantitativamente en la orina, fue a través del papel del pH. La determinación de la glucosa se realizó a través del método del reactivo Benedict. La albúmina se determinó en la orina, a través del método del ácido sulfosalicílico. Y la determinación de la acetona fue mediante el método de Imbert. La motivación para la investigación se debe a la incorporación del sable femenino en la esgrima contemporánea, lo que estudia las características y rendimiento del sexo femenino en el sable, arma bien rápida y fuerte. Los resultados demuestran cómo la carga aplicada durante una sesión de entrenamiento de un microciclo seleccionado de la preparación especial provocó variaciones en la mayoría de los indicadores, demostrando la aparición de un estado de acidosis en la orina, como consecuencia del trabajo realizado. Y se constató, además, la utilidad en la determinación de la albúmina para caracterizar la intensidad de la carga física.

RESUMO O presente estudo visa determinar o comportamento de alguns indicadores bioquímicos na urina de atletas do sabre feminino, de idade juvenil, após uma sessão de treino, entre os quais se destacam o pH (reação), glicose, albumina e um dos três corpos cetónicos (acetona). A amostra foi representada por sete atletas do sabre feminino, pertencentes à academia de esgrima provincial, categoria juvenil, com uma idade média de 16 anos e dois anos de experiência. A estatística utilizada para as comparações foi a média. A determinação do pH, quantitativamente na urina, foi feita através do papel de pH. A glicose foi determinada utilizando o método do reagente de Benedict. A albumina foi determinada na urina, através do método do ácido sulfosalicílico. E a acetona foi determinada pelo método de Imbert. A motivação para a investigação deve-se à incorporação do sabre feminino na esgrima contemporânea, que estuda as características e o desempenho do sexo feminino no sabre, uma arma muito rápida e forte. Os resultados mostram como a carga aplicada durante uma sessão de treino de um microciclo selecionado da preparação especial causou variações na maioria dos indicadores, demonstrando o aparecimento de um estado de acidose na urina, como consequência do trabalho realizado. Foi também confirmada a utilidade da determinação da albumina para caracterizar a intensidade da carga física.

ABSTRACT The present study aims to determine the behavior of some biochemical indicators in the urine of female sabre athletes, of juvenile age, after a training session, among which pH (reaction), glucose, albumin and one of the three ketone bodies (acetone) stand out. The sample was represented by seven female sabre athletes, belonging to the provincial fencing academy, youth category, with an average age of 16 years and two years of experience. The statistic used for comparisons was the mean. The determination of pH, quantitatively in urine, was through pH paper. Glucose was determined by the Benedict's reagent method. Albumin was determined in urine, through the sulfosalicylic acid method. In addition, acetone was determined by Imbert's method. The motivation for the research is due to the incorporation of the female sabre in contemporary fencing, which studies the characteristics and performance of the female sex in the sabre, a very fast and strong weapon. The results show how the load applied during a training session of a selected microcycle of the special preparation caused variations in most of the indicators, demonstrating the appearance of a state of acidosis in the urine, as a consequence of the work performed. The usefulness of the determination of albumin to characterize the intensity of the physical load was also confirmed.

Studies of binding by sulfonylureas with glyoxal- and methylglyoxal-modified albumin by immunoextraction using affinity microcolumns.

Diabetes is characterized by elevated levels of blood glucose, which can result in the modification of serum proteins. The modification of a protein by glucose, or glycation, can also lead to the formation of advanced glycated end-products (AGEs). One protein that can be modified through glycation and AGE formation is human serum albumin (HSA). In this study, immunoextraction based on polyclonal anti-HSA antibodies was used with high-performance affinity microcolumns to see how AGE-related modifications produced by glyoxal (Go) and methylglyoxal (MGo) affected the binding of HSA to several first- and second-generation sulfonylureas, a class of drugs used to treat type II diabetes and known to bind to HSA. With this approach, it was possible to use a single platform to examine drug interactions with several preparations of HSA. Each applied protein sample could be used over 20-50 experiments, and global affinity constants for most of the examined drugs could be obtained in less than 7.5 min. The binding constants measured for these drugs with normal HSA gave good agreement with global affinities based on the literature. Both Go- and MGo-related modifications at clinically relevant levels were found by this method to create significant changes in the binding by some sulfonylureas with HSA. The global affinities for many of the drugs increased by 1.4-fold or more; gliclazide and tolazamide had no significant change with some preparations of modified HSA, and a small-to-moderate decrease in binding strength was noted for glibenclamide and gliclazide with Go-modified HSA. This approach can be adapted for the study of other drug-protein interactions and alternative modified proteins by altering the antibodies that are employed for immunoextraction and within the affinity microcolumn.

