PyNAST: a flexible tool for aligning sequences to a template alignment

Motivation: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted as possible. Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API)

Subjective Report of Side Effects of Prescribed and Nonprescribed Psychostimulant Use in Young Adults

Background: Side effects of prescribed and nonprescribed psychostimulant use are understudied. Objectives: The study examined side effects of prescribed and nonprescribed psychostimulant use in a college sample with attention to possible gender differences. Methods: 2716 undergraduates (1448 male) between the ages of 17 and 57 years (M = 19.43 years, SD = 1.7 years) completed an online survey that included questions about the subjective side effects of prescribed and nonprescribed psychostimulant use. Results: Results suggested that prescribed users more frequently reported side effects, compared to nonprescribed users. For prescribed users, females more frequently reported appetite, somatic, and anxiety-related side effects compared to males. For nonprescribed users, while females reported more somatic and anxiety-related side effects, males more frequently reported loss of sex drive and sweating as side effects. Conclusions/Importance: These findings suggest prescribed users of psychostimulants more frequently report side effects with prominent gender differences in line with gender roles

Accurate Profiling of Microbial Communities from Massively Parallel Sequencing using Convex Optimization

We describe the Microbial Community Reconstruction ({\bf MCR}) Problem, which is fundamental for microbiome analysis. In this problem, the goal is to reconstruct the identity and frequency of species comprising a microbial community, using short sequence reads from Massively Parallel Sequencing (MPS) data obtained for specified genomic regions. We formulate the problem mathematically as a convex optimization problem and provide sufficient conditions for identifiability, namely the ability to reconstruct species identity and frequency correctly when the data size (number of reads) grows to infinity. We discuss different metrics for assessing the quality of the reconstructed solution, including a novel phylogenetically-aware metric based on the Mahalanobis distance, and give upper-bounds on the reconstruction error for a finite number of reads under different metrics. We propose a scalable divide-and-conquer algorithm for the problem using convex optimization, which enables us to handle large problems (with $\sim10^6$ species). We show using numerical simulations that for realistic scenarios, where the microbial communities are sparse, our algorithm gives solutions with high accuracy, both in terms of obtaining accurate frequency, and in terms of species phylogenetic resolution.Comment: To appear in SPIRE 1

Conserving the Mesoamerican herpetofauna: The most critical case of the priority level one endemic species

Of significant biodiversity importance, the Mesoamerican herpetofauna now increases at a rate of approximately 35 species annually. As its size increases, however, the global problem of biodiversity decline continues to worsen with time. Recently, a set of conservation priority levels was established for individual species based on a combination of physiographic distribution and Environmental Vulnerability Score (EVS). The 18 such levels identified range from level one, encompassing species that occupy a single physiographic region and with a high EVS, to level 18, including species that inhabit six physiographic regions and have a low EVS. For the Mesoamerican herpetofauna, the greatest number of species is placed in level one, amounting to 970 taxa with documentable distributions. From one to 149 priority level one species are found in 20 of the 21 physiographic regions recognized in Mesoamerica. Slightly more than three-quarters of the priority level one species of anurans, salamanders, and squamates are found in the Baja California Peninsula and six montane regions in Mexico and Central America. Conservation biology, thus far, has not been successful at reversing the steady loss of biodiversity nor at placing biodiversity decline on the global agenda. In addition, humans are becoming increasingly divorced from contact with the natural world and, thus, less aware of the life-threatening impact they are having on the planet’s life-support systems. Given this situation, the authors of this paper have become increasingly devoted to trying to understand why humans in general exhibit the highly dangerous anthropocentric worldview. As have other biologists, the authors ascribe this behavior to what is known as “the mismanagement of the human mind.” This mismanagement of the human mind is believed to result from a cascade of psychological ailments giving rise to increasingly restrictive forms of centristic thinking. In the final analysis, these types of thinking appear likely to doom to failure any efforts to establish for perpetuity protected areas that can harbor the priority level one species identified in this and earlier papers. Until and unless the anthropocentric worldview can be transformed into a worldview consonant with the realities of how life operates on planet Earth, we humans are not only endangering ourselves but also all other life. This article discusses the implications of this worldview for the potential conservation of the priority level one endemic species of the Mesoamerica herpetofauna

A Machine Learning Compatible Method For ordinal Propensity Score Stratification and Matching

