DIDA: Distributed Indexing Dispatched Alignment

One essential application in bioinformatics that is affected by the high-throughput sequencing data deluge is the sequence alignment problem, where nucleotide or amino acid sequences are queried against targets to find regions of close similarity. When queries are too many and/or targets are too large, the alignment process becomes computationally challenging. This is usually addressed by preprocessing techniques, where the queries and/or targets are indexed for easy access while searching for matches. When the target is static, such as in an established reference genome, the cost of indexing is amortized by reusing the generated index. However, when the targets are non-static, such as contigs in the intermediate steps of a de novo assembly process, a new index must be computed for each run. To address such scalability problems, we present DIDA, a novel framework that distributes the indexing and alignment tasks into smaller subtasks over a cluster of compute nodes. It provides a workflow beyond the common practice of embarrassingly parallel implementations. DIDA is a cost-effective, scalable and modular framework for the sequence alignment problem in terms of memory usage and runtime. It can be employed in large-scale alignments to draft genomes and intermediate stages of de novo assembly runs. The DIDA source code, sample files and user manual are available through http://www.bcgsc.ca/platform/bioinfo/software/dida. The software is released under the British Columbia Cancer Agency License (BCCA), and is free for academic use

A reliability-based approach for influence maximization using the evidence theory

The influence maximization is the problem of finding a set of social network users, called influencers, that can trigger a large cascade of propagation. Influencers are very beneficial to make a marketing campaign goes viral through social networks for example. In this paper, we propose an influence measure that combines many influence indicators. Besides, we consider the reliability of each influence indicator and we present a distance-based process that allows to estimate the reliability of each indicator. The proposed measure is defined under the framework of the theory of belief functions. Furthermore, the reliability-based influence measure is used with an influence maximization model to select a set of users that are able to maximize the influence in the network. Finally, we present a set of experiments on a dataset collected from Twitter. These experiments show the performance of the proposed solution in detecting social influencers with good quality.Comment: 14 pages, 8 figures, DaWak 2017 conferenc

Clinical grade human adipose tissue-derived mesenchymal stem cell banking

In this study, our aim was to produce a generation of GMP-grade adipose tissue-derived mesenchymal stem cells for clinical applications. According to our results, we fulfill to establish consistent and also reproducible current good manufacturing practice (cGMP) compliant adipose tissue-derived mesenchymal stem cells from five female donors. The isolated cells were cultured in DMEM supplemented with 10 fetal bovine serum and characterized by standard methods. Moreover, karyotyping was performed to evaluate chromosomal stability. Mean of donors� age was 47.6 ± 8.29 year, mean of cell viability was 95.6 ± 1.51, and cell count was between 9�106 and 14�106 per microliter with the mean of 12.2�106 ± 2863564.21 per microliter. The main aim of this project was demonstrating the feasibility of cGMP-compliant and clinical grade adipose tissue-derived mesenchymal stem cells preparation and banking for clinical cell transplantation trials. © 2015 Tehran University of Medical Sciences. All rights reserved

Clinical Grade Human Adipose Tissue-Derived Mesenchymal Stem Cell Banking

In this study, our aim was to produce a generation of GMP-grade adipose tissue-derived mesenchymal stem cells for clinical applications. According to our results, we fulfill to establish consistent and also reproducible current good manufacturing practice (cGMP) compliant adipose tissue-derived mesenchymal stem cells from five female donors. The isolated cells were cultured in DMEM supplemented with 10 fetal bovine serum and characterized by standard methods. Moreover, karyotyping was performed to evaluate chromosomal stability. Mean of donors' age was 47.6 ± 8.29 year, mean of cell viability was 95.6 ± 1.51, and cell count was between 9�106 and 14�106 per microliter with the mean of 12.2�106 ± 2863564.21 per microliter. The main aim of this project was demonstrating the feasibility of cGMP-compliant and clinical grade adipose tissue-derived mesenchymal stem cells preparation and banking for clinical cell transplantation trials

Effect of opium consumption on cardiovascular diseases � a cross- sectional study based on data of Rafsanjan cohort study