Analysis of curcumin and piperine in biological samples by reversed-phase liquid chromatography with multi-wavelength detection.

Widely accessible food phytochemicals such as curcumin have been reported to have anti-inflammatory and anticarcinogenic properties. However, curcumin has poor absorption in the gut, and piperine has been of interest as a dietary compound that can enhance curcumin bioavailability. The aim of this study was to develop and optimize a technique using reversed-phase chromatography with multi-wavelength detection for the simultaneous measurement of curcumin and piperine in various biological matrices. Emodin was used as an internal standard. Protein precipitation and liquid-liquid extraction based on acetonitrile provided good recovery of these analytes. A 150 mm × 4.6 mm I.D. Luna C18 column was used under isocratic conditions to separate curcumin, piperine, and emodin with baseline resolution, and with good separation from other sample components, in as little as 4 min. The detection limits for curcumin and piperine were 3 and 7 ng/mL, respectively. This method has been used to quantitate these compounds in samples such as human intestinal epithelial cell lysates and mouse plasma or GI tissues in research aimed at examining the bioavailability of curcumin in the presence of piperine.

Affinity chromatography: A review of trends and developments over the past 50 years.

The field of affinity chromatography, which employs a biologically-related agent as the stationary phase, has seen significant growth since the modern era of this method began in 1968. This review examines the major developments and trends that have occurred in this technique over the past five decades. The basic principles and history of this area are first discussed. This is followed by an overview of the various supports, immobilization strategies, and types of binding agents that have been used in this field. The general types of applications and fields of use that have appeared for affinity chromatography are also considered. A survey of the literature is used to identify major trends in these topics and important areas of use for affinity chromatography in the separation, analysis, or characterization of chemicals and biochemicals.

Development of an on-line immunoextraction/entrapment system for protein capture and use in drug binding studies by high-performance affinity chromatography.

An on-line purification and entrapment system was developed that could extract a protein from a sample such as serum and entrap this protein within a small column for use in high-performance affinity chromatography. Human serum albumin (HSA) was employed as a model protein for this work. Immunoextraction columns containing polyclonal anti-HSA antibodies were developed to capture and isolate HSA from applied samples. This was followed by the use of a strong cation-exchange column to recapture and focus HSA as it eluted from the immunoextraction columns. The recaptured HSA was entrapped within 1.0 cm × 2.1 mm I.D. columns containing hydrazide-activated silica and in the presence of oxidized glycogen as a capping agent. The binding and elution properties of HSA on the various components of this system were examined and optimized. The entrapped columns produced by this system were then evaluated for their use in binding studies with several sulfonylurea drugs. The HSA columns created by this approach typically contained 0.3-0.6 nmol HSA and were stable over several weeks and more than 50-60 sample injections. Drug binding constants could be determined with these columns in 8 min or less by zonal elution and gave good agreement with literature values. The same system could be used for the capture and entrapment of other proteins by utilizing antibodies against the given target for immunoextraction.

Managing genomic variant calling workflows with Swift/T.

