E. coli and colon cancer : Is mutY a culprit?

Peer reviewedPreprin

Unraveling the chloroplast genomes of two Prosopis species to identify its genomic information, comparative analyses and phylogenetic relationship

Genus Prosopis (family Fabaceae) are shrubby trees, native to arid and semi-arid regions of Asia, Africa, and America and known for nitrogen fixation. Here, we have sequenced the complete chloroplast (cp) genomes of two Prosopis species (P. juliflora and P. cineraria) and compared them with previously sequenced P. glandulosa, Adenanthera microsperma, and Parkia javanica belonging to the same family. The complete genome sequences of Prosopis species and related species ranged from 159,389 bp (A. microsperma) to 163,677 bp (P. cineraria). The overall GC contents of the genomes were almost the similar (35.9–36.6%). The P. juliflora and P. cineraria genomes encoded 132 and 131 genes, respectively, whereas both the species comprised of 85 protein-coding genes higher than other compared species. About 140, 134, and 129 repeats were identified in P. juliflora, P. cineraria and P. glandulosa cp genomes, respectively. Similarly, the maximum number of simple sequence repeats were determined in P. juliflora (88), P. cineraria (84), and P. glandulosa (78). Moreover, complete cp genome comparison determined a high degree of sequence similarity among P. juliflora, P. cineraria, and P. glandulosa, however some divergence in the intergenic spacers of A. microsperma and Parkia javanica were observed. The phylogenetic analysis showed that P. juliflora is closer to P. cineraria than P. glandulosa.publishedVersio

Factors affecting functional outcome after decompressive craniectomy performed for traumatic brain injury: A retrospective, cross-sectional study

Background: Factors affecting functional outcome after decompressive craniectomy (DC) performed for traumatic brain injury (TBI) remain poorly understood.Methods: We conducted a retrospective study of all patients who underwent primary DC for TBI at our hospital between 2010 and 2014. Multivariate regression analyses were used to determine the predictors of functional outcome and overall survival.Results: A total of 98 patients with severe (n = 81, 82.6%) or moderate (n = 17, 17.4%) TBI underwent primary DC and were included in this study. The 30-day and overall mortality rates were 15.3% and 25.5%, respectively. At a median follow-up of 90 (interquartile range (IQR): 38-180) days, median Karnofsky Performance Status (KPS) and Glasgow outcome scale-extended (GOSE) scores were 50 (IQR: 20-70) and 5 (IQR: 3-7), respectively. Young age and severe TBI were predictors of mortality. Glasgow coma scale (GCS) score on discharge was a strong predictor of KPS and GOSE scores.Conclusion: Primary DC afforded an acceptable functional outcome (GOSE score ≥5) in 45.9% of patients. Young age and lower GCS at presentation were associated with worse survival. GCS score on discharge was a strong predictor of functional outcome

Complete chloroplast genomes of Vachellia nilotica and Senegalia senegal : Comparative genomics and phylogenomic placement in a new generic system

Vachellia and Senegalia are the most important genera in the subfamily Mimosoideae (Fabaceae). Recently, species from both genera were separated from the long-characterized Acacia due to their macro-morphological characteristics. However, this morpho-taxonomic differentiation struggles to discriminate some species, for example, Vachellia nilotica and Senegalia senegal. Therefore, sequencing the chloroplast (cp) genomes of these species and determining their phylogenetic placement via conserved genes may help to validate the taxonomy. Hence, we sequenced the cp genomes of V. nilotica and S. senegal, and the results showed that the sizes of the genomes are 165.3 and 162.7 kb, respectively. The cp genomes of both species comprised large single-copy regions (93,849~91,791 bp) and pairs of inverted repeats (IR; 26,093~26,008 bp). The total numbers of genes found in the V. nilotica and S. senegal cp genomes were 135 and 132, respectively. Approximately 123:130 repeats and 290:281 simple sequence repeats were found in the S. senegal and V. nilotica cp genomes, respectively. Genomic characterization was undertaken by comparing these genomes with those of 17 species belonging to related genera in Fabaceae. A phylogenetic analysis of the whole genome dataset and 56 shared genes was undertaken by generating cladograms with the same topologies and placing both species in a new generic system. These results support the likelihood of identifying segregate genera from Acacia with phylogenomic disposition of both V. nilotica and S. senegal in the subfamily Mimosoideae. The current study is the first to obtain complete genomic information on both species and may help to elucidate the genome architecture of these species and evaluate the genetic diversity among species.publishedVersio

