Direct Band Gap Gallium Antimony Phosphide (GaSb\u3csub\u3ex\u3c/sub\u3eP\u3csub\u3e1-x\u3c/sub\u3e) Alloys

Here, we report direct band gap transition for Gallium Phosphide (GaP) when alloyed with just 1–2 at% antimony (Sb) utilizing both density functional theory based computations and experiments. First principles density functional theory calculations of GaSbxP1−x alloys in a 216 atom supercell configuration indicate that an indirect to direct band gap transition occurs at x = 0.0092 or higher Sb incorporation into GaSbxP1−x. Furthermore, these calculations indicate band edge straddling of the hydrogen evolution and oxygen evolution reactions for compositions ranging from x = 0.0092 Sb up to at least x = 0.065 Sb making it a candidate for use in a Schottky type photoelectrochemical water splitting device. GaSbxP1−x nanowires were synthesized by reactive transport utilizing a microwave plasma discharge with average compositions ranging from x = 0.06 to x = 0.12 Sb and direct band gaps between 2.21 eV and 1.33 eV. Photoelectrochemical experiments show that the material is photoactive with p-type conductivity. This study brings attention to a relatively uninvestigated, tunable band gap semiconductor system with tremendous potential in many fields

Design of intelligent mesoscale periodic array structures utilizing smart hydrogel

Mesoscale Periodic Array Structures (MPAS, also known as crystalline colloidal arrays), composed of aqueous or nonaqueous dispersions of self-assembled submicron colloidal spheres are emerging toward the development of advanced optical devices for technological applications. This is because of their unique optical diffraction properties and the ease with which these intriguing properties can be modulated experimentally. Moreover our recent advancements in this area which include 'locking' the liquid MPAS into solid or semisolid polymer matrices for greater stability with longer life span, and incorporation of CdS quantum dots and laser dyes into colloidal spheres to obtain nonlinear optical (NLO) responses further corroborate the use of MPAS in optical technology. Our long term goal is fabrication of all-optical and electro-optical devices such as spatial light modulators for optical signal processing and flat panel display devices by utilizing intelligent nonlinear periodic array structural materials. Here we show further progress in the design of novel linear MPAS which have the ability to sense and respond to an external source such as temperature. This is achieved by combining the self-assembly properties of polymer colloidal spheres and thermoshrinking properties of smart polymer gels. At selected temperatures the periodic array efficiently Bragg diffracts light and transmits most of the light at other temperatures. Hence these intelligent systems are of potential use as fixed notch filters optical switches or limiters to protect delicate optical sensors from high intensity laser radiation

Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data

Motivation: Single-nucleotide variants (SNVs) are the most common variations in the human genome. Recently developed methods for SNV detection from single-cell DNA sequencing data, such as SCI and scVILP, leverage the evolutionary history of the cells to overcome the technical errors associated with single-cell sequencing protocols. Despite being accurate, these methods are not scalable to the extensive genomic breadth of single-cell whole-genome (scWGS) and whole-exome sequencing (scWES) data. Results: Here, we report on a new scalable method, Phylovar, which extends the phylogeny-guided variant calling approach to sequencing datasets containing millions of loci. Through benchmarking on simulated datasets under different settings, we show that, Phylovar outperforms SCI in terms of running time while being more accurate than Monovar (which is not phylogeny-aware) in terms of SNV detection. Furthermore, we applied Phylovar to two real biological datasets: an scWES triple-negative breast cancer data consisting of 32 cells and 3375 loci as well as an scWGS data of neuron cells from a normal human brain containing 16 cells and approximately 2.5 million loci. For the cancer data, Phylovar detected somatic SNVs with high or moderate functional impact that were also supported by bulk sequencing dataset and for the neuron dataset, Phylovar identified 5745 SNVs with non-synonymous effects some of which were associated with neurodegenerative diseases. Availability and implementation: Phylovar is implemented in Python and is publicly available at https://github.com/NakhlehLab/Phylovar.National Science Foundation | Ref. IIS-1812822National Science Foundation | Ref. IIS-210683

Factors associated with failed treatment : an analysis of 121,744 women embarking on their first IVF cycles

Peer reviewedPublisher PD

Butyrate Enhances Disease Resistance of Chickens by Inducing Antimicrobial Host Defense Peptide Gene Expression