Bioinformatics research is frequently performed using complex workflows with multiple steps, fans, merges, and conditionals. This complexity makes management of the workflow difficult on a computer cluster, especially when running in parallel on large batches of data: hundreds or thousands of samples at a time. Scientific workflow management systems could help with that. Many are now being proposed, but is there yet the "best" workflow management system for bioinformatics? Such a system would need to satisfy numerous, sometimes conflicting requirements: from ease of use, to seamless deployment at peta- and exa-scale, and portability to the cloud. We evaluated Swift/T as a candidate for such role by implementing a primary genomic variant calling workflow in the Swift/T language, focusing on workflow management, performance and scalability issues that arise from production-grade big data genomic analyses. In the process we introduced novel features into the language, which are now part of its open repository. Additionally, we formalized a set of design criteria for quality, robust, maintainable workflows that must function at-scale in a production setting, such as a large genomic sequencing facility or a major hospital system. The use of Swift/T conveys two key advantages. (1) It operates transparently in multiple cluster scheduling environments (PBS Torque, SLURM, Cray aprun environment, etc.), thus a single workflow is trivially portable across numerous clusters. (2) The leaf functions of Swift/T permit developers to easily swap executables in and out of the workflow, which makes it easy to maintain and to request resources optimal for each stage of the pipeline. While Swift/T's data-level parallelism eliminates the need to code parallel analysis of multiple samples, it does make debugging more difficult, as is common for implicitly parallel code. Nonetheless, the language gives users a powerful and portable way to scale up analyses in many computing architectures. The code for our implementation of a variant calling workflow using Swift/T can be found on GitHub at https://github.com/ncsa/Swift-T-Variant-Calling, with full documentation provided at http://swift-t-variant-calling.readthedocs.io/en/latest/.

Piperine potentiates curcumin-mediated repression of mTORC1 signaling in human intestinal epithelial cells: implications for the inhibition of protein synthesis and TNFα signaling.

Persistent activation of the mechanistic target of rapamycin complex 1 (mTORC1) is linked to sustained inflammation and progression of colorectal cancer. Widely available dietary phenolics, curcumin and piperine are purported to have antiinflammatory and anticarcinogenic activities through yet-to-be-delineated multitarget mechanisms. Piperine is also known to increase the bioavailability of dietary components, including curcumin. The objective of the study was to determine whether curcumin and piperine have individual and combined effects in the setting of gut inflammation by regulating mTORC1 in human intestinal epithelial cells. Results show that curcumin repressed (a) mTORC1 activity (measured as changes in the phosphorylation state of p70 ribosomal protein S6 kinase B1 and 40S ribosomal protein S6) in a dose-dependent manner (2.5-20 µM, P<.007) and (b) synthesis of nascent proteins. Piperine inhibited mTORC1 activity albeit at comparatively higher concentrations than curcumin. The combination of curcumin + piperine further repressed mTORC1 signaling (P<.02). Mechanistically, curcumin may repress mTORC1 by preventing TSC2 degradation, the conserved inhibitor of mTORC1. Results also show that a functional mTORC1 was required for the transcription of TNFα as Raptor knockdown abrogated TNFα gene expression. Curcumin, piperine and their combination inhibited TNFα gene expression at baseline but failed to do so under conditions of mTORC1 hyperactivation. TNF∝-induced cyclooxygenase-2 expression was repressed by curcumin or curcumin + piperine at baseline and high mTORC1 levels. We conclude that curcumin and piperine, either alone or in combination, have the potential to down-regulate mTORC1 signaling in the intestinal epithelium with implications for tumorigenesis and inflammation.

High performance affinity chromatography and related separation methods for the analysis of biological and pharmaceutical agents.

The last few decades have witnessed the development of many high-performance separation methods that use biologically related binding agents. The combination of HPLC with these binding agents results in a technique known as high performance affinity chromatography (HPAC). This review will discuss the general principles of HPAC and related techniques, with an emphasis on their use for the analysis of biological compounds and pharmaceutical agents. Various types of binding agents for these methods will be considered, including antibodies, immunoglobulin-binding proteins, aptamers, enzymes, lectins, transport proteins, lipids, and carbohydrates. Formats that will be discussed for these methods range from the direct detection of an analyte to indirect detection based on chromatographic immunoassays, as well as schemes based on analyte extraction or depletion, post-column detection, and multi-column systems. The use of biological agents in HPLC for chiral separations will also be considered, along with the use of HPAC as a tool to screen or study biological interactions. Various examples will be presented to illustrate these approaches and their applications in fields such as biochemistry, clinical chemistry, and pharmaceutical research.

