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Sökning: WFRF:(Shahid Naeem)

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1.
  • Abbas, Syed Adeel, et al. (författare)
  • Spinel-type Na2MoO4 and Na2WO4 as promising optoelectronic materials : First-principle DFT calculations
  • 2020
  • Ingår i: Chemical Physics. - : Elsevier. - 0301-0104 .- 1873-4421. ; 538
  • Tidskriftsartikel (refereegranskat)abstract
    • The mechanical, thermodynamic, electronic, and optical properties of Na2MoO4 (NMO) and Na2WO4 (NWO) spinels are elaborated by density functional theory (DFT) based full potential augmented plane wave method (FP-LAPW + lo). Our optimized lattice constants for the studied spinels are in good agreement with that obtained experimentally. The enthalpy of formation ensures the thermodynamic stability of NMO and NWO in the cubic phase. The Born mechanical stability criteria guarantees their mechanical stability, while Poisson ratio (ν) and Pugh's ratio (B/G) infer their brittle behavior. The Debye temperature (θD) is significant for NMO than NWO. The wide bandgap of 3.5 eV for NMO and 4.4 eV for NWO show the maximum absorption in the ultraviolet region that increases their importance for optoelectronic applications. The optical properties are explained in term of dielectric constant, refractive index, absorption of light, reflection, and optical loss factor.
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2.
  • Ahmed, Naeem, et al. (författare)
  • Germination and growth improvement of papaya utilizing oxygen (O2) plasma treatment
  • 2022
  • Ingår i: Journal of Physics D. - : Institute of Physics (IOP). - 0022-3727 .- 1361-6463. ; 55:25
  • Tidskriftsartikel (refereegranskat)abstract
    • In general, cold plasma treatment improves crop germination and growth. The purpose of this research is to examine the impact of low-pressure O2 plasma treatment on the germination and growth kinetics of papaya seeds. Seeds were treated for 40 s at a discharge power of 80 W using O2 as a monomer. Physical and chemical changes were studied to understand the mechanism of germination and growth improvement. Furthermore, changes in phytohormones and antioxidant activity that were beneficial to germination were also examined. O2 plasma treatment improved wettability, surface etching, and oxidation, and affected other molecular-level changes leading to a 16% germination improvement in papaya.
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3.
  • Anand, Srinivasan, et al. (författare)
  • InP-based photonic crystal waveguide filters
  • 2010
  • Ingår i: 2010 Asia Communications and Photonics Conference and Exhibition, ACP 2010. - 9781424471119 ; , s. 104-105
  • Konferensbidrag (refereegranskat)
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4.
  • Anand, Srinivasan, et al. (författare)
  • InP-Based Photonic Crystal Waveguide Technology for Filtering and Sensing Applications
  • 2011
  • Ingår i: 2011 13TH INTERNATIONAL CONFERENCE ON TRANSPARENT OPTICAL NETWORKS (ICTON). - NEW YORK : IEEE. - 9781457708800
  • Konferensbidrag (refereegranskat)abstract
    • Photonic crystal (PhC) components in InP-based materials are of practical importance not only for their unique properties but also for integration with conventional optoelectronic components on InP substrate. Several PhC devices in the substrate approach such as filters, lasers, and waveguides have been demonstrated [1,2] and this has been possible due to the development of deep etching of PhCs in InP [3].
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5.
  • Berg, Alexander, et al. (författare)
  • Growth and optical properties of InxGa1−xP nanowires synthesized by selective-area epitaxy
  • 2017
  • Ingår i: Nano Research. - : Springer Science and Business Media LLC. - 1998-0124 .- 1998-0000. ; 10:2, s. 672-682
  • Tidskriftsartikel (refereegranskat)abstract
    • Ternary III–V nanowires (NWs) cover a wide range of wavelengths in the solar spectrum and would greatly benefit from being synthesized as position-controlled arrays for improved vertical yield, reproducibility, and tunable optical absorption. Here, we report on successful selective-area epitaxy of metal-particle-free vertical InxGa1−xP NW arrays using metal–organic vapor phase epitaxy and detail their optical properties. A systematic growth study establishes the range of suitable growth parameters to obtain uniform NW growth over a large array. The optical properties of the NWs were characterized by room-temperature cathodoluminescence spectroscopy. Tunability of the emission wavelength from 870 nm to approximately 800 nm was achieved. Transmission electron microscopy and energy dispersive X-ray measurements performed on cross-section samples revealed a pure wurtzite crystal structure with very few stacking faults and a slight composition gradient along the NW growth axis. [Figure not available: see fulltext.]
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6.
  • Dhaka, Veer, et al. (författare)
  • Protective capping and surface passivation of III-V nanowires by atomic layer deposition
  • 2016
  • Ingår i: AIP Advances. - : American Institute of Physics (AIP). - 2158-3226. ; 6:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Low temperature (similar to 200 degrees C) grown atomic layer deposition (ALD) films of AlN, TiN, Al2O3, GaN, and TiO2 were tested for protective capping and surface passivation of bottom-up grown III-V (GaAs and InP) nanowires (NWs), and top-down fabricated InP nanopillars. For as-grown GaAs NWs, only the AlN material passivated the GaAs surface as measured by photoluminescence (PL) at low temperatures (15K), and the best passivation was achieved with a few monolayer thick (2 angstrom) film. For InP NWs, the best passivation (similar to 2x enhancement in room-temperature PL) was achieved with a capping of 2nm thick Al2O3. All other ALD capping layers resulted in a de-passivation effect and possible damage to the InP surface. Top-down fabricated InP nanopillars show similar passivation effects as InP NWs. In particular, capping with a 2 nm thick Al2O3 layer increased the carrier decay time from 251 ps (as-etched nanopillars) to about 525 ps. Tests after six months ageing reveal that the capped nanostructures retain their optical properties. Overall, capping of GaAs and InP NWs with high-k dielectrics AlN and Al2O3 provides moderate surface passivation as well as long term protection from oxidation and environmental attack.
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7.
  • Jameel, Muhammad, et al. (författare)
  • A novel AP4M1 mutation in autosomal recessive cerebral palsy syndrome and clinical expansion of AP-4 deficiency
  • 2014
  • Ingår i: BMC Medical Genetics. - : Springer Science and Business Media LLC. - 1471-2350. ; 15, s. 133-
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND:Cerebral palsy (CP) is a heterogeneous neurodevelopmental disorder associated with intellectual disability in one-third of cases. Recent findings support Mendelian inheritance in subgroups of patients with the disease. The purpose of this study was to identify a novel genetic cause of paraplegic CP with intellectual disability in a consanguineous Pakistani family.METHODS:We performed whole-exome sequencing (WES) in two brothers with CP and intellectual disability. Analysis of AP4M1 mRNA was performed using quantitative real-time PCR on total RNA from cultured fibroblasts. The brothers were investigated clinically and by MRI.RESULTS:We identified a novel homozygous AP4M1 mutation c.194_195delAT, p.Y65Ffs*50 in the affected brothers. Quantitative RT-PCR analysis showed markedly reduced AP4M1 mRNA levels suggesting partial non-sense mediated mRNA decay. Several clinical and MRI features were consistent with AP-4 complex deficiency. However, in contrast to previously reported cases with AP4M1 mutations our patients show an aggressive behavior and a relatively late onset of disease.CONCLUSION:This study shows an AP4M1 mutation associated with aggressive behavior in addition to mild dysmorphic features, intellectual disability, spastic paraparesis and reduced head circumference. Our findings expand the clinical spectrum associated with AP-4 complex deficiency and the study illustrates the importance of MRI and WES in the diagnosis of patients with CP and intellectual disability.
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8.
  • Khan, Tahir Naeem, et al. (författare)
  • Evidence for autosomal recessive inheritance in SPG3A caused by homozygosity for a novel ATL1 missense mutation
  • 2014
  • Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 22:10, s. 1180-1184
  • Tidskriftsartikel (refereegranskat)abstract
    • Hereditary spastic paraplegias (HSPs) comprise a heterogeneous group of disorders characterized by progressive spasticity and weakness of the lower limbs. Autosomal dominant and 'pure' forms of HSP account for similar to 80% of cases in Western societies of whom 10% carry atlastin-1 (ATL1) gene mutations. We report on a large consanguineous family segregating six members with early onset HSP. The pedigree was compatible with both autosomal dominant and autosomal recessive inheritance. Whole-exome sequencing and segregation analysis revealed a homozygous novel missense variant c.353G>A, p.(Arg118Gln) in ATL1 in all six affected family members. Seven heterozygous carriers, five females and two males, showed no clinical signs of HSP with the exception of sub-clinically reduced vibration sensation in one adult female. Our combined findings show that homozygosity for the ATL1 missense variant remains the only plausible cause of HSP, whereas heterozygous carriers are asymptomatic. This apparent autosomal recessive inheritance adds to the clinical complexity of spastic paraplegia 3A and calls for caution using directed genetic screening in HSP.
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9.
  • Khan, Tahir Naeem, et al. (författare)
  • Novel missense mutation in the RSPO4 gene in congenital hyponychia and evidence for a polymorphic initiation codon (p.M1l)
  • 2012
  • Ingår i: BMC Medical Genetics. - : Springer Science and Business Media LLC. - 1471-2350. ; 13, s. 120-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Anonychia/hyponychia congenita is a rare autosomal recessive developmental disorder characterized by the absence (anonychia) or hypoplasia (hyponuchia) of finger- and/or toenails frequently caused by mutations in the R-spondin 4 (RSPO4) gene. Methods: Three hypo/anonychia consanguineous Pakistani families were ascertained and genotyped using microsatellite markers spanning the RSPO4 locus on chromosome 20p13. Mutation screening of the RSPO4 gene was carried out by direct sequencing of the entire coding region and all intron-exon boundaries. Results: Mutations in the RSPO4 gene were identified in all families including a novel missense mutation c.178C>T (p.R60W) and two recurrent variants c.353G>A (p.C118Y) and c.3G>A (p.M1l). The c.3G>A variant was identified in unaffected family members and a control sample in a homozygous state. Conclusions: This study raises to 17 the number of known RSPO4 mutations and further expands the molecular repertoire causing hypo/anonychia. The c.353G>A emerges as a recurrent change with a possible founder effect in the Pakistani population. Our findings suggest that c.3G>A is not sufficient to cause the disorder and could be considered a polymorphism.
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10.
  • Klar, Joakim, et al. (författare)
  • Whole exome sequencing identifies LRP1 as a pathogenic gene in autosomal recessive keratosis pilaris atrophicans
  • 2015
  • Ingår i: Journal of Medical Genetics. - : BMJ. - 0022-2593 .- 1468-6244. ; 52:9, s. 599-606
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Keratosis pilaris atrophicans (KPA) is a group of rare genodermatoses characterised by perifollicular keratosis and inflammation that progresses to atrophy and scars of the facial skin. Keratosis pilaris of extensor areas of limbs is a common associated finding. Most cases with KPA are sporadic and no consistent inheritance pattern has been documented.Methods A large consanguineous Pakistani pedigree segregating autosomal recessive KPA of a mixed type was subject to autozygosity mapping and whole exome sequencing. Quantification of mRNA and protein levels was performed on fibroblasts from affected individuals. Cellular uptake of the low-density lipoprotein (LDL) receptor-related protein 1 (LRP1) ligand alpha 2-macroglobulin (alpha M-2) was quantified using fluorescence confocal microscopy.Results Genetic analyses identified a unique homozygous missense variant (K1245R) in the LRP1 in all affected family members. LRP1 encodes the LRP1, a multifunctional cell surface receptor with endocytic functions that belongs to the LDL receptor family. The LRP1 mRNA and LRP1 protein levels in fibroblasts of affected individuals were markedly reduced when compared with controls. Similarly, the LRP1-mediated cellular uptake of alpha M-2 was reduced in patient fibroblasts. Conclusions This is the first report on LRP1 as a pathogenic gene for autosomal recessive KPA and keratosis pilaris. The inflammatory characteristics of the KPA entity in our family suggest a link to the immune-regulatory functions of LRP1.
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11.
  • Li, Mingyu, et al. (författare)
  • Fabrication of Submicrometer InP Pillars by Colloidal Lithography and Dry Etching
  • 2010
  • Ingår i: Journal of the Electrochemical Society. - : The Electrochemical Society. - 0013-4651 .- 1945-7111. ; 157:9, s. II896-II899
  • Tidskriftsartikel (refereegranskat)abstract
    • A simple method for the fabrication of submicrometer InP pillars with large surface area coverage has been developed based on a combination of colloidal lithography and inductively coupled plasma (ICP) etching technique using Cl-2/H-2/CH4/Ar chemistry. Pillars with different sizes could be fabricated by using colloidal SiO2 particles with different sizes dispersed on the sample serving as masks. Pillars with lateral diameters as small as 60 nm and aspect ratios as high as 10: 1 have been obtained. The effects of etch parameters such as radio-frequency power, ICP power, and etching time on pillar fabrication are investigated. By a suitable choice of etch parameters and utilizing erosion of colloidal (mask) SiO2 particle during etching, the height of the pillars as well as their shape can be modified from nearly cylindrical to conical shapes. Such a control on the shape of the structures in addition to the large surface coverage could be useful for applications in photovoltaics and for the fabrication of photonic crystals. For instance, continuous grading of the refractive index can be obtained for surfaces covered with conical pillars, which can be used as antireflecting surfaces in solar cells or for light extraction in light emitting diodes.
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12.
  • Masood, Asad, et al. (författare)
  • Atmospheric Pressure Plasma Polymerization of Carvone: A Promising Approach for Antimicrobial Coatings
  • 2023
  • Ingår i: Coatings. - : Mdpi. - 2079-6412. ; 13:6
  • Tidskriftsartikel (refereegranskat)abstract
    • Medical devices are often vulnerable to colonization by nosocomial pathogens (bacteria), leading to infections. Traditional sterilization methods may not always be effective, and as a result, alternative options are being explored to prevent microbial contamination. Recently, scientists are emphasizing using plant-derived essential oils that possess inherent antibacterial properties to produce antimicrobial coatings using plasma polymerization technology carried out at atmospheric pressure (AP). This approach shows promise compared to other coating strategies that need several processing steps, including a high-vacuum system, and are laborious, such as the immobilization of antimicrobial materials on precoated layers in the low-pressure plasma polymerization approach. The present study demonstrates the potential of AP plasma polymerization for producing thin films with excellent antibacterial properties and surface characteristics. The resulting coatings are stable, smooth, and have high wettability, making them ideal for repelling bacteria. The calculated zeta potential and deposition rate for the films are also favorable. These AP plasma-polymerized thin films created from carvone show a reduction rate of more than 90% for Escherichia coli and Staphylococcus aureus bacteria. Our computational docking studies also reveal strong binding interactions between the original carvone monomer and both bacteria. The study suggests that these AP plasma-produced coatings have great potential as antibacterial coatings for biomedical devices.
