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

Does COVID-19 Spread through Droplets Alone?

The world has been in the midst of a swiftly unfolding public health crisis that has turned deadly. The novel coronavirus disease 2019 (COVID-19), has turned out to be a rapidly expanding pandemic affecting the nations of the world. Most governments and their public health authorities worldwide have taken drastic measures to strictly contain the spread of this coronavirus. However, despite the aggressive preventative measures in place, COVID-19 has propagated exponentially across the world. Currently, the accepted mode of disease transmission is by droplets containing the virus. Here we provide epidemiological data in conjunction with biochemical molecular mechanisms of this Severe Acute Respiratory Syndrome- Coronavirus-2 (SARS-CoV-2) and explain the possible alternative modes of disease transmission. Our observed data, biochemical mechanisms, and inferences indicate that COVID-19 has a high probability of transmission through other routes as well, such as indirect routes; viz, fomites and aeros

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

Evaluating coverage bias in next-generation sequencing of Escherichia coli

Whole-genome sequencing is essential to many facets of infectious disease research. However, technical limitations such as bias in coverage and tagmentation, and difficulties characterising genomic regions with extreme GC content have created significant obstacles in its use. Illumina has claimed that the recently released DNA Prep library preparation kit, formerly known as Nextera Flex, overcomes some of these limitations. This study aimed to assess bias in coverage, tagmentation, GC content, average fragment size distribution, and de novo assembly quality using both the Nextera XT and DNA Prep kits from Illumina. When performing whole-genome sequencing on Escherichia coli and where coverage bias is the main concern, the DNA Prep kit may provide higher quality results; though de novo assembly quality, tagmentation bias and GC content related bias are unlikely to improve. Based on these results, laboratories with existing workflows based on Nextera XT would see minor benefits in transitioning to the DNA Prep kit if they were primarily studying organisms with neutral GC content

Titanium Alloyed with Boron

Small additions of boron to conventional titanium alloys have been found to produce significant changes to the microstructures and associated properties. Grain refinement and improved strength and stiffness are first-order effects, which lead to possibilities for developing novel and affordable processing methodologies and to enhance performance over conventional titanium alloys. In this article, we introduce this new class of titanium alloys and describe unique formability benefits achieved via engineering microstructures

Spectroscopic observations of novae V1065 CEN and V1280 SCO using 45 cm cassegrain telescope at Arthur C Clarke Institute

The spectroscopic observations of two novae namely V1065 CEN and V1280 SCO were made by 45 cm Cassegrain telescope in high resolution ($\lambda/\delta\lambda$=22000) at H$\alpha$ (6563 \r{A}) region. V1065 CEN is He/N-type spectra which characterize a broad (Gaussian FWHM 49 \r{A}), saddle shaped and asymmetric H$\alpha$ emission line without prominent P-Cyg absorption component. Completely different H$\alpha$ profile of V1280 SCO shows prominent P-Cyg absorption and narrow emission line (Gaussian FWHM 26 \r{A}) which can be classified as Fe II type nova. The expansion velocities of these two systems measured from the minima of the P-Cyg profiles are close to 2300 km/s for V1065 CEN, and 716 km/s for V1280 SCO. Based on the photometric analysis, the Nova V1065 CEN can be classified as fast (11$<$t${_2}$$<$25) nova. The derived absolute magnitudes at maximum for nova V1065 CEN to be M$_{o,V}$ = -7.58$\pm$0.18 and M$_{o,B}$= -7.75$\pm$0.25 correspond to a distance 8.51$\pm$0.33 kpc. The parameters t$_{2V}$=12 days and t$_{3V}$=14 days of nova V1280 SCO determine that the nova is in between very fast and fast nova. The mean absolute magnitude at maximum is calculated to be M$_{o,V}$=-8.7$\pm$0.1 and the estimated distance to the nova V1280 SCO is 3.2$\pm$0.2 kpc

Biopsychosocial and Spiritual Implications of Patients with COVID-19 Dying in Isolation

