Ultrasound renal stone diagnosis based on convolutional neural network and VGG16 features

This paper deals with the classification of the kidneys for renal stones on ultrasound images. Convolutional neural network (CNN) and pre-trained CNN (VGG16) models are used to extract features from ultrasound images. Extreme gradient boosting (XGBoost) classifiers and random forests are used for classification. The features extracted from CNN and VGG16 are used to compare the performance of XGBoost and random forest. An image with normal and renal stones was classified. This work uses 630 real ultrasound images from Al-Diwaniyah General Teaching Hospital (a lithotripsy center) in Iraq. Classifier performance is evaluated using its accuracy, recall, and F1 score. With an accuracy of 99.47%, CNN-XGBoost is the most accurate model

Isolation and antimicrobial activity of rutin and its derivatives from Ruta chalepensis (Rutaceae) growing in Iraq

Rutin (1), rutin 3'-methyl ether (2), and a new flavonol glycoside, 6-hydroxy-rutin 3',7-dimethyl ether (3), were isolated from the methanol extract of the fruits of Ruta chalepensis, collected from Diyala, Iraq. Their structures were elucidated by spectroscopic analyses, including 1D-, 2D-NMR and HRESIMS. Antimicrobial activity of compounds 1-3 was tested against four Gram +ve and Gram –ve bacterial strains, and the only fungal strain, Candida albicans, using the 96-well based resazurin microtitre assay

Variation in gas chromatography (GC) analysis in setting up laboratory protocols for waste to energy novel fixed bed reactor setups

Gas Chromatography coupled with Mass Spectrometry (GC/MS) has been applied in various analytical chemistry works. However, to fine tune a system that can serve the purposes of pyrolysis oil identification has proven to be a laborious effort, especially when considering the fact that no standard protocol exists for such analysis. In addition, obtained products were yielded from a newly commissioned unit with a unique and novel design. In this study, a US patent office claimed reactor [SULTAN-1, Pyrolysis Reactor System for the Conversion and Analysis of Organic Solid Waste, Patent application number: 15,487,351] that degrades polyolefinc virgin and waste materials to obtain petroleum refinery and petrochemical feedstock, has been commissioned. The reactor produces three distinct physical states of matter products accumulated as testing specimens, i.e. solids, gaseous and oil. The samples analysed in this work were of the gas and oil produced by pyrolysis of end of life tyre (ELTs) shavings that required to have a special recipe to work with in the laboratory. Various MS cords were utilised and experimental setups to fine tune the process, and special emphasis was given on the gas samples variation in this communication. To reach the desired analysis results with high repeatability, a plethora of experiences of lab personnel and laboratory-based experimental work was accumulated. Laboratory protocols were also setup for this work. These will be detailed along the process execution which yielded a standard laboratory best practice analytical method as part of the State of Kuwait newly initiated Government Initiative project

Why honey is effective as a medicine. 1. Its use in modern medicine

Honey has been used as a medicine for thousands of years and its curative properties are well documented. However, modern medicine turned its back on honey and it is only now, with the advent of multi-resistant bacteria, that the antibiotic properties of honey are being rediscovered

Quantum dynamics in strong fluctuating fields

A large number of multifaceted quantum transport processes in molecular systems and physical nanosystems can be treated in terms of quantum relaxation processes which couple to one or several fluctuating environments. A thermal equilibrium environment can conveniently be modelled by a thermal bath of harmonic oscillators. An archetype situation provides a two-state dissipative quantum dynamics, commonly known under the label of a spin-boson dynamics. An interesting and nontrivial physical situation emerges, however, when the quantum dynamics evolves far away from thermal equilibrium. This occurs, for example, when a charge transferring medium possesses nonequilibrium degrees of freedom, or when a strong time-dependent control field is applied externally. Accordingly, certain parameters of underlying quantum subsystem acquire stochastic character. Herein, we review the general theoretical framework which is based on the method of projector operators, yielding the quantum master equations for systems that are exposed to strong external fields. This allows one to investigate on a common basis the influence of nonequilibrium fluctuations and periodic electrical fields on quantum transport processes. Most importantly, such strong fluctuating fields induce a whole variety of nonlinear and nonequilibrium phenomena. A characteristic feature of such dynamics is the absence of thermal (quantum) detailed balance.Comment: review article, Advances in Physics (2005), in pres

Graphene Nano-, Micro-and Macro-Photonics

ABSTRACT Graphene has already become an established medium for novel photonic devices and their applications. In some cases, e.g. the use of graphene as a non-linear medium with saturable absorption properties, it is experimentally convenient to use the readily available form that is known as graphene oxide. Moreover, technological and scientific developments that are advancing control of the properties of graphene for electronic applications are also likely to be applicable in photonic and optoelectronic devices. This presentation will review research in the field of graphene photonics across the world. It will address, in particular, its application as a saturable absorber, e.g. for pulsed operation of fibre lasers -as well as work on materials characterisation of deposited graphene films. Patterning of graphene films with precision at the microand nano-scales will be an important requirement -and will be considered in this presentation

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Genetic programming of macrophages generates an in vitro model for the human erythroid island niche

In vitro differentiation of red blood cells (RBCs) is a desirable therapy for various disorders. Here the authors develop a culture system using stem cell-derived macrophages to show that inducible expression of a transcription factor, KLF1, enhances RBC production, potentially through the induction of three soluble factors, ANGPTL7, IL33 and SERPINB2

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer