Efficient Algorithms for Prokaryotic Whole Genome Assembly and Finishing

De-novo genome assembly from DNA fragments is primarily based on sequence overlap information. In addition, mate-pair reads or paired-end reads provide linking information for joining gaps and bridging repeat regions. Genome assemblers in general assemble long contiguous sequences (contigs) using both overlapping reads and linked reads until the assembly runs into an ambiguous repeat region. These contigs are further bridged into scaffolds using linked read information. However, errors can be made in both phases of assembly due to high error threshold of overlap acceptance and linking based on too few mate reads. Identical as well as similar repeat regions can often cause errors in overlap and mate-pair evidence. In addition, the problem of setting the correct threshold to minimize errors and optimize assembly of reads is not trivial and often requires a time-consuming trial and error process to obtain optimal results. The typical trial-and-error with multiple assembler, which can be computationally intensive, and is very inefficient, especially when users must learn how to use a wide variety of assemblers, many of which may be serial requiring long execution time and will not return usable or accurate results. Further, we show that the comparison of assembly results may not provide the users with a clear winner under all circumstances. Therefore, we propose a novel scaffolding tool, Correlative Algorithm for Repeat Placement (CARP), capable of joining short low error contigs using mate pair reads, computationally resolved repeat structures and synteny with one or more reference organisms. The CARP tool requires a set of repeat sequences such as insertion sequences (IS) that can be found computationally found without assembling the genome. Development of methods to identify such repeating regions directly from raw sequence reads or draft genomes led to the development of the ISQuest software package. ISQuest identifies bacterial ISs and their sequence elements—inverted and direct repeats—in raw read data or contigs using flexible search parameters. ISQuest is capable of finding ISs in hundreds of partially assembled genomes within hours; making it a valuable high-throughput tool for a global search of IS and repeat elements. The CARP tool matches very low error contigs with strong overlap using the ambiguous partial repeat sequence at the ends of the contig annotated using the repeat sequences discovered using ISQuest. These matches are verified by synteny with genomes of one or more reference organisms. We show that the CARP tool can be used to verify low mate pair evidence regions, independently find new joins and significantly reduce the number of scaffolds. Finally, we are demonstrate a novel viewer that presents to the user the computationally derived joins along with the evidence used to make the joins. The viewer allows the user to independently assess their confidence in the joins made by the finishing tools and make an informed decision of whether to invest the resources necessary to confirm a particular portion of the assembly. Further, we allow users to manually record join evidence, re-order contigs, and track the assembly finishing process

Comparative study of copper, zinc, iron, ferritin, calcium and magnesium levels in pregnancy induced hypertension and normotensive primigravida mothers

Background: Exact pathophysiology of pregnancy induced hypertension (PIH) is still unknown but there is a definite relationship between trace elements and preeclampsia. Several studies in this context have conflicting reports. So, a comparative study of serum levels of copper (Cu), zinc (Zn), iron (Fe), ferritin, calcium (Ca) and magnesium (Mg), in PIH and normotensive primipara mothers was conducted.Methods: Study was conducted in Department of Biochemistry & Department of Gynaecology and Obstetrics, R. G. Kar Medical College & Hospital, Kolkata over 1 year from September 2013 to August 2014 on fifty PIH patients as cases and fifty normotensive primipara mother without proteinuria as controls, both having ages ranging between 15-35 years in 2nd and 3rd trimesters.Results: Serum Ca, Mg, Cu and Zn levels were found to be significantly reduced (<0.05) in the PIH group compared to the normal pregnant group. Serum ferritin was markedly increased in the cases (mean 90.41±47.39, p<0.00001). No significant correlation was found in serum Fe levels.Conclusions: Alteration of serum Cu, Zn, Ca, Mg and ferritin levels can be considered to have a role in the etiopathogenesis and severity of PIH.

A Novel Regularity Criterion For The three-dimensional Navier-Stokes Equations Based On Finitely many observations

In this paper we present two results: (1) A data assimilation algorithm for the 3D Navier-Stokes equation (3D NSE) using nodal data, and, as a consequence (2) a novel regularity criterion for the 3D NSE based on finitely many observations of the velocity. The data assimilation algorithm we employ utilizes nudging, a method based on a Newtonian relaxation scheme motivated by feedback-control. The observations, which may be either modal, nodal or volume elements, are drawn from a weak solution of the 3D NSE and are collected almost everywhere in time over a finite grid and our results, including the regularity criterion, hold for data of any of the aforementioned forms. The regularity criterion we propose follows from our data assimilation algorithm and is hence intimately connected to the notion of determining functionals (modes, nodes and volume elements). To the best of our knowledge, all existing regularity criteria require knowing the solution of the 3D NSE almost everywhere in space. Our regularity criterion is fundamentally different from any preexisting regularity criterion as it is based on finitely many observations (modes, nodes and volume elements). We further prove that the regularity criterion we propose is both a necessary and sufficient condition for regularity. Thus our result can be viewed as a natural generalization of the notion of determining modes, nodes and volume elements as well as the asymptotic tracking property of the nudging algorithm for the 2D NSE to the 3D setting

A Fuzzy EPQ Model for Non-Instantaneous Deteriorating Items where Production Depends on Demand which is Proportional to Population, Selling Price as well as Advertisement

