Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

หนงสอเรอง การออกแบบการวจย: วธการวจยเชงคณภาพ วธการวจยเชงปรมาณ และวธการวจยแบบผสม (Research Design: Qualitative, Quantitative, and Mixed Method Approaches) เปนหนงสอทเรยบเรยงเพออธบายเกยวกบความแตกตางของกระบวนทศนการวจยทง 2 แบบ ไดแก การวจย เชงปรมาณ และการวจยเชงคณภาพ และความจำเปนของประเดนปญหาการวจยทตองนำกระบวนทศนทง 2 มารวมกนหาขอคนพบเพอนำไปสผลการวจยทสามารถนำผลการวจยไปใชประโยชนไดอยางจรงมากยงขน เรยกวา “การวจยแบบผสมผสาน” ซงเปนหนงสอทอธบายวธการวจยทง 2 ประเภทไดอยางชดเจน และการรวมกนของกระบวนทศนการวจยทง 2 แบบอยางลงตว

Research Design: Qualitative, Quantitative, and Mixed Method Approaches

The four Visegrad states — Poland, the Czech Republic, Slovakia (until 1993 Czechoslovakia) and Hungary — form a compact area between Germany and Austria in the west and the states of the former USSR in the east. They are bounded by the Baltic in the north and the Danube river in the south. They are cut by the Sudeten and Carpathian mountain ranges, which divide Poland off from the other states. Poland is an extension of the North European plain and like the latter is drained by rivers that flow from south to north west — the Oder, the Vlatava and the Elbe, the Vistula and the Bug. The Danube is the great exception, flowing from its source eastward, turning through two 90-degree turns to end up in the Black Sea, forming the barrier and often the political frontier between central Europe and the Balkans. Hungary to the east of the Danube is also an open plain. The region is historically and culturally part of western Europe, but its eastern Marches now represents a vital strategic zone between Germany and the core of the European Union to the west and the Russian zone to the east.

Economy and Society

With the continued interest in the role of the gut microbiota in health, attention has now turned to how to harness the microbiota for the benefit of the host. This Consensus Statement outlines the definition and scope of the term 'prebiotic' as determined by an expert panel convened by the International Scientific Association for Probiotics and Prebiotics in December 2016. In December 2016, a panel of experts in microbiology, nutrition and clinical research was convened by the International Scientific Association for Probiotics and Prebiotics to review the definition and scope of prebiotics. Consistent with the original embodiment of prebiotics, but aware of the latest scientific and clinical developments, the panel updated the definition of a prebiotic: a substrate that is selectively utilized by host microorganisms conferring a health benefit. This definition expands the concept of prebiotics to possibly include non-carbohydrate substances, applications to body sites other than the gastrointestinal tract, and diverse categories other than food. The requirement for selective microbiota-mediated mechanisms was retained. Beneficial health effects must be documented for a substance to be considered a prebiotic. The consensus definition applies also to prebiotics for use by animals, in which microbiota-focused strategies to maintain health and prevent disease is as relevant as for humans. Ultimately, the goal of this Consensus Statement is to engender appropriate use of the term 'prebiotic' by relevant stakeholders so that consistency and clarity can be achieved in research reports, product marketing and regulatory oversight of the category. To this end, we have reviewed several aspects of prebiotic science including its development, health benefits and legislation.

/pdf/expert-consensus-document-the-international-scientific-304wp8k7i9.pdf

Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics

Detection of selected arboviral infections in patients with history of persistent fever in Pakistan.

Several outbreaks of avian influenza (AI) caused by H9N2 subtype, have been reported in the poultry industry during 1990 around the globe. Currently, H9N2 are endemic in the large area of Middle and Far East, including Pakistan. Since H9N2 AI viruses are sporadically reported from humans, extensive incidence of H9N2 in poultry imposes a great risk for human health. In this context, continuous monitoring of the poultry and determining the genetic nature of these viruses are fundamental to predict any future threat. Thus gene sequences of one isolate of H9N2, isolated from commercial poultry flocks, were analyzed. The results of this investigation, based on hemagglutinin (HA), neuraminidase (NA) and non-structural genes, showed that Pakistani H9N2 isolates are closely related to each other and to other H9N2 isolates from the Middle East. However, several unusual substitutions with unknown functional consequences were observed in HA and NA proteins and thus warrant further investigations for their possible role in viral biology. In conclusion, these findings provide information regarding the genetic nature of H9N2 avian influenza viruses in Pakistani poultry and necessitate the sequencing of more H9N2 viruses from both naturally infected and vaccinated flocks.