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13.
  • Naureen, Shagufta, et al. (författare)
  • Carrier dynamics in InP nanopillar arrays fabricated by low-damage etching
  • 2013
  • Ingår i: Applied Physics Letters. - : American Institute of Physics (AIP). - 0003-6951 .- 1077-3118. ; 102:21, s. 212106-
  • Tidskriftsartikel (refereegranskat)abstract
    • We present a comprehensive characterization of the optical quality of InP nanopillars (NPs) fabricated by a top down approach using micro-photoluminescence (mu-PL), time-resolved PL, and cathodoluminescence (CL). A lattice matched InGaAs layer provided beneath the 1 mu m tall NPs functions as a "detector" in CL for monitoring carrier diffusion in InP NP. Carrier feeding to the InGaAs layer indicated by a double exponential PL decay is confirmed through CL mapping. Carrier lifetimes of over 1 ns and the appreciably long diffusion lengths (400-700 nm) in the InP NPs indicate very low surface damage making them attractive for optoelectronic applications.
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14.
  • Naureen, Shagufta, et al. (författare)
  • Generation of substrate-free III-V nanodisks from user-defined multilayer nanopillar arrays for integration on Si
  • 2013
  • Ingår i: Nanotechnology. - : IOP Publishing. - 0957-4484 .- 1361-6528. ; 24:22, s. 225301-
  • Tidskriftsartikel (refereegranskat)abstract
    • High material quality InP-based multilayer nanopillar (NP) arrays are fabricated using a combination of self-assembly of silica particles for mask generation and dry etching. In particular, the NP arrays are made from user-defined epitaxial multilayer stacks with specific materials and layer thicknesses. An additional degree of flexibility in the structures is obtained by changing the lateral diameters of the NP multilayer stacks. Pre-defined NP arrays made from InGaAsP/InP and InGaAs/InP NPs are then used to generate substrate-free nanodisks of a chosen material from the stack by selective etching. A soft-stamping method is demonstrated to transfer the generated nanodisks with arbitrary densities onto Si. The transferred nanodisks retain their smooth surface morphologies and their designed geometrical dimensions. Both InP and InGaAsP nanodisks display excellent photoluminescence properties, with line-widths comparable to unprocessed reference epitaxial layers of similar composition. The multilayer NP arrays are potentially attractive for broad-band absorption in third-generation solar cells. The high optical quality, substrate-free InP and InGaAsP nanodisks on Si offer a new path to explore alternative ways to integrate III-V on Si by bonding nanodisks to Si. The method also has the advantage of re-usable III-V substrates for subsequent layer growth.
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15.
  • Naureen, Shagufta, et al. (författare)
  • Generation of substrate free III-V nanodisksfrom user-defined multilayer nanopillar arrays
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • High material quality InP-based multilayer nanopillar (NP) arrays are fabricated using a combination of self-assembly of silica particles for mask generation and dry etching. In particular, the NP arrays are made from user-defined epitaxial multi-layer stacks with specific materials and layer thickness. Additional degree of flexibility in the structures is obtained by changing the lateral diameters of the NP multi-layer stacks. Pre-defined NP arrays made in InGaAsP/InP and InGaAs/InP NPs are then used to generate substrate-free nanodisks of a chosen material from the stack by selective etching. A soft-stamping method is demonstrated to transfer the generated nanodisks with arbitrary densities onto Si. It is shown that the transferred nanodisks retain their smooth surface morphologies and their designed geometrical dimensions. Both InP and InGaAsP nanodisks display excellent photo-luminescence properties, with line-widths comparable to unprocessed reference epitaxial layers of similar composition. The multilayer NP arrays are potentially attractive for broad-band absorption in third-generation solar-cells. The high optical quality, substrate-free InP and InGaAsP nanodisks on Si offer a new path to explore alternative ways to integrate III-V on Si by bonding nanodisks to Si. The method also has the advantage of re-usable III-V substrates for subsequent layer growth.
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16.
  • Naureen, Shagufta, et al. (författare)
  • High Optical Quality InP-Based Nanopillars Fabricated by a Top-Down Approach
  • 2011
  • Ingår i: Nano letters (Print). - : American Chemical Society (ACS). - 1530-6984 .- 1530-6992. ; 11:11, s. 4805-4811
  • Tidskriftsartikel (refereegranskat)abstract
    • Dense and uniform arrays of Top-based nanopillars were fabricated by dry etching using self-assembly of colloidal silica particles for masking. The pillars, both single and arrays, fabricated from epitaxially grown InP and InP/GaInAsP/InP quantum well structures :how excellent photoluminescence (PL) even at room temperature. The measured PL line widths are comparable to the as-grown wafer indicating high quality fabricated pillars. A stamping technique enables transfer with arbitrary densities of the nanopillars freed from the substrate by selectively etching a sacrificial InGaAs layer.