Frequency of Myocardial Infarction in Type 2 Diabetic Patients with Peripheral Arterial Disease

Objective:  This study aimed at determining the frequency of MI in diabetic Pakistani patients with PAD in a Pakistani tertiary care hospital. Methodology: A cross-sectional study carried out at Diabetes Research Centre, Nishtar Hospital Multan for six months from July 10, 2018 to January 09, 2019. The study was approved from the institutional ethics committee. As per study inclusion/exclusion criteria, the patients suffering from DM with PAD were enrolled, after signing the study informed consent. Each patient underwent electrocardiogram (ECG) recording under PI supervision. Patients having pathological Q waves (0.04 seconds wide and 2 mm deep) in two relevant leads were labeled as having myocardial infarction. Results: A total of 290 patients (men: 56.2% and women: 43.8%) were included in the study. Mean age of the patients was 51.29 ± 8.54 years with age range of 40-85 years. There were 71 (24%) smokers and 219 (76%) non-smoker patients. Fifty percent of the total patients were obese. Mean duration of diabetes was 7.39 ± 0.36 years whereas mean duration of peripheral arterial disease was 1.604 ± 0.005 years. The frequency of MI among diabetic patients with PAD was 14.8%. Conclusion: Prevalence of 14.8% MI in the present study alarms to diagnose and treat diabetes and PAD patients at earlier stage

Measuring the BDARX architecture by agent oriented system a case study

Distributed systems are progressively designed as multi-agent systems that are helpful in designing high strength complex industrial software. Recently, distributed systems cooperative applications are openly access, dynamic and large scales. Nowadays, it hardly seems necessary to emphasis on the potential of decentralized software solutions. This is because the main benefit lies in the distributed nature of information, resources and action. On the other hand, the progression in multi agent systems creates new challenges to the traditional methodologies of fault-tolerance that typically relies on centralized and offline solution. Research on multi-agent systems had gained attention for designing software that operates in distributed and open environments, such as the Internet. DARX (Dynamic Agent Replication eXtension) is one of the architecture which aimed at building reliable software that would prove to be both flexible and scalable and also aimed to provide adaptive fault tolerance by using dynamic replication methodologies. Therefore, the enhancement of DARX known as BDARX can provide dynamic solution of byzantine faults for the agent based systems that embedded DARX. The BDARX architecture improves the fault tolerance ability of multi-agent systems in long run and strengthens the software to be more robust against such arbitrary faults. The BDARX provide the solution for the Byzantine fault tolerance in DARX by making replicas on the both sides of communication agents by using BFT protocol for agent systems instead of making replicas only on server end and assuming client as failure free. This paper shows that the dynamic behaviour of agents avoid us from making discrimination between server and client replicas

Expanded inverted repeat region with large scale inversion in the first complete plastid genome sequence of Plantago ovata

Plantago ovata (Plantaginaceae) is an economically and medicinally important species, however, least is known about its genomics and evolution. Here, we report the first complete plastome genome of P. ovata and comparison with previously published genomes of related species from Plantaginaceae. The results revealed that P. ovata plastome size was 162,116 bp and that it had typical quadripartite structure containing a large single copy region of 82,084 bp and small single copy region of 5,272 bp. The genome has a markedly higher inverted repeat (IR) size of 37.4 kb, suggesting large-scale inversion of 13.8 kb within the expanded IR regions. In addition, the P. ovata plastome contains 149 different genes, including 43 tRNA, 8 rRNA, and 98 protein-coding genes. The analysis revealed 139 microsatellites, of which 71 were in the non-coding regions. Approximately 32 forward, 34 tandem, and 17 palindromic repeats were detected. The complete genome sequences, 72 shared genes, matK gene, and rbcL gene from related species generated the same phylogenetic signals, and phylogenetic analysis revealed that P. ovata formed a single clade with P. maritima and P. media. The divergence time estimation as employed in BEAST revealed that P. ovata diverged from P. maritima and P. media about 11.0 million years ago (Mya; 95% highest posterior density, 10.06-12.25 Mya). In conclusion, P. ovata had significant variation in the IR region, suggesting a more stable P. ovata plastome genome than that of other Plantaginaceae species.publishedVersio

Complete chloroplast genome sequencing and comparative analysis of threatened dragon trees Dracaena serrulata and Dracaena cinnabari

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