/pdf/isolation-and-characterization-of-low-pathogenic-h9n2-avian-1mxh8g8gco.pdf

Isolation and characterization of low pathogenic H9N2 avian influenza A viruses from a healthy flock and its comparison to other H9N2 isolates.

To evaluate the results of augmentative plate fixation for femoral non union after intramedullary nailing. This study was conducted in the department of orthopaedic and Trauma KTH, Peshawar from December 1995 to December 2003. We have found this method a useful treatment for the non unio of femoral shaft fracture after intra medullary nailijng. Teh technique is simple and does not require any special instrument. it facilitates an early weight bearing and gives a quick recovery from non union.

/pdf/augmentative-plate-fixation-for-the-management-of-femoral-237orcc5b9.pdf

Augmentative Plate Fixation for the management of Femoral Non-union After intramedullary Nailing

Newcastle disease, caused by Avian avulavirus 1 (AAvV 1), is endemic to many developing countries around the globe including Pakistan. Frequent epidemics are not uncommon even in vaccinated populations and are largely attributed to the genetic divergence of prevailing isolates and their transmission in the environment. With the strengthening of laboratory capabilities in Pakistan, a number of genetically diverse AAvV 1 strains have recently been isolated and individually characterized in comparison with isolates reported elsewhere in the world. However, there lacks sufficient comparative genomic and phylogenomic analyses of field circulating strains that can elucidate the evolutionary dynamics over a period of time. Herein, we enriched the whole genome sequences of AAvV reported so far (n = 35) from Pakistan and performed comparative genomic, phylogenetic and evolutionary analyses. Based on these analyses, we found only isolates belonging to genotypes VI, VII and XIII of AAvV 1 in a wide range of avian and human hosts. Comparative phylogeny revealed the concurrent circulation of avulaviruses representing different sub-genotypes such as VIg, VIm, VIIa, VIIb, VIIe, VIIf, VIIi, XIIIb and XIIId. We found that the isolates of genotype VII were more closely associated with viruses of genotype XIII than genotype VI. An inter-genotype comparative residue analysis revealed a few substitutions in structurally and functionally important motifs. Putative recombination events were reported for only one of the captive-wild bird (pheasant)-origin isolates. The viruses of genotype VII had a high genetic diversity as compared to isolates from genotypes VI and XIII and, therefore, have more potential to evolve over a period of time. Taken together, the current study provides an insight into the genetic diversity and evolutionary dynamics of AAvV 1 strains circulating in Pakistan. Such findings are expected to facilitate better intervention strategies for the prevention and control of ND in disease-endemic countries across the globe particularly Pakistan.

/pdf/a-comparative-genomic-and-evolutionary-analysis-of-1riwjlnmya.pdf

A comparative genomic and evolutionary analysis of circulating strains of Avian avulavirus 1 in Pakistan

Using data for SAARC region, we found real GDP per capita is nonlinear stationary implying that shocks to economy by economic policies (external or internal) have permanent effects on real per capita GDP of SAARC countries. This finding reveals that classical growth model works better to boost economic growth in long run.

https://mpra.ub.uni-muenchen.de/29109/1/MPRA_paper_29109.pdf

Muhammad Zubair Shabbir

Papers

Detection of selected arboviral infections in patients with history of persistent fever in Pakistan.

Isolation and characterization of low pathogenic H9N2 avian influenza A viruses from a healthy flock and its comparison to other H9N2 isolates.

Augmentative Plate Fixation for the management of Femoral Non-union After intramedullary Nailing

A comparative genomic and evolutionary analysis of circulating strains of Avian avulavirus 1 in Pakistan

Is per capita GDP non-linear stationary in SAARC countries?