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17.
  • Naureen, Shagufta, et al. (författare)
  • Nanostructuring of InP by colloidal lithography and ICP etching for photovoltaic applications
  • 2011
  • Ingår i: Conference Proceedings - International Conference on Indium Phosphide and Related Materials. - 9783800733569
  • Konferensbidrag (refereegranskat)abstract
    • We demonstrate a simple and cost effective method to fabricate InP nanopillars using silica particles as masks for etching InP. Oxygen plasma treatment of InP surfaces before dispersion of colloidal mask particles improved surface wettability significantly and helped in uniform coverage of the particles over large areas. Pillars with varied sizes were fabricated by dispersing colloidal SiO2 with different sizes on the sample and/or by reducing size of particles after dispersion. Nanopillars with different heights and shapes from near cylindrical to conical were obtained by varying etch process parameters and by progressive erosion of colloidal SiO 2 particle (mask). Pillars with aspect ratios in excess of 15:1 have been obtained. Investigations are also made on regular close packed hexagonal structures with wide area coverage. Size reduction of colloidal particles after dispersion is used to overcome the lag effect observed in the etching of close packed structures. The demonstrated nanostructuring method is attractive for producing photonic crystals and antireflecting surfaces in solar cells.
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18.
  • Naureen, Shagufta, et al. (författare)
  • Top-Down Fabrication of High Quality III–V Nanostructures by Monolayer Controlled Sculpting and Simultaneous Passivation
  • 2013
  • Ingår i: Advanced Functional Materials. - : Wiley. - 1616-301X .- 1616-3028. ; 23:13, s. 1620-1627
  • Tidskriftsartikel (refereegranskat)abstract
    • In the fabrication of IIIV semiconductor nanostructures for electronic and optoelectronic devices, techniques that are capable of removing material with monolayer precision are as important as material growth to achieve best device performances. A robust chemical treatment is demonstrated using sulfur (S)-oleylamine (OA) solution, which etches layer by layer in an inverse epitaxial fashion and simultaneously passivates the surface. The application of this process to push the limits of top-down nanofabrication is demonstrated by the realization of InP-based high optical quality nanowire arrays, with aspect ratios more than 50, and nanostructures with new topologies. The findings are relevant for other IIIV semiconductors and have potential applications in IIIV device technologies.
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19.
  • Nawaz, Sadia, et al. (författare)
  • Report of a recurrent mutation in ARS (component B) gene with severe Mal de Meleda in a large consanguineous Pakistani family
  • 2011
  • Ingår i: Pakistan journal of medical sciences print. - 1682-024X .- 1681-715X. ; 27:3, s. 686-689
  • Tidskriftsartikel (refereegranskat)abstract
    • Objective: To characterize the disease causing mutation in a large consanguineous Pakistani family with severe Mat de Meleda (MDM) or keratosis palmoplantaris transgrediens, a rare autosomal recessive skin disorder. Methodology: Single nucleotide polymorphism (SNPs) genotyping was performed using the Gene Chip Mapping 250K array (Affymetrix). Homozygosity mapping and sorting of genomic regions were performed with dedicated software called AutoSNPa. Selected regions were further investigated by genotyping with microsatellite markers derived from known and novel pOlymorphic repeats. Two-point LOD score calculation was performed by using the MLINK of Fast link computer package. All three coding exons of ARS (component B) gene were amplified by PCR and sequenced. Conclusion: Sequencing of all the coding exons of ARS (component B) gene in the affected individuals revealed a recurrent missense mutation in exon 3 at base pair 256 from Guanine to Alanine (256G>A) and as a result the amino acid Glycine is replaced by Arginine at position 86 (G86R). This finding will facilitate control of affected MDM births in the Pakistani families.
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20.
  • Perrings, Charles, et al. (författare)
  • Ecosystem services, targets, and indicators for the conservation and sustainable use of biodiversity
  • 2011
  • Ingår i: Frontiers in Ecology and the Environment. - : Wiley. - 1540-9295 .- 1540-9309. ; 9:9, s. 512-520
  • Tidskriftsartikel (refereegranskat)abstract
    • After the collective failure to achieve the Convention on Biological Diversity's (CBD's) 2010 target to substantially reduce biodiversity losses, the CBD adopted a plan composed of five strategic goals and 20 “SMART” (Specific, Measurable, Ambitious, Realistic, and Time-bound) targets, to be achieved by 2020. Here, an interdisciplinary group of scientists from DIVERSITAS – an international program that focuses on biodiversity science – evaluates these targets and considers the implications of an ecosystem-services-based approach for their implementation. We describe the functional differences between the targets corresponding to distinct strategic goals and identify the interdependency between targets. We then discuss the implications for supporting research and target indicators, and make several specific suggestions for target implementation.
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21.