Critically ill patients with the Coronavirus disease 2019 (COVID-19) are dying in isolation without the comfort of their family or other social support in unprecedented numbers. Recently, healthcare teams at COVID-19 epicenters have been inundated with critically ill patients. Patients isolated for COVID-19 have had no contact with their family or loved ones and may have likely experienced death without closure. This situation highlights concerns about the psychological and spiritual well-being of patients with COVID-19 and their families, as they permanently part ways. While palliative care has advanced to address these patients\u27 needs adequately, the COVID-19 pandemic presents several barriers that force healthcare teams to deprioritize these essential aspects of patient care. The severe acute respiratory syndrome (SARS) outbreak in 2003 gave us a glimpse of these challenges as these patients were also isolated in hospitals. Here, we discuss the importance of the biopsychosocial spiritual model in end-of-life care and its implications on patients dying with COVID-19. Furthermore, we outline an integrative approach to address the unique and holistic needs of critically ill patients dying with COVID-19. These include intentional and increased coordination with trained palliative care staff, early and frequent goals of care including discussion of end-of-life plans, broader use of technology to improve connectedness and shared decision making with patients’ families

IMECE2002-33784 PROCESS MODELING OF SHAPE ROLLING FOR AEROSPACE INDUSTRY

ABSTRACT Shape rolling of seamless rings constitutes an efficient manufacturing process offering excellent material yield, energy conservation, and component production, which require a minimum of subsequent machining operations. An increasing number of rings are being produced from high temperature Titanium and Nickel based super alloy materials for gas turbine engine parts such as vane and fan casings, exhaust casings, turbine shrouds, and combustion liners. With the increasing cost of super alloy raw materials and growing demand for costcompetitive parts, the importance of ring rolling to contoured shape becomes an increasingly important factor. This paper describes a new process modeling technique based on Upper Bound Elemental Technique (UBET) for shape rolling of super alloys. This tool provides a new design paradigm for an industry relying to heavily on designer experience and cut-and-try methods. As a rapid software tool to aid designers in developing ring-rolling process schedules thereby helping in reducing the design and analysis cycle time, the potential to capture the unique 3-D flow situation experienced in shape rolling of seamless rings is being explored. Numerical results have been compared with data available for high temperature alloys such as IN718 and Ti6Al-4V

Microbiological analysis of skin and soft tissue infections in cancer patients at Apeksha Hospital, Sri Lanka

Background: Skin and soft tissue infections (SSTIs) in patients with malignancies are common and frequently have serious consequences. These infections are caused by a wide range of microorganisms with variable anti-microbial susceptibilities.Objectives: To analyse skin and soft tissue infections in cancer patients at Apeksha Hospital with regard to causative agents, antibiotic susceptibility and associated factors.Methods: A descriptive cross sectional study was carried out for 18-month period. Specimens from adult cancer patients admitted to Apeksha Hospital, Maharagama with SSTIs were analysed. Aerobic and anaerobic bacterial culture, fungal culture, species identification and antibiotic susceptibility testing were performed. Clinical data were obtained from patient records.Results: A total of 85 patients were included with a male: female ratio of 1:1.1.Majority (75%) were >50 years old. Out of the 80 aerobic bacterial isolates most (69%) were Gram negatives, majority being Enterobateriaceae (42/80) followed by Pseudomonas (11/80). Escherichia coli was the commonest bacterial species. Staphylococcus aureus was the commonestGram positive organism (22/80). No strict anaerobic bacteria were yielded however, 3 fungi (two Candida albicans, one Fusarium species) were isolated. Enterobacteria showed lowest resistance to amikacin (7%) and meropenem (10%). Pseudomonas species had highest resistance to ticarcillin-clavulanate (64%). Methicillin resistant Staphylococcus aureus (MRSA) rate was 61%. None had resistance to anti-MRSA agents. Gram-negative bacteria caused 74% of wound infections while 54% of the abscesses were caused by Gram positives. Gram negatives were prevalent (73%) in patients with solid organ cancers and Gram positives in haematological malignancies (83%). Gram-negative infections (69%) predominate in patients on radiotherapy while chemoptherapy had similar rates of infections by the two types of organisms.Conclusion: SSTIs in the cancer patients at Apeksha Hospital, Maharagama are mainly caused by Gram negative bacteria however, Gram positives predominate in haematological malignancies. Multi-drug resistance is prevalent in all commonly isolated pathogens.Acknowledgements: University of Sri Jayewardenepura research grant ASP/01/R/MED/2016/61 (Centre for Cancer Research