PhyBin: binning trees by topology

A major goal of many evolutionary analyses is to determine the true evolutionary history of an organism. Molecular methods that rely on the phylogenetic signal generated by a few to a handful of loci can be used to approximate the evolution of the entire organism but fall short of providing a global, genome-wide, perspective on evolutionary processes. Indeed, individual genes in a genome may have different evolutionary histories. Therefore, it is informative to analyze the number and kind of phylogenetic topologies found within an orthologous set of genes across a genome. Here we present PhyBin: a flexible program for clustering gene trees based on topological structure. PhyBin can generate bins of topologies corresponding to exactly identical trees or can utilize Robinson-Fould’s distance matrices to generate clusters of similar trees, using a user-defined threshold. Additionally, PhyBin allows the user to adjust for potential noise in the dataset (as may be produced when comparing very closely related organisms) by pre-processing trees to collapse very short branches or those nodes not meeting a defined bootstrap threshold. As a test case, we generated individual trees based on an orthologous gene set from 10 Wolbachia species across four different supergroups (A–D) and utilized PhyBin to categorize the complete set of topologies produced from this dataset. Using this approach, we were able to show that although a single topology generally dominated the analysis, confirming the separation of the supergroups, many genes supported alternative evolutionary histories. Because PhyBin’s output provides the user with lists of gene trees in each topological cluster, it can be used to explore potential reasons for discrepancies between phylogenies including homoplasies, long-branch attraction, or horizontal gene transfer events

Adaptive Lock-Free Data Structures in Haskell: A General Method for Concurrent Implementation Swapping

A key part of implementing high-level languages is providing built-in and default data structures. Yet selecting good defaults is hard. A mutable data structure's workload is not known in advance, and it may shift over its lifetime - e.g., between read-heavy and write-heavy, or from heavy contention by multiple threads to single-threaded or low-frequency use. One idea is to switch implementations adaptively, but it is nontrivial to switch the implementation of a concurrent data structure at runtime. Performing the transition requires a concurrent snapshot of data structure contents, which normally demands special engineering in the data structure's design. However, in this paper we identify and formalize an relevant property of lock-free algorithms. Namely, lock-freedom is sufficient to guarantee that freezing memory locations in an arbitrary order will result in a valid snapshot. Several functional languages have data structures that freeze and thaw, transitioning between mutable and immutable, such as Haskell vectors and Clojure transients, but these enable only single-threaded writers. We generalize this approach to augment an arbitrary lock-free data structure with the ability to gradually freeze and optionally transition to a new representation. This augmentation doesn't require changing the algorithm or code for the data structure, only replacing its datatype for mutable references with a freezable variant. In this paper, we present an algorithm for lifting plain to adaptive data and prove that the resulting hybrid data structure is itself lock-free, linearizable, and simulates the original. We also perform an empirical case study in the context of heating up and cooling down concurrent maps.Comment: To be published in ACM SIGPLAN Haskell Symposium 201

Deterministic Threshold Queries of Distributed Data Structures

Abstract. Convergent replicated data types, or CvRDTs, are latticebased data structures for enforcing the eventual consistency of replicated objects in a distributed system. Although CvRDTs are provably eventually consistent, queries of CvRDTs nevertheless allow inconsistent intermediate states of replicas to be observed; and although in practice, many systems allow a mix of eventually consistent and strongly consistent queries, CvRDTs only support the former. Taking inspiration from our previous work on LVars for deterministic parallel programming, we show how to extend CvRDTs to support deterministic, strongly consistent queries using a mechanism called threshold queries. The threshold query technique generalizes to any lattice, and hence any CvRDT, and allows deterministic observations to be made of replicated objects before the replicas ’ states have converged

Linear Haskell: practical linearity in a higher-order polymorphic language

Linear type systems have a long and storied history, but not a clear path forward to integrate with existing languages such as OCaml or Haskell. In this paper, we study a linear type system designed with two crucial properties in mind: backwards-compatibility and code reuse across linear and non-linear users of a library. Only then can the benefits of linear types permeate conventional functional programming. Rather than bifurcate types into linear and non-linear counterparts, we instead attach linearity to function arrows. Linear functions can receive inputs from linearly-bound values, but can also operate over unrestricted, regular values. To demonstrate the efficacy of our linear type system - both how easy it can be integrated in an existing language implementation and how streamlined it makes it to write programs with linear types - we implemented our type system in GHC, the leading Haskell compiler, and demonstrate two kinds of applications of linear types: mutable data with pure interfaces; and enforcing protocols in I/O-performing functions

Dilute Bose gases interacting via power-law potentials

Neutral atoms interact through a van der Waals potential which asymptotically falls off as r^{-6}. In ultracold gases, this interaction can be described to a good approximation by the atom-atom scattering length. However, corrections arise that depend on the characteristic length of the van der Waals potential. We parameterize these corrections by analyzing the energies of two- and few-atom systems under external harmonic confinement, obtained by numerically and analytically solving the Schrodinger equation. We generalize our results to particles interacting through a longer-ranged potential which asymptotically falls off as r^{-4}.Comment: 7 pages, 4 figure

Detection of Multi-drug Resistant \u3cem\u3eEscherichia coli\u3c/em\u3e in the Urban Waterways of Milwaukee, WI

