2,823 research outputs found
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 =
1.36 GeV at CELSIUS-WASA. At near-threshold energies the total and differential
distributions for the and channels are dominated by
Roper excitation and its decay into and channels. At beam
energies 1.1 GeV the excitation governs the two-pion
production process. In the channel evidence is found for the
excitation of a higher-lying I=3/2 resonance, favorably the . The
isovector fusion processes leading to the deuteron and to quasi-stable 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 -invariant
mass spectrum, and can be described by conventional -channel
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
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
Health-related quality-of-life results from the randomised phase II TAVAREC trial on temozolomide with or without bevacizumab in 1p/19q intact first-recurrence World Health Organization grade 2 and 3 glioma (European Organization for Research and Treatment of Cancer 26091)
Background: In an international randomised controlled phase II study of temozolomide (TMZ) versus TMZ in combination with bevacizumab (BEV) in locally diagnosed non-1p/19q co-deleted World Health Organization grade 2 or 3 gliomas with a first and contrast-enhancing recurrence after initial radiotherapy, and overall survival at 12 months was not significantly different (61% in the TMZ arm and 55% in the TMZ + BEV arm). Objectives: Health-related quality of life (HRQoL) was a key secondary end-point in this trial, and the main objective of this study was to determine the impact of the addition of BEV to TMZ on HRQoL. Methods: HRQoL was assessed using the European Organization for Research and Treatment of Cancer QLQ-C30 (version 3) and QLQ-BN20 at baseline, and then every 12 weeks until disease progression. The pre-selected primary HRQoL end-point was the QLQ-C30 global health scale, with self-perceived cognitive functioning and pain selected as secondary HRQoL issues. Analysis was undertaken using linear mixed modelling and complemented with sensitivity analyses using summary statistics. A difference was considered clinically relevant with ≥10 points difference on a 100-point scale. Results: Baseline compliance was high at 94% and remained above 60% until 72 weeks, limiting the analysis to 60 weeks. Compliance was similar in both arms. We found no statistically significant or clinically significant differences between the primary HRQoL end-point in both treatment arms (p = 0.2642). The sensitivity analyses confirmed this finding. The overall test for post-baseline differences between the two treatment arms also showed no statistically or clinically significant differences regarding the selected secondary end-point scales. Interpretation: The addition of BEV to TMZ in this patient group neither improves nor negatively impacts HRQoL.</p
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