Background: There are differences of opinion about the beneficial or detrimental effects of opium consumption on cardiovascular diseases (CVDs). So, we aimed to study the association between opium use and CVDs. Methods: We used data obtained from the Rafsanjan Cohort Study (RCS), as a part of the prospective epidemiological research studies in IrAN (PERSIAN), with detailed, validated data on opium consumption and some other exposures. A total of 10,000 adults were enrolled in the study. Logistic regression models were used to assess the possible relationships of opium consumption with the prevalence of ischemic heart diseases (IHD) and myocardial infarction (MI). Results: In this study, 9990 participants in the baseline phase of the Rafsanjan adult cohort study were included according to their completed questionnaire. Among all participants, 870 and 296 individuals were found to suffer from IHD and MI, respectively. Opium consumption was found to be relatively high in the RCS participants, especially in men (men = 2150 and women = 228). Opium use was associated with a higher odds of IHD and MI, with the adjusted odds ratios (95 CI) of 1.51 (1.22�1.86) and 1.79 (1.31�2.45), respectively. Also, dose-response increases were observed with the highest odds ratios in the 4th quartile for MI and IHD (p-values for trend < 0.001). Increased odds were observed for the two main methods of opium consumption, i.e. oral and smoking, but oral administration had higher odds ratio. Conclusions: Opium consumption is associated with the increased odds of both IHD and MI diseases. © 2021, The Author(s)

Different references for valgus cut angle in Total Knee Arthroplasty

Background: The valgus cut angle (VCA) of the distal femur in Total Knee Arthroplasty (TKA) is measured preoperatively on three-joint alignment radiographs. The anatomical axis of the femur can be described as the anatomical axis of the full length of the femur or as the anatomical axis of the distal half of the femur, which may result in different angles in some cases. During TKA, the anatomical axis of the femur is determined by intramedullary femoral guides, which may follow the distal half or near full anatomical axis, based on the length of the femoral guide. The aim of this study was to compare using the anatomical axis of the full length of the femur versus the anatomical axis of the distal half of the femur for measuring VCA, in normal and varus aligned femurs. We hypothesized that the VCA would be different based upon these two definitions of the anatomical axis of the femur. Methods: Full-length weight bearing radiographs were used to determine three-joint alignment in normal aligned (Lateral Distal Femoral Angle; LDFA = 87° ± 2°) and varus aligned (LDFA > 89°) femurs. Full-length anatomical axismechanical axis angle (angle 1) and distal half anatomical axis-mechanical axis angle (angle 2) were measured in all subjects by two independent orthopedic surgeons using a DICOM viewer software (PACS). Angles 1 and 2 were compared in normal and varus aligned subjects to determine whether there was a significant difference. Results: Ninety-seven consecutive subjects with normally aligned femurs and 97 consecutive subjects with varus aligned femurs were included in this study. In normally aligned femurs, the mean value of angle 1 was 5.05° ± 0.76° and for angle 2 was 3.62° ± 1.19°, which were statistically different (P= 0.0001). In varus aligned femurs, the mean value of angle 1 was 5.42° ± 0.85° and for angle 2 was 4.23° ± 1.27°, which were also statistically different (P= 0.0047). Conclusion: The two different methods of outlining the anatomical axis of the femur lead to different results in both normal and varus-aligned femurs. This should be considered in determination of the valgus cut angle on preoperative radiographs and be adjusted according to the length of the intramedullary guide. © 2018 By The Archives of Bone and Joint Surgery

Sinteza, in vitro antitumorsko ispitivanje i radiosenzitirajuće vrednovanje novih derivata 4-[3-(supstituiranih)tioureido]-N-(kinoksalin-2-il)benzensulfonamida

Sulfonamides and quinoxaline derivatives possess many types of biological activities and have been recently reported to show substantial antitumor activity. This paper reports the synthesis of novel thioureidosulfaquinoxaline derivatives. All the newly synthesized compounds were evaluated for their in vitro anticancer activity against a human liver cell line (HEPG2) and showed higher activity than the reference drug doxorubicin. 4-(3-(4-Ethylbenzoate)thioureido)-N-(quinoxalin-2-yl)benzenesulfonamide (9) (IC50 = 15.6 µmol L1), N-(pyridin-2-yl)-4-(3-(4-(N-quinoxalin-2-yl-sulfamoyl)phenyl)thioureido)benzene-sulfonamide (10) (IC50 = 26.8 µmol L1) and N-(quinoxalin-2-yl)-4-(3-(4-(N-thiazol-2-ylsulfamoyl)phenyl)thioureido)benzenesulfonamide (11) (IC50 = 24.4 µmol L1) were the most potent compared to doxorubicin (IC50 = 71.8 µmol L1). The most potent compounds 9, 10 and 11 were evaluated as radiosensitizing agents by subjecting the compounds to γ-irradiation (8 kGy).Derivati sulfonamida i kinoksalina imaju raznoliko biološko djelovanje, između ostalog i antitumorsko djelovanje. U radu je opisana sinteza novih derivata tioureido sulfakinoksalina. Svim novim spojevima ispitano je antitumorsko djelovanje in vitro na humanoj staničnoj liniji jetre (HEPG 2). Svi ispitani spojevi pokazuju jači učinak nego referentni lijek doksorubicin. Najjači učinak imali su 4-(3-(4-etilbenzoat)tioureido)-N-(kinoksalin-2-il)benzen-sulfonamid (9) (IC50 = 15,6 µmol L1), N-(piridin-2-il)-4-(3-(4-(N-kinoksalin-2-il-sulfamoil)fenil)tioureido)-benzen-sulfonamid (10) (IC50 = 26,8 µmol L1) i N-(kinoksalin-2-il)-4-(3-(4-(N-tiazol-2-ilsulfamoil)fenil)tioureido)benzen-sulfonamid (11) (IC50 = 24,4 µmol L1), dok je IC50 vrijednost bila 71,8 µmol L1. Najaktivniji spojevi 9, 10 i 11 evaluirani su kao radziosenzitirajuća sredstva nakon izlaganja spojeva γ-zračenju (8 kGy)