Urban waterways represent a natural reservoir of antibiotic resistance which may provide a source of transferable genetic elements to human commensal bacteria and pathogens. The objective of this study was to evaluate antibiotic resistance of Escherichia coli isolated from the urban waterways of Milwaukee, WI compared to those from Milwaukee sewage and a clinical setting in Milwaukee. Antibiotics covering 10 different families were utilized to determine the phenotypic antibiotic resistance for all 259 E. coli isolates. All obtained isolates were determined to be multi-drug resistant. The E. coli isolates were also screened for the presence of the genetic determinants of resistance including ermB (macrolide resistance), tet(M) (tetracycline resistance), and β-lactamases (blaOXA, blaSHV, and blaPSE). E. coli from urban waterways showed a greater incidence of antibiotic resistance to 8 of 17 antibiotics tested compared to human derived sources. These E. coli isolates also demonstrated a greater incidence of resistance to higher numbers of antibiotics compared to the human derived isolates. The urban waterways demonstrated a greater abundance of isolates with co-occurrence of antibiotic resistance than human derived sources. When screened for five different antibiotic resistance genes conferring macrolide, tetracycline, and β-lactam resistance, clinical E. coli isolates were more likely to harbor ermB and blaOXA than isolates from urban waterway. These results indicate that Milwaukee’s urban waterways may select or allow for a greater incidence of multiple antibiotic resistance organisms and likely harbor a different antibiotic resistance gene pool than clinical sources. The implications of this study are significant to understanding the presence of resistance in urban freshwater environments by supporting the idea that sediment from urban waterways serves as a reservoir of antibiotic resistance

Strategies for improving mental health and wellbeing used by adults ageing with HIV from the Kenyan coast: a qualitative exploration

Background: Physical and mental health problems are common among older adults living with HIV (OALWH). Adaptive coping strategies play a vital role in improving these adults\u27 mental health and well-being despite the deleterious effects of HIV and ageing. However, in sub-Saharan Africa, limited evidence exists on the commonly utilized coping strategies in this population. We explore the coping strategies used by Kenyan OALWH to improve their mental health and wellbeing. Methods: Semi-structured in-depth interviews were conducted between October and December 2019 with 56 participants: 34 OALWH (53% female), 11 healthcare providers (63% female) and 11 primary caregivers (73% female) in Kilifi County. All interviews were audiorecorded and transcribed verbatim. We used the framework approach to synthesize the qualitative data. Results: Five major themes emerged from the analysis of participants’ narratives, including self-care practices, religion and spirituality, relational living (social connectedness), generativity, identity, and mastery. Our study further revealed maladaptive coping strategies, including reliance on over-the-counter medications, self-isolation, waiting to see if symptoms would subside despite doing nothing, and HIV treatment interruptions during prolonged periods of prayer and fasting. Conclusions: Our findings provide an initial understanding of the coping strategies used by OALWH to confront HIV and ageing challenges in a low-literacy, low socio-economic Kenyan setting. Our results suggest that interventions designed to enhance personal capacity, social support, positive religiosity and spirituality, and intergenerational connections may be beneficial in improving the mental health and well-being of OALWH

Efficient Tree-Traversals: Reconciling Parallelism and Dense Data Representations

Recent work showed that compiling functional programs to use dense, serialized memory representations for recursive algebraic datatypes can yield significant constant-factor speedups for sequential programs. But serializing data in a maximally dense format consequently serializes the processing of that data, yielding a tension between density and parallelism. This paper shows that a disciplined, practical compromise is possible. We present Parallel Gibbon, a compiler that obtains the benefits of dense data formats and parallelism. We formalize the semantics of the parallel location calculus underpinning this novel implementation strategy, and show that it is type-safe. Parallel Gibbon exceeds the parallel performance of existing compilers for purely functional programs that use recursive algebraic datatypes, including, notably, abstract-syntax-tree traversals as in compilers

Strategies for improving mental health and well being used by adults ageing with HIV: a qualitative exploration

Background: Physical and mental health problems are common among older adults living with HIV (OALWH). Adaptive coping strategies play a vital role in improving these adults\u27 mental health and well-being despite the deleterious effects of HIV and ageing. However, in sub-Saharan Africa, limited evidence exists on the commonly utilized coping strategies in this population. We explore the coping strategies used by Kenyan OALWH to improve their mental health and wellbeing. Methods: Semi-structured in-depth interviews were conducted between October and December 2019 with 56 participants: 34 OALWH (53% female), 11 healthcare providers (63% female) and 11 primary caregivers (73% female) in Kilifi County. All interviews were audio - recorded and transcribed verbatim. We used the framework approach to synthesize the qualitative data. Results: Five major themes emerged from the analysis of participants’ narratives, including self-care practices, religion and spirituality, relational living (social connectedness), generativity, identity, and mastery. Our study further revealed maladaptive coping strategies, including reliance on over-the-counter medications, self-isolation, waiting to see if symptoms would subside despite doing nothing, and HIV treatment interruptions during prolonged periods of prayer and fasting. Conclusions: Our findings provide an initial understanding of the coping strategies used by OALWH to confront HIV and ageing challenges in a low-literacy, low socio-economic Kenyan setting. Our results suggest that interventions designed to enhance personal capacity, social support, positive religiosity and spirituality, and intergenerational connections may be beneficial in improving the mental health and well-being of OALWH