  • Raykova, Doroteya, et al. (författare)
  • Autosomal Recessive Transmission of a Rare KRT74 Variant Causes Hair and Nail Ectodermal Dysplasia : Allelism with Dominant Woolly Hair/Hypotrichosis
  • 2014
  • Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:4, s. e93607-
  • Tidskriftsartikel (refereegranskat)abstract
    • Pure hair and nail ectodermal dysplasia (PHNED) comprises a heterogeneous group of rare heritable disorders characterized by brittle hair, hypotrichosis, onychodystrophy and micronychia. Autosomal recessive (AR) PHNED has previously been associated with mutations in either KRT85 or HOXC13 on chromosome 12p11.1-q14.3. We investigated a consanguineous Pakistani family with AR PHNED linked to the keratin gene cluster on 12p11.1 but without detectable mutations in KRT85 and HOXC13. Whole exome sequencing of affected individuals revealed homozygosity for a rare c.821T> C variant (p.Phe274Ser) in the KRT74 gene that segregates AR PHNED in the family. The transition alters the highly conserved Phe274 residue in the coil 1B domain required for long-range dimerization of keratins, suggesting that the mutation compromises the stability of intermediate filaments. Immunohistochemical (IHC) analyses confirmed a strong keratin-74 expression in the nail matrix, the nail bed and the hyponychium of mouse distal digits, as well as in normal human hair follicles. Furthermore, hair follicles and epidermis of an affected family member stained negative for Keratin-74 suggesting a loss of function mechanism mediated by the Phe274Ser substitution. Our observations show for the first time that homozygosity for a KRT74 missense variant may be associated with AR PHNED. Heterozygous KRT74 mutations have previously been associated with autosomal dominant woolly hair/ hypotrichosis simplex (ADWH). Thus, our findings expand the phenotypic spectrum associated with KRT74 mutations and imply that a subtype of AR PHNED is allelic with ADWH.
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22.
  • Schuster, Jens, et al. (författare)
  • Exome sequencing circumvents missing clinical data and identifies a BSCL2 mutation in congenital lipodystrophy
  • 2014
  • Ingår i: BMC Medical Genetics. - Uppsala : Springer Science and Business Media LLC. - 1471-2350. ; 15
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Exome sequencing has become more and more affordable and the technique has emerged as an important diagnostic tool for monogenic disorders at early stages of investigations, in particular when clinical information is limited or unspecific as well as in cases of genetic heterogeneity.METHODS: We identified a consanguineous Pakistani family segregating an autosomal recessive phenotype characterized by muscular hypertrophy, mild mental retardation and skeletal abnormalities. The available clinical information was incomplete and we applied whole exome sequencing in an affected family member for the identification of candidate gene variants.RESULTS: Exome sequencing identified a previously unreported homozygous mutation in the acceptor splice site of intron 5 in the BSCL2 gene (c.574-2A > G). Expression analysis revealed that the mutation was associated with skipping of exon 6. BSCL2 mutations are associated with Berardinelli-Seip congenital lipodystrophy and a clinical re-evaluation of affected individuals confirmed the diagnosis.CONCLUSIONS: Exome sequencing is a powerful technique for the identification of candidate gene variants in Mendelian traits. We applied this technique on a single individual affected by a likely autosomal recessive disorder without access to complete clinical details. A homozygous and truncating mutation was identified in the BSCL2 gene suggesting congenital generalized lipodystrophy. Incomplete phenotypic delineations are frequent limiting factors in search for a diagnosis and may lead to inappropriate care and follow-up. Our study exemplifies exome sequencing as a powerful diagnostic tool in Mendelian disorders that may complement missing clinical information and accelerate clinical diagnosis.
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23.
  • Shahid, Naeem, et al. (författare)
  • Effect of hole shapes on the reliability of deeply-etched InP-based photonic crystal devices
  • 2012
  • Ingår i: Physica Status Solidi. C, Current topics in solid state physics. - : Wiley. - 1610-1634 .- 1610-1642. ; 9:7, s. 1670-1673
  • Tidskriftsartikel (refereegranskat)abstract
    • We present systematic evaluation of the optical transmission characteristics of a set of photonic crystal waveguides (PhCWs) fabricated by two schemes. An optimized hole-reshaping process to obtain cylindrical holes was applied in one scheme and a comparison is made with as-etched PhCWs. The spectral characteristics of the transmission mini- stopband (MSB) in identical waveguides show that the reliability, in terms of spectral position and shape, of fabricated PhCWs using the hole reshaping process is significantly improved in comparison to the as-etched waveguides. The obtained MSB characteristics are attractive for coarse WDM filtering and wavelength selective mirrors.
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24.
