ORFanID: A Web-Based Search Engine for the Discovery and Identification of Orphan and Taxonomically Restricted Genes

With the multiplicity of genomes sequenced today, it has been shown that significant percentages of genes in any given taxon do not possess orthologous sequences in other taxa. These sequences are typically designated as orphans/ORFans when found as singletons in one species only or taxonomically restricted genes (TRGs) when found at higher taxonomic ranks. Quantitative and collective studies of these genes are necessary for understanding their biological origins. Currently, orphan gene identifying software is limited, and those previously available are either not functional, are limited in their database search range, or are very complex algorithmically. Thus, an interested researcher studying orphan genes must harvest their data from many disparate sources. ORFanID is a graphical web-based search engine that efficiently finds both orphan genes and TRGs at all taxonomic levels, from DNA or amino acid sequences in the entire NCBI database cluster and other large bioinformatics repositories. This algorithm allows the easy identification of both orphan genes and TRGs using both nucleotide and protein sequences in any species of interest. ORFanID identifies genes unique to any taxonomic rank, from species to a domain, using standard NCBI systematic classifiers. The software allows for user control of the NCBI database search parameters. The results of the search are provided in a spreadsheet as well as a graphical display. All the tables in the software are sortable by column, and results can be easily filtered with fuzzy search functionality. In addition, the visual presentation is expandable and collapsible by taxonomy

Quantum Magnetic Properties in Perovskite with Anderson Localized Artificial Spin-1/2

Quantum magnetic properties in a geometrically frustrated lattice of spin-1/2 magnet, such as quantum spin liquid or solid and the associated spin fractionalization, are considered key in developing a new phase of matter. The feasibility of observing the quantum magnetic properties, usually found in geometrically frustrated lattice of spin-1/2 magnet, in a perovskite material with controlled disorder is demonstrated. It is found that the controlled chemical disorder, due to the chemical substitution of Ru ions by Co-ions, in a simple perovskite CaRuO3 creates a random prototype configuration of artificial spin-1/2 that forms dimer pairs between the nearest and further away ions. The localization of the Co impurity in the Ru matrix is analyzed using the Anderson localization formulation. The dimers of artificial spin-1/2, due to the localization of Co impurities, exhibit singlet-to-triplet excitation at low temperature without any ordered spin correlation. The localized gapped excitation evolves into a gapless quasi-continuum as dimer pairs break and create freely fluctuating fractionalized spins at high temperature. Together, these properties hint at a new quantum magnetic state with strong resemblance to the resonance valence bond system.Comment: 8 pages, 6 figure

Sigmoid sinus thrombosis presenting with posterior alexia in a patient with Behçet's disease and polycythaemia: a case report

<p>Abstract</p> <p>Introduction</p> <p>A 59-year-old Caucasian woman presented with an acute onset of alexia, noticed whilst driving. She described how while she could read car number plates, she had lost the ability to read and understand words on roadside advertisements and car window stickers.</p> <p>Case presentation</p> <p>Neurological examination was unremarkable apart from the inability to read full words or sentences. Imaging of the brain, initially computed tomography, followed by magnetic resonance venography, confirmed a diagnosis of sigmoid sinus thrombosis with associated venous infarction. The patient's past medical history revealed that she had suffered an ischemic stroke and following investigation for this, had undergone a nephrectomy for renal cell carcinoma. This was complicated by postoperative deep venous thrombosis. She had a persistent polycythaemia that was managed with venesection, and recently she had been diagnosed with Behçet's disease. Prior to this presentation, she had recently stopped her prophylactic antiplatelet medication as she was due to undergo a total knee replacement for osteoarthritis. She was managed with weight-adjusted, low molecular weight heparin followed by oral anticoagulation, and made a good recovery from her symptoms.</p> <p>Conclusion</p> <p>This case illustrates a classical neurological syndrome, highlights the importance of cerebral venous and sinus thrombosis as a cause of stroke, and the importance of remaining vigilant to a person's changing risk of venous thrombosis with evolving comorbidity.</p

The 23.01 release of Cloudy

We announce the C23.01 update of Cloudy. This corrects a simple coding error, present since $\sim$ 1990, in one routine that required a conversion from the line-center to the mean normalization of the Ly$\alpha$ optical depth. This affects the destruction of H I Ly$\alpha$ by background opacities. Its largest effect is upon the Ly$\alpha$ intensity in high-ionization dusty clouds, where the predicted intensity is now up to three times stronger. Other properties that depend on Ly$\alpha$ destruction, such as grain infrared emission, change in response.Comment: 4 pages, 1 figur