Nanomaterials as stationary phases and supports in liquid chromatography.

The development of various nanomaterials over the last few decades has led to many applications for these materials in liquid chromatography (LC). This review will look at the types of nanomaterials that have been incorporated into LC systems and the applications that have been explored for such systems. A number of carbon-based nanomaterials and inorganic nanomaterials have been considered for use in LC, ranging from carbon nanotubes, fullerenes and nanodiamonds to metal nanoparticles and nanostructures based on silica, alumina, zirconia and titanium dioxide. Many ways have been described for incorporating these nanomaterials into LC systems. These methods have included covalent immobilization, adsorption, entrapment, and the synthesis or direct development of nanomaterials as part of a chromatographic support. Nanomaterials have been used in many types of LC. These applications have included the reversed-phase, normal-phase, ion-exchange, and affinity modes of LC, as well as related methods such as chiral separations, ion-pair chromatography and hydrophilic interaction liquid chromatography. Both small and large analytes (e.g., dyes, drugs, amino acids, peptides and proteins) have been used to evaluate possible applications for these nanomaterial-based methods. The use of nanomaterials in columns, capillaries and planar chromatography has been considered as part of these efforts. Potential advantages of nanomaterials in these applications have included their good chemical and physical stabilities, the variety of interactions many nanomaterials can have with analytes, and their unique retention properties in some separation formats.

Affinity monolith chromatography: A review of general principles and applications.

Affinity monolith chromatography, or AMC, is a liquid chromatographic method in which the support is a monolith and the stationary phase is a biological-binding agent or related mimic. AMC has become popular for the isolation of biochemicals, for the measurement of various analytes, and for studying biological interactions. This review will examine the principles and applications of AMC. The materials that have been used to prepare AMC columns will be discussed, which have included various organic polymers, silica, agarose, and cryogels. Immobilization schemes that have been used in AMC will also be considered. Various binding agents and applications that have been reported for AMC will then be described. These applications will include the use of AMC for bioaffinity chromatography, immunoaffinity chromatography, dye-ligand affinity chromatography, and immobilized metal-ion affinity chromatography. The use of AMC with chiral stationary phases and as a tool to characterize biological interactions will also be examined.

Chromatographic immunoassays: strategies and recent developments in the analysis of drugs and biological agents.

A chromatographic immunoassay is a technique in which an antibody or antibody-related agent is used as part of a chromatographic system for the isolation or measurement of a specific target. Various binding agents, detection methods, supports and assay formats have been developed for this group of methods, and applications have been reported that range from drugs, hormones and herbicides to peptides, proteins and bacteria. This review discusses the general principles and applications of chromatographic immunoassays, with an emphasis being given to methods and formats that have been developed for the analysis of drugs and biological agents. The relative advantages or limitations of each format are discussed. Recent developments and research in this field, as well as possible future directions, are also considered.

Studies of metabolite-protein interactions: a review.

The study of metabolomics can provide valuable information about biochemical pathways and processes at the molecular level. There have been many reports that have examined the structure, identity and concentrations of metabolites in biological systems. However, the binding of metabolites with proteins is also of growing interest. This review examines past reports that have looked at the binding of various types of metabolites with proteins. An overview of the techniques that have been used to characterize and study metabolite-protein binding is first provided. This is followed by examples of studies that have investigated the binding of hormones, fatty acids, drugs or other xenobiotics, and their metabolites with transport proteins and receptors. These examples include reports that have considered the structure of the resulting solute-protein complexes, the nature of the binding sites, the strength of these interactions, the variations in these interactions with solute structure, and the kinetics of these reactions. The possible effects of metabolic diseases on these processes, including the impact of alterations in the structure and function of proteins, are also considered.