ComPhy: Prokaryotic Composite Distance Phylogenies Inferred from Whole-Genome Gene Sets

doi:10.1186/1471-2105-10-S1-S5With the increasing availability of whole genome sequences, it is becoming more and more important to use complete genome sequences for inferring species phylogenies. We developed a new tool ComPhy, 'Composite Distance Phylogeny', based on a composite distance matrix calculated from the comparison of complete gene sets between genome pairs to produce a prokaryotic phylogeny. The composite distance between two genomes is defined by three components: Gene Dispersion Distance (GDD), Genome Breakpoint Distance (GBD) and Gene Content Distance (GCD). GDD quantifies the dispersion of orthologous genes along the genomic coordinates from one genome to another; GBD measures the shared breakpoints between two genomes; GCD measures the level of shared orthologs between two genomes. The phylogenetic tree is constructed from the composite distance matrix using a neighbor joining method. We tested our method on 9 datasets from 398 completely sequenced prokaryotic genomes. We have achieved above 90% agreement in quartet topologies between the tree created by our method and the tree from the Bergey's taxonomy. In comparison to several other phylogenetic analysis methods, our method showed consistently better performance. ComPhy is a fast and robust tool for genome-wide inference of evolutionary relationship among genomes."This work was supported in part by NSF/ITR-IIS-0407204.

Automated image registration for dynamic contrast-enhanced breast magnetic resonance imaging

Treballs Finals de Grau d'Enginyeria Informàtica, Facultat de Matemàtiques, Universitat de Barcelona, Any: 2024, Director: Oliver Díaz[en] This thesis presents an automated approach to image registration for dynamic contrastenhanced breast magnetic resonance imaging (MRI), a critical task in medical diagnostics that enhances the analysis and interpretation of sequential image data. Image registration, particularly within the domain of breast MRI, faces significant challenges due to the deformable nature of breast tissue and the high degree of accuracy required for effective diagnosis and treatment planning. The work employs advanced machine learning models to develop an efficient and robust system capable of aligning multiple MRI scans over time with high precision. The primary methodological contribution of this thesis is the integration of a convolutional neural network model, designed to adapt to the unique complexities presented by the high variability and dynamic changes in breast MRI scans. This approach facilitates improved diagnostic capabilities by enhancing the temporal analysis of contrast patterns in breast tissue, which is crucial for identifying and monitoring various pathological conditions. Experimental results demonstrate the effectiveness of the proposed system, which achieved a Dice score of 0.782 ± 0.009 in one of the models and demonstrate substantial improvements in alignment efficiency compared to traditional image registration techniques. The system’s ability to provide rapid and precise alignments promises significant benefits for clinical practices, including better monitoring of disease progression and more tailored treatment strategies for breast cancer patients

Pallada-Electrocatalyzed Non-Directed C–H Alkenylation and Double C–H Arylation

The merger of electrooxidation and transition metal-catalyzed C–H activation has emerged as an increasingly viable platform in molecular syntheses that can avoid stoichiometric chemical redox agents and circuitous functional group operations. Despite significant progress, these electrochemical C−H activations generally require directing groups, of which the installation and removal call for additional synthesis steps, leading to undesired waste with reduced step and atom economy. In his thesis, we present palladium-electrochemical C−H olefinations of simple arenes devoid of exogenous directing groups. The robust electrocatalysis protocol proved amenable to a wide range of both electron-rich and electron-deficient arenes under exceedingly mild reaction conditions, avoiding chemical oxidants. This study points to an interesting approach of two electrochemical transformations for the success of outstanding levels of position-selectivities in direct olefinations of electron-rich anisoles. Furthermore, late-stage2024-12-2

In a pilot study, reduced fatty acid desaturase 1 function was associated with nonalcoholic fatty liver disease and response to treatment in children

BACKGROUND: FADS1 gene encodes delta 5 desaturase, a rate-limiting enzyme in the metabolism of n-3 and n-6 polyunsaturated fatty acids (PUFAs). Minor alleles of FADS1 locus polymorphisms are associated with reduced FADS1 expression and intra-hepatic fat accumulation. However, the relationship between FADS1 expression and pediatric nonalcoholic fatty liver disease (NAFLD) risk remains to be explored. METHODS: We analyzed FADS1 transcription levels and their association with intra-hepatic fat and histology in children, and we performed pathway enrichment analysis on transcriptomic profiles associated with FADS1 polymorphisms. We also evaluated the weight of FADS1 alleles on the response to combined docosahexaenoic acid, choline, and vitamin E (DHA-CHO-VE) treatment. RESULTS: FADS1 mRNA level was significantly and inversely associated with intra-hepatic fat (p = 0.004), degree of steatosis (p = 0.03), fibrosis (p = 0.05), and NASH (p = 0.008) among pediatric livers. Transcriptomics demonstrated a significant enrichment of a number of pathways strongly related to NAFLD (e.g., liver damage, fibrosis, and hepatic stellate cell activation). Compared to children who are common allele homozygotes, children with FADS1 minor alleles had a greater reduction in steatosis, fibrosis, and NAFLD activity score after DHA-CHO-VE. CONCLUSION: This study suggests that decreased FADS1 expression may be associated with NAFLD in children but an increased response to DHA-CHO-VE

Multi-dimensional Channel Parameter Estimation for mmWave Cylindrical Arrays

University of Technology Sydney. Faculty of Engineering and Information Technology.Millimeter-wave (mmWave) large-scale antenna arrays, standardized for the fifth-generation (5G) communication networks, have the potential to estimate channel parameters with unprecedented accuracy, due to their high temporal resolution and excellent directivity. However, most existing techniques have very high complexities in hardware and software, and they cannot effectively exploit the properties of mmWave large-array systems for channel estimation. As a result, their application in 5G mmWave large array systems is limited in practice. This thesis develops new and efficient solutions to channel parameter estimation using large-scale mmWave uniform cylindrical arrays (UCyAs). The key contributions of this thesis are on the following four aspects: We first present a channel compression-based channel estimation method, which reduces the computational complexity substantially at a negligible cost of estimation accuracy. By capitalizing on the sparsity of mmWave channel, the method effectively filters out the useless signal components. As a result, the dimension of the element space of the received signals can be reduced. Next, we extend the channel estimation to the hybrid UCyA case, and design new hybrid beamformers. By exploiting the convergence property of the Bessel function, the designed beamformers can preserve the recurrence relationship of the received signals with a small number of radio frequency (RF) chains. We then arrange the received signals in a tensor form and propose a new tensor-based channel estimation algorithm. By suppressing the receiver noises in all dimensions (time, frequency, and space), the algorithm can achieve substantially higher estimation accuracy than existing matrix-based techniques. Finally, to reduce cost and power consumption while maintaining a high network access capability, we develop a novel nested hybrid UCyA and present the corresponding parameter estimation algorithm based on the second-order channel statistics. Simulation results show that by exploiting the sparse array technique to design the RF chain connection network, the angles of a large number of devices can be accurately estimated with much fewer RF chains than antennas. Overall, this thesis presents several applicable UCyA design schemes and proposes the efficient channel parameter estimation algorithms. The presented new UCyAs can significantly reduce the hardware cost of the system with a marginal accuracy loss, and the proposed algorithms are capable of accurately estimating the channel parameters with low computational complexities. By employing the presented UCyAs and implementing the proposed novel algorithms cohesively, the different communication and deployment requirements of a variety of mmWave communication scenarios can be met