Host defense peptides (HDPs) constitute a large group of natural broad-spectrum antimicrobials and an important first line of immunity in virtually all forms of life. Specific augmentation of synthesis of endogenous HDPs may represent a promising antibiotic-alternative approach to disease control. In this study, we tested the hypothesis that exogenous administration of butyrate, a major type of short-chain fatty acids derived from bacterial fermentation of undigested dietary fiber, is capable of inducing HDPs and enhancing disease resistance in chickens. We have found that butyrate is a potent inducer of several, but not all, chicken HDPs in HD11 macrophages as well as in primary monocytes, bone marrow cells, and jejuna and cecal explants. In addition, butyrate treatment enhanced the antibacterial activity of chicken monocytes against Salmonella enteritidis, with a minimum impact on inflammatory cytokine production, phagocytosis, and oxidative burst capacities of the cells. Furthermore, feed supplementation with 0.1% butyrate led to a significant increase in HDP gene expression in the intestinal tract of chickens. More importantly, such a feeding strategy resulted in a nearly 10-fold reduction in the bacterial titer in the cecum following experimental infections with S. enteritidis. Collectively, the results indicated that butyrate-induced synthesis of endogenous HDPs is a phylogenetically conserved mechanism of innate host defense shared by mammals and aves, and that dietary supplementation of butyrate has potential for further development as a convenient antibiotic-alternative strategy to enhance host innate immunity and disease resistance

Structure and properties of ilmenite from first principles

Published versio

A multi-centre randomised controlled study of pre-IVF outpatient hysteroscopy in women with recurrent IVF implantation failure: Trial of Outpatient Hysteroscopy - [TROPHY] in IVF

<p>Abstract</p> <p>Background</p> <p>The success rate of IVF treatment is low. A recent systematic review and meta-analysis found that the outcome of IVF treatment could be improved in patients who have experienced recurrent implantation failure if an outpatient hysteroscopy (OH) is performed before starting the new treatment cycle. However, the trials were of variable quality, leading to a call for a large and high-quality randomised trial. This protocol describes a multi-centre randomised controlled trial to test the hypothesis that performing an OH prior to starting an IVF cycle improves the live birth rate of the subsequent IVF cycle in women who have experienced two to four failed IVF cycles.</p> <p>Methods and design</p> <p>Eligible and consenting women will be randomised to either OH or no OH using an internet based trial management programme that ensures allocation concealment and employs minimisation for important stratification variables including age, body mass index, basal follicle stimulating hormone level and number of previous failed IVF cycles. The primary outcome is live birth rate per IVF cycle started. Other outcomes include implantation, clinical pregnancy and miscarriage rates.</p> <p>The sample size for this study has been estimated as 758 participants with 379 participants in each arm. Interim analysis will be conducted by an independent Data Monitoring Committee (DMC), and final analysis will be by intention to treat. A favourable ethical opinion has been obtained (REC reference: 09/H0804/32).</p> <p>Trail Registration</p> <p>The trial has been assigned the following ISRCTN number: ISRCTN35859078</p

Novel IgG-degrading enzymes of the IgdE protease family link substrate specificity to host tropism of <i>Streptococcus</i> species

Recently we have discovered an IgG degrading enzyme of the endemic pig pathogen S. suis designated IgdE that is highly specific for porcine IgG. This protease is the founding member of a novel cysteine protease family assigned C113 in the MEROPS peptidase database. Bioinformatical analyses revealed putative members of the IgdE protease family in eight other Streptococcus species. The genes of the putative IgdE family proteases of S. agalactiae, S. porcinus, S. pseudoporcinus and S. equi subsp. zooepidemicus were cloned for production of recombinant protein into expression vectors. Recombinant proteins of all four IgdE family proteases were proteolytically active against IgG of the respective Streptococcus species hosts, but not against IgG from other tested species or other classes of immunoglobulins, thereby linking the substrate specificity to the known host tropism. The novel IgdE family proteases of S. agalactiae, S. pseudoporcinus and S. equi showed IgG subtype specificity, i.e. IgdE from S. agalactiae and S. pseudoporcinus cleaved human IgG1, while IgdE from S. equi was subtype specific for equine IgG7. Porcine IgG subtype specificities of the IgdE family proteases of S. porcinus and S. pseudoporcinus remain to be determined. Cleavage of porcine IgG by IgdE of S. pseudoporcinus is suggested to be an evolutionary remaining activity reflecting ancestry of the human pathogen to the porcine pathogen S. porcinus. The IgG subtype specificity of bacterial proteases indicates the special importance of these IgG subtypes in counteracting infection or colonization and opportunistic streptococci neutralize such antibodies through expression of IgdE family proteases as putative immune evasion factors. We suggest that IgdE family proteases might be valid vaccine targets against streptococci of both human and veterinary medical concerns and could also be of therapeutic as well as biotechnological use