The inventory system has been drawing more intrigue because this system deals with the decision that minimizes the total average cost or maximizes the total average profit. For any farm, the demand for any items depends upon population, selling price and frequency of advertisement etc. Most of the model, it is assumed that deterioration of any item in inventory starts from the beginning of their production. But in reality, many goods are maintaining their good quality or original condition for some time. So, price discount is availed for defective items. Our target is to calculate the total optimal cost and the optimal inventory level for this inventory model in a crisp and fuzzy environment. Here Holding cost taken as constant and no-shortages are allowed. The cost parameters are considered as Triangular Fuzzy Numbers and to defuzzify the model Signed Distance Method is applied. A numerical example of the optimal solution is given to clarify the model. The changes of different parameters effect on the optimal total cost are presented and sensitivity analysis is given.JEL Classification: C44, Y80, C61Mathematics Subject Classification: 90B0

Multi-objective economic production quantity model for fully backlogged problem where demand depend on some conditions and permissible delay in payment

For any business, inventory system takes a monumental part. Keep this aspect in mind, we formulate multi-objective displayed EPQ model consider with non-instantaneous deteriorating things where production depends on demand and variable demand pattern depends on display self-space, selling price and frequency of advertisement of the item. The customers are more attracted to buy an item by observing self-space, selling price and advertisement. Imperfect materials are now and again come back to providers for a discount or credit. Here price discount is available for deteriorated and defective items. Holding cost varies with time where shortages are allowed and fully backlogged. Fuzzy environment touches the reality instead of the crisp environment. So, we assumed the cost components as Triangular Fuzzy Numbers and Nearest Interval Approximation Method is used to defuzzify the model. Finally, numerical examples as well as  sketches are given to illustrate the model

A Dynamic Programming Algorithm for Finding the Optimal Placement of a Secondary Structure Topology in Cryo-EM Data

The determination of secondary structure topology is a critical step in deriving the atomic structures from the protein density maps obtained from electron cryomicroscopy technique. This step often relies on matching the secondary structure traces detected from the protein density map to the secondary structure sequence segments predicted from the amino acid sequence. Due to inaccuracies in both sources of information, a pool of possible secondary structure positions needs to be sampled. One way to approach the problem is to first derive a small number of possible topologies using existing matching algorithms, and then find the optimal placement for each possible topology. We present a dynamic programming method of Θ(Nq2h) to find the optimal placement for a secondary structure topology. We show that our algorithm requires significantly less computational time than the brute force method that is in the order of Θ(qN h)

TLR2 polymorphisms, Arg753Gln and Arg677Trp, are not associated with increased burden of tuberculosis in Indian patients

<p>Abstract</p> <p>Background</p> <p>In view of the role of TLR2 activation in host defense against mycobacteria, the present study was conducted to examine whether TLR2 polymorphisms could account for the increased prevalence of tuberculosis in Indian patients. Detection of such polymorphisms would help in assessing the risk of developing active tuberculosis among contacts or HIV positive patients and in identifying candidates for chemoprophylaxis.</p> <p>Findings</p> <p>One hundred patients with tuberculosis and 100 controls were investigated for the presence of two TLR2 polymorphisms, viz. Arg753Gln and Arg677Trp, using PCR-RFLP of a 340 bp region of the TLR2 gene, followed by DNA sequencing of a randomly selected group of 35 patients. While these polymorphisms were found to be non-existent in our study groups, we observed a novel polymorphism Phe749Tyr in 2 patients. However, this polymorphism was associated with negligible deviation in Delphi electrostatic potential and structural alignment from the wild-type TLR2 protein, making it an unlikely candidate for any significant structural or functional alteration at the protein level.</p> <p>Conclusion</p> <p>Hence we conclude that, contrary to reported associations in other populations, TLR2 polymorphisms are not responsible for the increased prevalence of TB in the Indian population.</p

Parametric Influences on Heat Affected Zone in Micro-channel Milling Process of Zirconia Ceramic

Zirconia, a bio-ceramic, is widely utilized in bioengineering, biomedical implants, dentistry, and the automotive industry due to high hardness, excellent wear resistance, etc. However, it is difficult to attain micro features on zirconia utilizing a laser machining system for&nbsp;the aforesaid properties. The paper deals with the study of the Heat Affected Zone (HAZ) formation during the micro-channel milling (V-shaped cross-sections) of zirconia utilizing a nanosecond fiber laser system. Experiments are accomplished to&nbsp;examine the&nbsp;consequence of control variables namely transverse feed, pulse frequency, laser power, scan number, and scan speed. The&nbsp;influence of each of the laser process variables on response parameter are studied in order to get the significant trends of laser parameters. With&nbsp;the increment of laser power, the number of pass and transverse feed, HAZ width dimensions tend to&nbsp;increase. The reverse phenomena are observed for pulse frequency and scan speed. The lower HAZ width which is achieved as&nbsp;31.74&nbsp;μm at a parametric setting of average power at&nbsp;10&nbsp;W, pulse frequency at 65&nbsp;kHz, scanning speed at 11&nbsp;mm/s, a number of pass at 1, transverse feed at&nbsp;0.005&nbsp;mm