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

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

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

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

Ecteinascidin-743: Evidence of Activity in Advanced, Pretreated Soft Tissue and Bone Sarcoma Patients

Purpose. To evaluate the activity and safety of ecteinascidin (ET-743) in pretreated patients with advanced or metastatic soft tissue and bone sarcoma. Patients or subjects. Eighty-nine patients received ET-743 as a 24-hour continuous infusion at a dose of 900–1500 μg/m(2) every 3 weeks. Results. We observed one complete remission, 5 partial remissions, one minimal response, and 16 patients with a disease stabilization of 6 months or more. The objective response rate was 6.7% and the clinical benefit rate at 3 and 6 months was 37.7% and 23.4%, respectively. Responses were noted in patients with lipo-, leiomyo-, osteo-, and myogenic sarcoma, with a median duration of 9.85 months. Toxicity mainly involved an asymptomatic elevation of transaminases and neutropenia. Estimated 1- and 2-year survival rates were 39.4% and 15.8%. Median overall survival was 8.25 months. Discussion. This retrospective analysis confirms that ET-743 induces objective responses and progression arrest in a clinically relevant proportion of patients

De novo Assembly of the Burying Beetle Nicrophorus orbicollis (Coleoptera: Silphidae) Transcriptome Across Developmental Stages with Identification of Key Immune Transcripts

Burying beetles (Nicrophorus spp.) are among the relatively few insects that provide parental care while not belonging to the eusocial insects such as ants or bees. This behavior incurs energy costs as evidenced by immune deficits and shorter life-spans in reproducing beetles. In the absence of an assembled transcriptome, relatively little is known concerning the molecular biology of these beetles. This work details the assembly and analysis of the Nicrophorus orbicollis transcriptome at multiple developmental stages. RNA-Seq reads were obtained by next-generation sequencing and the transcriptome was assembled using the Trinity assembler. Validation of the assembly was performed by functional characterization using Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Differential expression analysis highlights developmental stage-specific expression patterns, and immunity-related transcripts are discussed. The data presented provides a valuable molecular resource to aid further investigation into immunocompetence throughout this organism’s sexual development

Measurement of the Eta Production in Proton Proton Collisions with the COSY Time of Flight Spectrometer

The reaction pp -> pp eta was measured at excess energies of 15 and 41 MeV at an external target of the Juelich Cooler Synchrotron COSY with the Time of Flight Spectrometer. About 25000 events were measured for the excess energy of 15 MeV and about 8000 for 41 MeV. Both protons of the process pp eta were detected with an acceptance of nearly 100% and the eta was reconstructed by the missing mass technique. For both excess energies the angular distributions are found to be nearly isotropic. In the invariant mass distributions strong deviations from the pure phase space distributions are seen.Comment: 15 pages, 14 figures, 4 table

Strategies to improve spinal cord ischemia in endovascular thoracic aortic repair: Outcomes of a prospective cerebrospinal fluid drainage protocol

PurposeAlthough endovascular repair of thoracic aortic aneurysm has been shown to reduce the morbidity and mortality rates, spinal cord ischemia remains a persistent problem. We evaluated our experience with spinal cord protective measures using a standardized cerebrospinal fluid (CSF) drainage protocol in patients undergoing endovascular thoracic aortic repair.MethodsFrom 2004 to 2006, 121 patients underwent elective (n = 52, 43%) and emergent (n = 69, 57%) endovascular thoracic aortic stent graft placement for thoracic aortic aneurysm (TAA) (n = 94, 78%), symptomatic penetrating ulceration (n = 11, 9%), pseudoaneurysms (n = 5, 4%) and traumatic aortic transactions (n = 11, 9%). In 2005, routine use of a CSF drainage protocol was established to minimize the risks of spinal cord ischemia. The CSF was actively drained to maintain pressures <15 mm Hg and the mean arterial blood pressures were maintained at ≥90 mm Hg. Data was prospectively collected in our vascular registry for elective and emergent endovascular thoracic aortic repair and the patients were divided into 2 groups (+CSF drainage protocol, −CSF drainage protocol). A χ2 statistical analysis was performed and significance was assumed for P < .05.ResultsOf the 121 patients with thoracic stent graft placement, the mean age was 72 years, 62 (51%) were male, and 56 (46%) underwent preoperative placement of a CSF drain, while 65 (54%) did not. Both groups had similar comorbidities of coronary artery disease (24 [43%] vs 27 [41%]), hypertension (44 [79%] vs 50 [77%]), chronic obstructive pulmonary disease (18 [32%] vs 22 [34%]), and chronic renal insufficiency (10 [17%] vs 12 [18%]). None of the patients with CSF drainage developed spinal cord ischemia (SCI), and 5 (8%) of the patients without CSF drainage developed SCI within 24 hours of endovascular repair (P< .05). All patients with clinical symptoms of SCI had CSF drain placement and augmentation of systemic blood pressures to ≥90 mm Hg, and 60% (3 of 5 patients) demonstrated marked clinical improvement.ConclusionPerioperative CSF drainage with augmentation of systemic blood pressures may have a beneficial role in reducing the risk of paraplegia in patients undergoing endovascular thoracic aortic stent graft placement. However, selective CSF drainage may offer the same benefit as mandatory drainage