Active Fault System and the Related Seismicity in Pakistan

Earthquakes in Pakistan are generated along the active fault system due to neo-tectonic process, emerged from the colliding plate boundaries of the Indian, Eurasian and Arabian plates. Based on this progression many active seismic zones in Pakistan, e.g., the Hindu Kush-Karakoram and Indus-Kohistan seismic zones emerged. Consequently, the 8th October 2005 earthquake occurred along the Indus-Kohistan active seismic zone that killed more than 80000 people. The subsequent studies revealed that he causative faults for earthquakes are mainly active thrust faults with a strike slip component and purely the strike slip faults. Based on the seismic hazard zones, prepared after 8th October 2005 earthquake, Islamabad, the capital of Pakistan has been up-graded from Zone 2 to Zone 3 having “g” factor between 0.1-0.3 with moderate to severe damage

Post Aswan High Dam flash floods in Egypt: Causes, consequences and mitigation strategies

Flash floods become one of the most recent common forms of natural disaster in recent-day Egypt. These floods are made up of sudden, unexpected and heavy rains or a strong surge of water, which usually hit the steep sloped mountainous catchments and inundate many regions, particularly along the Red Sea Coast and Sinai, Egypt. These floods often carry rocks, soil, and other debris, a matter which make them pose a significant risk to people and infrastructure, leading to death and destruction. Egypt recognized the challenges posed by disasters and strengthened and developed its national institutions and policy to meet the tasks of the Hyogo Framework for Action (HFA) on the Crisis Management and Disaster Risk Reduction (DRR). Egypt established a Crisis Management Affairs (CEMA) entity in 2000 and some good signs of progress have been made along several areas and sectors. The multi-sectoral approach is to be adopted and operationalized to ensure the full integration and harmony. Furthermore, in 2009, Egypt in collaboration with Belgium has installed the first early warning system called Flash Flood Manager (FlaFloM) in Wadi Watir, Southern Sinai

Mineralogy and geochemical properties of dust storm in Sistan region and Khuzestan Province, Iran

In recent years, dust storms coming from western neighboring countries are drastically increased dust storms and affecting western and eastern part of Iran. This phenomenon is caused a lot of environmental and socio-economic problems. Sistan is a region located in southeast Iran with extensive wind erosion. X-Ray Diffraction (XRD) analysis of airborne and soil dust samples from Sistan shows that the dust mineralogy is dominated mainly by quartz (30-40%), calcite (18-23%), muscovite (10-17%), plagioclase (9-12%), chlorite (~6%) and enstatite (~3%), with minor components of dolomite, microcline, halite and gypsum. X-Ray Fluorescence (XRF) analyses of all the samples indicate that the most important oxide compositions of the airborne and soil dust are SiO2, CaO, Al2O3, Na2O, MgO and Fe2O3, exhibiting similar percentages for both stations and soil samples. However Khuzestan Province is located in southwest Iran with sandy deserts. XRD result from Khuzestan show that mineralogical composition of these dust particles can be divided into three groups: (1) Carbonate group (calcite mineral), (2) Silicate group (quartz mineral) and (3) Clay group (Kaoline mineral). The most important minor phase is Gypsum. SEM studies indicate that these particles were found in rounded, irregular, prismatic and rhombic shapes. XRF and ICP analyses of the samples show that the most important oxide compositions of airborne dusts are SiO2, Al2O3, Fe2O3, CaO and MgO. This research can be help to find the impact of geological units on the wind erosion lands for finding dust storm sources in the states of western and eastern parts of Iran

Environmental impacts and mineralogical characteristics of dust storm in Middle-East

Middle Earth, including Iran, Iraq, China and Syria has been recognized as one of the most important primary sources of dust. Intensive investigations have been conducted to study the chemical composition, sources and deposition of Middle Earth particles. However, analysis of individual Middle Earth particles show that about one fifth of all the particles are mineral aggregates, and at least one fourth of the particles contain sulfur. X-ray diffraction (XRD) is used to quantify the phase and the clay mineral compositions of Middle Earth samples. Phases in the Middle Earth sample collected during the 20 March 2002 dust storm episode included clay minerals, noncrystalline materials, quartz, calcite, plagioclase, potassium feldspar, pyrite, hornblende, and gypsum in descending order. Clay minerals are mainly illite/smectite mixed layers (78%), followed by illite (9%), kaolinite (6%), and chlorite (7%). Particulate matter (PM) less than 10 mm are enriched with clay minerals and deficient with quartz by mass compared with the total suspended particulates collected during an Middle Earth episode. The PM less than 10 mm collected during the two severe dust storm episodes is characterized by the absence of dolomite, high quartz/clay ratio, and dominance of illite/smectite mixed layers in clay minerals

Host cell species-specific effect of cyclosporine A on simian immunodeficiency virus replication