Although machine learning techniques that estimate propensity scores for observational studies with multivalued treatments have advanced rapidly in recent years, the development of propensity score adjustment techniques has not kept pace. While machine learning propensity models provide numerous benefits, they do not produce a single variable balancing score that can be used for propensity score stratification and matching. This issue motivates the development of a flexible ordinal propensity scoring methodology that does not require parametric assumptions for the propensity model. The proposed method fits a one-parameter power function to the cumulative distribution function (CDF) of the generalized propensity score (GPS) vector resulting from any machine learning propensity model, and is henceforth called the GPS-CDF method. The estimated parameter from the GPS-CDF method

Signed Laplacian Deep Learning with Adversarial Augmentation for Improved Mammography Diagnosis

Computer-aided breast cancer diagnosis in mammography is limited by inadequate data and the similarity between benign and cancerous masses. To address this, we propose a signed graph regularized deep neural network with adversarial augmentation, named \textsc{DiagNet}. Firstly, we use adversarial learning to generate positive and negative mass-contained mammograms for each mass class. After that, a signed similarity graph is built upon the expanded data to further highlight the discrimination. Finally, a deep convolutional neural network is trained by jointly optimizing the signed graph regularization and classification loss. Experiments show that the \textsc{DiagNet} framework outperforms the state-of-the-art in breast mass diagnosis in mammography.Comment: To appear in MICCAI October 201

Histochemical analysis of glycoconjugates in the domestic cat testis

The localization and characterization of oligosaccharide sequences in the cat testis was investigated using 12 lectins in combination with the ßelimination reaction, N-Glycosidase F and sialidase digestion. Leydig cells expressed O-linked glycans with terminal aGalNAc (HPA reactivity) and N-glycans with terminal/internal aMan (Con A affinity). The basement membrane showed terminal Neu5Aca2,6Gal/GalNAc, Galß1,3GalNAc, a/ßGalNAc, and GlcNAc (SNA, PNA, HPA, SBA, GSA II reactivity) in O-linked oligosaccharides, terminal Galß1,4GlcNAc (RCA120 staining) and aMan in N-linked oligosaccharides; in addition, terminal Neu5Aca2,3Galß1,4GlcNac, Forssman pentasaccharide, aGal, aL-Fuc and internal GlcNAc (MAL II, DBA, GSA I-B4, UEA I, KOH-sialidase-WGA affinity) formed both O- and N-linked oligosaccharides. The Sertoli cells cytoplasm contained terminal Neu5Ac- Galß1,4GlcNAc, Neu5Ac-ßGalNAc as well as internal GlcNAc in O-linked glycans, aMan in N-linked glycoproteins and terminal Neu5Aca2,6Gal/ GalNAc in both O- and N-linked oligosaccharides. Spermatogonia exhibited cytoplasmic N-linked glycoproteins with aMan residues. The spermatocytes cytoplasm expressed terminal Neu5Aca2,3Galß1,4 GlcNAc and Galß1,3GalNAc in O-linked oligosaccharides, terminal Galß1,4GlcNAc and a/ßGalNAc in N-linked glycoconjugates. The Golgi region showed terminal Neu5aca2,3Galß1,4GlcNac, Galß1,4GlcNAc, Forssman pentasaccharide, and aGalNAc in O-linked oligosaccharides, aMan and terminal ßGal in N-linked oligosaccharides. The acrosomes of Golgi-phase spermatids expressed terminal Galß1,3GalNAc, Galß1,4GlcNAc, Forssmann pentasaccharide, a/ßGalNAc, aGal and internal GlcNAc in O-linked oligosaccharides, terminal a/ßGalNAc, aGal and terminal/internal aMan in N-linked glycoproteins. The acrosomes of cap-phase spermatids lacked internal Forssman pentasaccharide and aGal, while having increased a/ßGalNAc. The acrosomes of elongated spermatids did not show terminal Galß1,3GalNAc, displayed terminal Galß1,4GlcNAc and a/ßGalNAc in N-glycans and Neu5Ac-Galß1,3GalNAc in O-linked oligosaccharides

Worsening Glycemia increases the Odds of intermittent But Not Persistent Staphylococcus aureus Nasal Carriage in Two Cohorts of Mexican american adults

Numerous host and environmental factors contribute to persistent and intermittent nasal Staphylococcus aureus carriage in humans. The effects of worsening glycemia on the odds of S. aureus intermittent and persistent nasal carriage was established in two cohorts from an adult Mexican American population living in Starr County, Texas. The anterior nares were sampled at two time points and the presence of S. aureus determined by laboratory culture an