  • Shahid, Naeem, et al. (författare)
  • Engineering mode-gaps in photonic crystal waveguides for filtering applications
  • 2011
  • Ingår i: Conf. Lasers Electro-Opt. Europe Eur. Quantum Electron. Conf., CLEO EUROPE/EQEC. - 9781457705335
  • Konferensbidrag (refereegranskat)abstract
    • Photonic crystal (PhC) components in InP-based materials are of practical importance not only for their unique properties but also for integration with conventional optoelectronic components on InP substrate. PhC waveguides have been investigated extensively for their unique waveguiding and dispersive properties. One such interesting property is the mode-gap which results in a transmission mini-stop band (MSB) [1] and has been investigated for applications such as coarse wavelength selection [2]. However, the optical characteristics of the MSB have to be improved significantly. Single heterojunction PhC waveguides have received much less attention [3] and in particular the internal MSB effect due to mode-coupling could bring new functions in such waveguides.
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25.
  • Shahid, Naeem, et al. (författare)
  • High quality photonic crystal waveguide filters based on mode-gap effect
  • 2011
  • Ingår i: Conference Proceedings. - 9783800733569
  • Konferensbidrag (refereegranskat)abstract
    • We demonstrate that the side-wall profiles of high-aspect-ratio two-dimensional (2D) photonic crystals (PhCs) in InP-based materials can be made vertical by reshaping through annealing. The annealing reduces depth and shape irregularities which are inherent to the etch-process. The efficacy of the reshaping is demonstrated by comparing the optical properties of PhC waveguides having as-etched and reshaped PhC-hole geometries. Spectral characteristics of ministop-bands (MSBs), due to coupling of third and fifth order modes with the fundamental mode, are used to qualify PhC fabrication. We demonstrate high optical quality filters based on the MSB effect (first and fifth order modes) and also use the spectral characteristics as a quality indicator of PhC fabrication. The MSBs transmission spectrum shows very sharp cut-offs for reshaped PhC waveguides. It is proposed that the reshaping process using annealing may also be beneficial for other PhC devices, nanostructure geometries and materials.
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26.
  • Shahid, Naeem, et al. (författare)
  • Junction-type photonic crystal waveguides for notch- and pass-band filtering
  • 2011
  • Ingår i: Optics Express. - 1094-4087. ; 19:21, s. 21074-21080
  • Tidskriftsartikel (refereegranskat)abstract
    • Evolution of the mode gap and the associated transmission mini stop-band (MSB) as a function of photonic crystal (PhC) waveguide width is theoretically and experimentally investigated. The change of line-defect width is identified to be the most appropriate way since it offers a wide MSB wavelength tuning range. A high transmission narrow-band filter is experimentally demonstrated in a junction-type waveguide composed of two PhC waveguides with slightly different widths. The full width at half maximum is 5.6 nm; the peak transmission is attenuated by only 5 dB and is 20 dB above the MSBs. Additionally, temperature tuning of the filter were also performed. The results show red-shift of the transmission peak and the MSB edges with a gradient of dλ/dT $=$ 0.1 nm/°C. It is proposed that the transmission MSBs in such junction-type cascaded PhC waveguides can be used to obtain different types of filters.
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27.
  • Shahid, Naeem, et al. (författare)
  • Mini-stop bands in single heterojunction photonic crystal waveguides
  • 2013
  • Ingår i: AIP Advances. - : AIP Publishing. - 2158-3226. ; 3:3, s. 032136-
  • Tidskriftsartikel (refereegranskat)abstract
    • Spectral characteristics of mini-stop bands (MSB) in line-defect photonic crystal (PhC) waveguides and in heterostructure PhC waveguides having one abrupt interface are investigated. Tunability of the MSB position by air-fill factor heterostructure PhC waveguides is utilized to demonstrate different filter functions, at optical communication wavelengths, ranging from resonance-like to wide band pass filters with high transmission. The narrowest filter realized has a resonance-like transmission peak with a full width at half maximum of 3.4 nm. These devices could be attractive for coarse wavelength selection (pass and drop) and for sensing applications.
  •  
28.
  • Shahid, Naeem, et al. (författare)
  • Novel postetch process to realize high quality photonic crystals in InP
  • 2011
  • Ingår i: Journal of Vacuum Science & Technology B. - : American Vacuum Society. - 1071-1023 .- 1520-8567. ; 29:3, s. 031202-
  • Tidskriftsartikel (refereegranskat)abstract
    • Thermally driven reflow of material during annealing was positively used to obtain near-vertical sidewall profiles for high-aspect-ratio nanostructures in InP fabricated by dry etching. This is very promising for achieving high optical quality in photonic crystal (PhC) components. Nearly cylindrical profiles were obtained for high-aspect-ratio PhC holes with diameters as small as 200350 nm. Mini stop bands (MSBs) in line-defect PhC waveguides were experimentally investigated for both as-etched and reshaped hole geometries, and their spectral characteristics were used to assess the quality of PhC fabrication. The spectral characteristics of the MSB in PhC waveguides with reshaped holes showed significant improvement in performance with a transmission dip as deep as 35 dB with sharp edges dropping in intensity more than 30 dB for similar to 4 nm of wavelength change. These results show potential for using high extinction drop-filters in InP-based monolithic photonic integrated circuit applications. Finally, it is proposed that other nanostructure geometries may also benefit from this reshaping process.
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29.