Incidence, mortality, and burden of hepatitis B and C and geographical distribution in Iran during 2008-2015

Background: This study aimed at estimating the incidence, mortality, and burden of Hepatitis B (HBV) and Hepatitis C (HCV) viruses and their trends from 2008 to 2015. Methods: The Disability Adjusted Life Year (DALYs) index was applied to calculate the burden of the diseases by age, sex, time, and locations. The incidence and demographic data were obtained from HBV and HCV surveillance system, and the data on natural history was extracted from the cohort studies; moreover, the data on the standard life expectancy was obtained from the Iranian life table 2016. The two values of 0.03 and 21.5 yr were set as the discount rate and mean standard duration of the disease for both types of hepatitis. Results: The burden of HBV decreased from 13735 to 78277.6 yr, but there was an increase in the burden of HCV from 5174 to 14395 yr over the studied period. The burden of both types of hepatitis was higher among males than females. The incidence of HBV increased from 46611 to 22996 cases, and the incidence of HCV increased from 1210 to 3939 cases. The HBV decreased from 1925 to 1394 cases; however, the number of deaths caused by HCV increased from 197 to 583 cases over the studied period. The share of YLLs raised from 5 to 10 for HBV whereas it changed from 23 to 62 for HCV over the studied years. Tehran, Khorasan Razavi, and Golestan had the highest and Chaharmahal and Bakhtiari, Kurdistan, and Kermanshah had the lowest adjusted burden of HBV per 1000 population. Conclusion: Although the incidence, mortality, and burden of HBV declined over the eight studied years, these values increased dramatically for HCV. © 2019, Iranian Journal of Public Health. All rights reserved

Indications and outcome of repeat penetrating keratoplasty in India

BACKGROUND: Repeat penetrating keratoplasty is quite often required as there is high chance of failure of the primary graft particularly in the developing world. We planned a study to analyze the indications and outcome of repeat penetrating keratoplasty in a tertiary care centre in India. METHODS: A retrospective analysis of all the patients who underwent repeat penetrating keratoplasty, between January 1999 and December 2001 was performed. The parameters evaluated were indication for the primary penetrating keratoplasty, causes of failure of the previous graft, and final visual outcome and clarity of the repeat corneal grafts. RESULTS: Of fifty-three eyes of 50 patients with repeat penetrating keratoplasty (three patients underwent bilateral corneal regrafts), 37 eyes had undergone one regraft each, 14 eyes two regrafts and two eyes had three regrafts. The follow-up of the patients ranged from one to three years. The most common primary etiologic diagnosis was vascularized corneal scars (66%), of which the scars related to infection were most common (68.5%). Twenty-eight regrafts (52.8%) remained clear at a mean follow-up of 1.54 ± 0.68 years, of which 25 were single regrafts (89.3%). The commonest cause of failure of regraft was infection to the corneal graft (recurrence of herpetic infection in 9 eyes and perforated graft ulcers in 3 eyes). Three (18.6%) of the 16 eyes with multiple corneal regrafts achieved a BCVA of 6/60. Overall, only five eyes (all with single regraft) achieved a BCVA of 6/18 or better at the end of follow-up. CONCLUSION: Graft infection is the leading cause of failure of repeat keratoplasty in this part of the world. Prognosis for visual recovery and graft survival is worse in eyes undergoing multiple regrafts

Predicting the outcome of conservative treatment with physiotherapy in adults with shoulder pain associated with partial-thickness rotator cuff tears – a prognostic model development study

Model coefficient statistics (DOCX 21 kb