University of Jordan

About: University of Jordan is a education organization based out in Amman, Jordan. It is known for research contribution in the topics: Population & Medicine. The organization has 7796 authors who have published 13764 publications receiving 213526 citations.

Electronic properties of interfaces and defects from many-body perturbation theory: Recent developments and applications

Abstract: We review some recent developments in many-body perturbation theory (MBPT) calculations that have enabled the study of interfaces and defects. Starting from the theoretical basis of MBPT, Hedin’s equations are presented, leading to the GW and GWΓ approximations. We introduce the perturbative approach, that is the one most commonly used for obtaining quasiparticle (QP) energies. The practical strategy presented for dealing with the frequency dependence of the self-energy operator is based on either plasmon-pole models (PPM) or the contour deformation technique, with the latter being more accurate. We also discuss the extrapolar method for reducing the number of unoccupied states which need to be included explicitly in the calculations. The use of the PAW method in the framework of MBPT is also described. Finally, results which have been obtained using MBPT for band offsets at interfaces and for defects are presented, with emphasis on the main difficulties and caveats.

Influence of sediment permeability and mineral composition on organic matter degradation in three sediments from the Gulf of Aqaba, Red Sea

Abstract: In order to investigate the influence of sediment physical and chemical characteristics on the degradation of deposited organic matter, decomposition in three sediments from the Gulf of Aqaba (Red Sea) that differ in permeability and mineral composition were compared. Freeze-dried Spirulina was added to coarse carbonate and silicate sands from a shallow nearshore region and silt-clay sediment from the deeper center region of the Gulf incubated in laboratory chambers. The stirring in the chambers caused higher solute exchange in the coarse permeable sands relative to the fine less permeable silt due to the generation of advective fluid exchange between the sediment and overlying water. This enhanced exchange increased the decomposition rates of organic matter in the incubated sands. The decomposition rates of total organic carbon in the permeable carbonate (3.0 mg C m −2 d −1 ) and silicate sands (2.0 mg C m −2 d −1 ) exceeded that in the fine-grained sediment (1.4 mg C m −2 d −1 ). Oxygen consumption in the coarse sands was 3-fold higher than in the silt-clay sediment, with highest rates in the carbonate sand. In carbonate and silicate sands of the same grain size, the carbonate sediment was more permeable than the silicate, resulting in 1.4-fold higher fluid exchange rates and 1.4-fold larger sedimentary organic matter mineralization rates. An in situ experiment comparing trapping efficiencies in carbonate and silicate sands showed that the higher fluid exchange rate in the carbonate sand results in larger filtration rates and a faster accumulation of particulate organic matter from the boundary layer. These experiments demonstrate that with respect to sedimentary mineralization rates, higher transport rates in permeable coarse sediments can outweigh the effect of a higher specific surface area in fine-grained silt sediments. In permeable sands, however, the higher specific surface area and fluid exchange in biogenic carbonate sands result in higher mineralization rates than in silicate sands of the same grain size.

Diagnostic Exome Sequencing to Elucidate the Genetic Basis of Likely Recessive Disorders in Consanguineous Families

Abstract: Rare, atypical, and undiagnosed autosomal-recessive disorders frequently occur in the offspring of consanguineous couples. Current routine diagnostic genetic tests fail to establish a diagnosis in many cases. We employed exome sequencing to identify the underlying molecular defects in patients with unresolved but putatively autosomal-recessive disorders in consanguineous families and postulated that the pathogenic variants would reside within homozygous regions. Fifty consanguineous families participated in the study, with a wide spectrum of clinical phenotypes suggestive of autosomal-recessive inheritance, but with no definitive molecular diagnosis. DNA samples from the patient(s), unaffected sibling(s), and the parents were genotyped with a 720K SNP array. Exome sequencing and array CGH (comparative genomic hybridization) were then performed on one affected individual per family. High-confidence pathogenic variants were found in homozygosity in known disease-causing genes in 18 families (36%) (one by array CGH and 17 by exome sequencing), accounting for the clinical phenotype in whole or in part. In the remainder of the families, no causative variant in a known pathogenic gene was identified. Our study shows that exome sequencing, in addition to being a powerful diagnostic tool, promises to rapidly expand our knowledge of rare genetic Mendelian disorders and can be used to establish more detailed causative links between mutant genotypes and clinical phenotypes.