<p>Abstract</p> <p>Background</p> <p>An understanding of host cell factors that affect viral replication contributes to elucidation of the mechanism for determination of viral tropism. Cyclophilin A (CypA), a peptidyl-prolyl <it>cis-trans </it>isomerase (PPIase), is a host factor essential for efficient replication of human immunodeficiency virus type 1 (HIV-1) in human cells. However, the role of cyclophilins in simian immunodeficiency virus (SIV) replication has not been determined. In the present study, we examined the effect of cyclosporine A (CsA), a PPIase inhibitor, on SIV replication.</p> <p>Results</p> <p>SIV replication in human CEM-SS T cells was not inhibited but rather enhanced by treatment with CsA, which inhibited HIV-1 replication. CsA treatment of target human cells enhanced an early step of SIV replication. CypA overexpression enhanced the early phase of HIV-1 but not SIV replication, while CypA knock-down resulted in suppression of HIV-1 but not SIV replication in CEM-SS cells, partially explaining different sensitivities of HIV-1 and SIV replication to CsA treatment. In contrast, CsA treatment inhibited SIV replication in macaque T cells; CsA treatment of either virus producer or target cells resulted in suppression of SIV replication. SIV infection was enhanced by CypA overexpression in macaque target cells.</p> <p>Conclusions</p> <p>CsA treatment enhanced SIV replication in human T cells but abrogated SIV replication in macaque T cells, implying a host cell species-specific effect of CsA on SIV replication. Further analyses indicated a positive effect of CypA on SIV infection into macaque but not into human T cells. These results suggest possible contribution of CypA to the determination of SIV tropism.</p

Comprehensive Genomic Profiling of Neuroendocrine Carcinomas of the Gastrointestinal System

The neuroendocrine carcinoma of the gastrointestinal system (GIS-NEC) is a rare but highly malignant neoplasm. We analyzed 115 cases using whole-genome/exome sequencing, transcriptome sequencing, DNA methylation assays, and/or ATAC-seq and found GIS-NECs to be genetically distinct from neuroendocrine tumors (GIS-NET) in the same location. Clear genomic differences were also evident between pancreatic NECs (Panc-NEC) and nonpancreatic GIS-NECs (Nonpanc-NEC). Panc-NECs could be classified into two subgroups (i.e., "ductal-type" and "acinar-type") based on genomic features. Alterations in TP53 and RB1 proved common in GIS-NECs, and most Nonpanc-NECs with intact RB1 demonstrated mutually exclusive amplification of CCNE1 or MYC. Alterations of the Notch gene family were characteristic of Nonpanc-NECs. Transcription factors for neuroendocrine differentiation, especially the SOX2 gene, appeared overexpressed in most GIS-NECs due to hypermethylation of the promoter region. This first comprehensive study of genomic alterations in GIS-NECs uncovered several key biological processes underlying genesis of this very lethal form of cancer. SIGNIFICANCE: GIS-NECs are genetically distinct from GIS-NETs. GIS-NECs arising in different organs show similar histopathologic features and share some genomic features, but considerable differences exist between Panc-NECs and Nonpanc-NECs. In addition, Panc-NECs could be classified into two subgroups (i.e., "ductal-type" and "acinar-type") based on genomic and epigenomic features. This article is highlighted in the In This Issue feature, p. 587

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Egg parasitoids of Arboridia apicalis (Nawa, 1913) (Hemiptera, Cicadellidae), a leafhopper pest of grapevines in Japan, with description of a new species of Anagrus Haliday, 1833 (Hymenoptera, Mymaridae)

Several species of egg parasitoids (Hymenoptera: Mymaridae and Trichogrammatidae) of the leafhopper pest of grapevines in Japan, Arboridia (Arboridia) apicalis (Nawa) (Hemiptera, Cicadellidae), were reared and identified for the first time. Using a combination of genetic and morphological evidence, Anagrus (Anagrus) arboridiae Triapitsyn & Adachi-Hagimori, sp. nov. (Mymaridae) is described and illustrated from Honshu Island (Shimane Prefecture) and Kyushu Island (Miyazaki Prefecture). It is shown to be different from Anagrus (Anagrus) japonicus Sahad and A. flaviapex Chiappini & Lin, to which it is most similar; the latter species was originally described from China and is newly recorded here from Okinawa Island, Japan. Mitochondrial and nuclear ribosomal DNA sequence data provide clear evidence for the separation of A. arboridiae from A. flaviapex, A. japonicus, and some other members of the Anagrus (Anagrus) atomus (L.) species group. Two other species of Anagrus Haliday, A. (Anagrus) avalae Soyka and A. atomus, are also identified in Japan from eggs of the leafhoppers Edwardsiana ishidae (Matsumura) and Eurhadina ? betularia Anufriev, respectively. An updated key to females of the Japanese species of Anagrus is given. Oligosita pallida Kryger (a new record for Japan), Oligosita sp., and an Aphelinoidea (Aphelinoidea) sp. (Trichogrammatidae) were the other, although much less abundant, apparent egg parasitoids of A. apicalis in Shimane Prefecture, mainly in non-organic vineyards