Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs

We present kleuren, a novel assembly-free method to reconstruct phylogenetic trees using the Colored de Bruijn Graph. kleuren works by constructing the Colored de Bruijn Graph and then traversing it, finding bubble structures in the graph that provide phylogenetic signal. The bubbles are then aligned and concatenated to form a supermatrix, from which a phylogenetic tree is inferred. We introduce the algorithms that kleuren uses to accomplish this task, and show its performance on reconstructing the phylogenetic tree of 12 Drosophila species. kleuren reconstructed the established phylogenetic tree accurately, and is a viable tool for phylogenetic tree reconstruction using whole genome sequences. Software package available at: https://github.com/Colelyman/kleurenComment: 6 pages, 3 figures, accepted at BIBE 2017. Minor modifications to the text due to reviewer feedback and fixed typo

The high-intensity hyperon beam at CERN

A high-intensity hyperon beam was constructed at CERN to deliver Sigma- to experiment WA89 at the Omega facility and operated from 1989 to 1994. The setup allowed rapid changeover between hyperon and conventional hadron beam configurations. The beam provided a Sigma-flux of 1.4 x 10^5 per burst at mean momenta between 330 and 345 Gev/c, produced by about 3 x 10^10 protons of 450 GeV/c . At the experiment target the beam had a Sigma-/pi- ratio close to 0.4 and a size of 1.6 x 3.7 cm^2. The beam particle trajectories and their momenta were measured with a scintillating fibre hodoscope in the beam channel and a silicon microstrip detector at the exit of the channel. A fast transition radiation detector was used to identify the pion component of the beam.Comment: 20 pages, 13 figures. Submitted to Nucl. Instr. Meth.

Systematic Study of Two-Pion Production in NN Collisions -- from Single-Baryon to Di-Baryon Excitations

The two-pion production in nucleon-nucleon collisions has been studied by exclusive and kinematically complete experiments from threshold up to $T_p$ = 1.36 GeV at CELSIUS-WASA. At near-threshold energies the total and differential distributions for the $\pi^+\pi^-$ and $\pi^0\pi^0$ channels are dominated by Roper excitation and its decay into $N\sigma$ and $\Delta\pi$ channels. At beam energies $T_p >$ 1.1 GeV the $\Delta\Delta$ excitation governs the two-pion production process. In the $\pi^+\pi^+$ channel evidence is found for the excitation of a higher-lying I=3/2 resonance, favorably the $\Delta(1600)$. The isovector fusion processes leading to the deuteron and to quasi-stable $^2$He, respectively, %with the production of an isovector pion-pair exhibit no or only a modest ABC-effect, {\it i.e.} low-mass enhancement in the $\pi\pi$-invariant mass spectrum, and can be described by conventional $t$-channel $\Delta\Delta$ excitation. On the other hand, the isoscalar fusion process to the deuteron %with the production of an isoscalar pion-pair exhibits a dramatic ABC-effect correlated with a narrow resonance-like energy dependence in the total cross section with a width of only 50 MeV and situated at a mass 90 MeV below the $\Delta\Delta$ mass.Comment: Proceedings HADRON0

Surrogate approach to determine heavy metal loads in a moss species – Barbula lambaranensis

AbstractBiomonitoring using a moss species Barbula lambaranensis is an economical method for continuous assessment of atmospheric metal pollution. However, frequent measurement of common heavy metals such as Zn, Cd, Cr, Pb, Cu and Ni in moss can be costly for monitoring large areas. Thus, the aim of the study was to use the surrogate approach to reduce the number of heavy metals required for monitoring. The study found that the Zn load in moss was higher; Pb, Cu and Ni loads were moderate; while Cd and Cr were relatively lower across the study sites. Further, the following surrogates were identified based on PCA: Cu for Cr; Pb for Cd, Cu and Ni; and Cu and Pb for Zn. Quantitative relationships between surrogate loads and the loads of other heavy metals were developed by performing Multiple Linear Regression on a data set constructed using a four level full factorial design. The equations had a relative prediction error and standard error of cross validation below 25% and 1.5%, respectively, indicating that the equations are accurate. However, the cross validated coefficient of determination is relatively low suggesting that the precision of prediction using the equations is low, possibly due to the influence of factors such as climatic conditions on bioaccumulation of heavy metals by moss. Nevertheless, the developed equations can be useful for preliminary investigations

Learning the Language of Genes: Representing Global Codon Bias with Deep Language Models

Codon bias, the usage patterns of synonymous codons for encoding a protein sequence as nucleotides, is a biological phenomenon that is not well understood. Current methods that measure and model the codon bias of an organism exist for usage in codon optimization. In synthetic biology, codon optimization is a task the involves selecting the appropriate codons to reverse translate a protein sequence into a nucleotide sequence to maximize expression in a vector. These features include codon adaptation index (CAI) [1], individual codon usage (ICU), hidden stop codons (HSC) [2] and codon context (CC) [3]. While explicitly modeling these features has helped us to engineer high synthesis yield proteins, it is unclear what other biological features should be taken into account during codon selection for protein synthesis maximization. In this article, we present a method for modeling global codon bias through deep language models that is more robust than current methods by providing more contextual information and long-range dependencies to be considered during codon selection

Geophysical Surveys Across the Boise Hydrogeophysical Research Site to Determine Geophysical Parameters of a Shallow, Alluvial Aquifer