  • Shahid, Naeem, 1978- (författare)
  • Technology and properties of InP-based photonic crystal structures and devices
  • 2012
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Photonic crystals (PhCs) are periodic dielectric structures that exhibit a photonic band gap; a range of wavelengths for which light propagation is forbidden. 2D PhCs exhibit most of the properties as their three dimension counterparts with a compatibility with standard semiconductor processing techniques such as epitaxial growth, electron beam lithography, Plasma deposition/etching and electromechanical lapping/polishing. Indium Phosphide (InP) is the material of choice for photonic devices especially when it comes to realization of coherent light source at 1.55 μm wavelength. Precise engineering of the nanostructures in the PhC lattice offers novel ways to confine, guide and control light in phonic integrated circuits (PICs). Strong confinement of light in PhCs offer novel opportunities in many areas of physics and engineering.Dry etching, a necessary process step in PhC device manufacturing, is known to introduce damage in the etched material. Process induced damage and its impact on the electrical and optical properties of PhCs depends on the etched material, the etching technique and process parameters. We have demonstrated a novel post-etch process based on so-called mass-transport (MT) technology for the first time on InP-based PhCs that has significantly improved side-wall verticality of etched PhC holes. A statistical analysis performed on several devices fabricated by MT process technology shows a great deal of improvement in the reliability of optical transmission characteristics which is very promising for achieving high optical quality in PhC components. Several PhC devices were manufactured using MT technology.Broad enough PhC waveguides that operate in the mono/multi-mode regime are interesting for coarse wavelength de-multiplexing. The fundamental mode and higher order mode interaction creates mini-stop band (MSB) in the dispersion diagram where the higher order mode has a lower group velocity which can be considered as slow light regime. In this thesis work, the phenomena of MSBs and its impact on transmission properties have been evaluated. We have proposed and demonstrated a method that enables spectral tuning with sub-nanometer accuracy which is based on the transmission MSB. Along the same lines most of the thesis work relates to broad enough PhC guides that operated in the multimode regime. Temperature tuning experiments on these waveguides reveals a clear red-shift with a gradient of dλ/dT=0.1 nm/˚C. MSBs in these waveguides have been studied by varying the width in incremental amounts.Analogous to semiconductors heterostructures, photonic heterostructures are composed of two photonic crystals with different band-gaps obtained either by changing the air-fill factor or by the lattice constant. Juxtaposing two PhC and the use of heterostructures in waveguide geometry has been experimentally investigated in this thesis work. In particular, in multimode line defect waveguides the “internal” MSB effect brings a new dimension in single junction-type photonic crystal waveguide (JPCW) and heterostructure W3 (HW3) for fundamental physics and applications. We have also fabricated an ultra-compact polarization beam splitter (PBS) realized by combining a multimode waveguide with internal PhC. MSBs in heterostructure waveguides have shown interesting applications such as designable band-pass flat-top filters, and resonance-like filters with high transmission.In the course of this work, InGaAsP suspended membrane technology was developed. An H2 cavity with a linewidth of ~0.4 nm, corresponding to a Q value of ~3675 has been shown. InGaAsP PhC membrane is an ideal platform to study coupled quantum well/dot-nanocavity system.
  •  
30.
  • Shahid, Naeem, et al. (författare)
  • Ultrasharp ministop-band edge for subnanometer tuning resolution
  • 2011
  • Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 98:8, s. 081112-
  • Tidskriftsartikel (refereegranskat)abstract
    • We propose and demonstrate a method that enables spectral tuning with subnanometer accuracy, and is based on the transmission ministop-band (MSB) in line-defect multimode photonic crystal (PhC) waveguides. The fabricated MSB filter has ultrasharp edges which show a 30 dB drop in transmission in a 4 nm wavelength span. The use of the ultrasharp MSB edge to (optically) determine PhC fabrication accuracy is demonstrated. The wavelength position of the MSB could be tuned by temperature, with a coefficient of 0.1 nm/degrees C. The spectral characteristics of the MSB realized in this work are promising for sensing, tuning, and modulation applications.
  •  
31.
  • Shi, Yaocheng, et al. (författare)
  • Experimental demonstration of an ultracompact polarization beamsplitter based on a multimode interference coupler with internal photonic crystals
  • 2010
  • Ingår i: Optical Engineering. - : SPIE-Intl Soc Optical Eng. - 0091-3286 .- 1560-2303. ; 49:6, s. 060503-
  • Tidskriftsartikel (refereegranskat)abstract
    • The fabrication and characterization of a compact InP-based polarization beamsplitter (PBS) is presented. A multimode interference (MMI) coupler with an internal air hole photonic crystal (PhC) section is utilized to separate the two polarizations. The PhC structure in the middle of the MMI is polarization dependent, so that one polarization is reflected and the other one is transmitted; both are collected by the respective output ports of the MMI coupler. The obtained experimental results show that the PBS as short as similar to 400 mu m has an extinction ratio as large as 15 dB.
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32.
  • 2021
  • swepub:Mat__t
  •  
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