At the Boise Hydrogeophysical Research Site (BHRS), we are characterizing the hydrogeophysical parameters of a cobble-and-sand, unconfined aquifer using a wide variety of geophysical methods. Our goal is to develop methods for mapping variations in permeability by combining non-invasive geophysical data with hydrologic measurements. We are using seismic, ground penetrating radar, and electrical methods in a variety of configurations to provide images of and parameter distributions at the BHRS. Issues such as resolution, depth of penetration, and the ability to image the desired parameters will help determine the most effective methods. Supporting data sets from the BHRS include core analyses and geophysical logs from 18 wells at the site. We will use these data to verify our geophysical interpretations. The various geophysical methods and acquisition geometries, combined with the well control, will provide an outstanding data set to characterize the heterogeneity of the subsurface beneath this alluvial aquifer, and find ways to map permeability with geophysical information

Measuring the Electrical Stapedius Reflex with Stapedius Muscle Electromyogram Recordings

Previous studies have demonstrated a correlation between cochlear implant recipients' comfort levels ( C level, upper limit of dynamic range of stimulation) and the contralateral electrical stapedius reflex (ESR) threshold, detected by acoustic impedance change. However, the utility of the approach is limited because many recipients have no detectable impedance change. The goals of this study were to investigate the utility of the stapedial electromyogram (EMG) for estimating onset and strength of the ESR. Ketamine-anesthetized guinea pigs were implanted with Nucleus electrode arrays and stimulated with biphasic current pulse trains (250 pps) via a Cochlear Corporation CI24M stimulator. Typical EMG recordings (obtained with bipolar microwire electrodes) contained easily detectable unit potentials up to 300 μV in amplitude. Growth response curves (obtained from threshold-crossing counts or rms of the EMG signal) were typically monotonic with dynamic ranges spanning 700 μA or 8 dB. Based on adaptation and temporal properties, the stimulus protocol (500 ms duration with 4–5 s interstimulus intervals) was adequate for producing independent responses. The data presented are consistent with ESR characteristics (acoustic impedance technique) of cochlear implant recipients and with EMG properties of acoustically stimulated guinea pigs. Use of the EMG for characterizing the ESR may eventually be applied to human cochlear implant recipients as a guide in setting the upper limit of the dynamic range. © 2002 Biomedical Engineering Society.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43999/1/10439_2004_Article_482671.pd

Age-related changes in femoral head trabecular microarchitecture

Osteoporosis is a prevalent bone condition, characterised by low bone mineral density and increased fracture risk. Currently, the gold standard for identifying osteoporosis and increased fracture risk is through quantification of bone mineral density using dual energy X-ray absorption. However, many studies have shown that bone strength, and consequently the probability of fracture, is a combination of both bone mass and bone ‘quality’ (architecture and material chemistry). Although the microarchitecture of both non-fracture and osteoporotic bone has been previously investigated, many of the osteoporotic studies are constrained by factors such as limited sample number, use of ovariectomised animal models, and lack of male and female discrimination. This study reports significant differences in bone quality with respect to the microarchitecture between fractured and non-fractured human femur specimens. Micro-computed tomography was utilised to investigate the microarchitecture of femoral head trabecular bone from a relatively large cohort of non-fracture and fracture human donors. Various microarchitectural parameters have been determined for both groups, providing an understanding of the differences between fracture and non -fracture material. The microarchitecture of non-fracture and fracture bone tissue is shown to be significantly different for many parameters. Differences between sexes also exist, suggesting differences in remodelling between males and females in the fracture group. The results from this study will, in the future, be applied to develop a fracture model which encompasses bone density, architecture and material chemical properties for both female and male tissues

More on Massive 3D Supergravity

Completing earlier work on three dimensional (3D) N=1 supergravity with curvature-squared terms, we construct the general supergravity extension of cosmological massive gravity theories. We expand about supersymmetric anti-de Sitter vacua, finding the conditions for bulk unitarity and the critical points in parameter space at which the spectrum changes. We discuss implications for the dual conformal field theory.Comment: v1 : 53 pages, 1 figure; v2 : significantly shortened, 42 p., version published in Class. Quant. Gra

Research ethics capacity building in Sub-Saharan Africa: a review of NIH Fogarty-funded programs 2000–2012

The last fifteen years have witnessed a significant increase in investment in research ethics capacity development throughout the world. We examine nine research ethics training programs that are focused on Sub-Saharan Africa and supported by the US National Institutes of Health. We collected data from grants awards' documents and annual reports supplemented by questionnaires completed by the training program directors. Together, these programs provided long-term training in research ethics to 275 African professionals, strengthened research ethics committees in 19 countries in Sub-Saharan Africa, and created research ethics curricula at many institutions and bioethics centers within Africa. Trainees' leadership resulted in new national systems and policies on research ethics, human tissue storage and export, and methods of monitoring compliance with research ethics guidelines. Training programs adapted to challenges that arose due to varied trainees' background knowledge in ethics, duration of time available for training, spoken and written English language skills, administrative obstacles, and the need to sustain post-training research ethics activities. Our report showcases the development of awareness of research ethics and building/strengthening of basic research ethics infrastructure in Sub-Saharan Africa. Nevertheless, the increasing amount and complexity of health research being conducted in Sub-Saharan Africa suggests the need for continued investment in research ethics capacity development in this region. This paper is part of a collection of papers analyzing the Fogarty International Center's International Research Ethics Education and Curriculum Development program