Multi-criteria decision making to validate performance of RBC-based formulae to screen [Formula: see text]-thalassemia trait in heterogeneous haemoglobinopathies.

BACKGROUND: India has the most significant number of children with thalassemia major worldwide, and about 10,000-15,000 children with the disease are born yearly. Scaling up e-health initiatives in rural areas using a cost-effective digital tool to provide healthcare access for all sections of people remains a challenge for government or semi-governmental institutions and agencies. METHODS: We compared the performance of a recently developed formula SCS[Formula: see text] and its web application SUSOKA with 42 discrimination formulae presently available in the literature. 6,388 samples were collected from the Postgraduate Institute of Medical Education and Research, Chandigarh, in North-Western India. Performances of the formulae were evaluated by eight different measures: sensitivity, specificity, Youden's Index, AUC-ROC, accuracy, positive predictive value, negative predictive value, and false omission rate. Three multi-criteria decision-making (MCDM) methods, TOPSIS, COPRAS, and SECA, were implemented to rank formulae by ensuring a trade-off among the eight measures. RESULTS: MCDM methods revealed that the Shine & Lal and SCS[Formula: see text] were the best-performing formulae. Further, a modification of the SCS[Formula: see text] formula was proposed, and validation was conducted with a data set containing 939 samples collected from Nil Ratan Sircar (NRS) Medical College and Hospital, Kolkata, in Eastern India. Our two-step approach emphasized the necessity of a molecular diagnosis for a lower number of the population. SCS[Formula: see text] along with the condition MCV[Formula: see text] 80 fl was recommended for a higher heterogeneous population set. It was found that SCS[Formula: see text] can classify all BTT samples with 100% sensitivity when MCV[Formula: see text] 80 fl. CONCLUSIONS: We addressed the issue of how to integrate the higher-ranked formulae in mass screening to ensure higher performance through the MCDM approach. In real-life practice, it is sufficient for a screening algorithm to flag a particular sample as requiring or not requiring further specific confirmatory testing. Implementing discriminate functions in routine screening programs allows early identification; consequently, the cost will decrease, and the turnaround time in everyday workflows will also increase. Our proposed two-step procedure expedites such a process. It is concluded that for mass screening of BTT in a heterogeneous set of data, SCS[Formula: see text] and its web application SUSOKA can provide 100% sensitivity when MCV[Formula: see text] 80 fl.

Recycling of animal protein wastes in the formulation of feed for Labeo rohita and Mystus vittatus-a comparative evaluation.

Lactic acid bacteria (LAB) are key players in the fermentation of organic wastes and their recycling as feedstuff for fish. Whey, a common dairy byproduct in India, is a cheap source of LAB and can be used to ferment animal byproducts. An experimental study was designed to explore whether the whey fermented animal protein blend (WFAPB) could be used as a fishmeal replacer in the formulation of feed for both stomach-less carp fish Labeo rohita and stomach-bearing catfish Mystus vittatus. Experiments were performed with five isoproteinous, isolipidous, and isoenergetic feeds with WFAPB replacing fishmeal (FM) by 0% (T1), 25% (T2), 50% (T3), 75% (T4), and 100% (T5). Fifteen days of laboratory experiments with these experimental feeds revealed that more than 50% FM replacement level could result in excess postprandial absorption (6 h) of some essential and non-essential amino acids in the plasma of both fish. The postprandial absorption was more in M. vittatus than L. rohita. Ninety-day experiments were conducted in outdoor cement vats to measure growths and deposition of amino acids (AA) in muscle. Regression analysis was performed to find the optimal FM replacement based on four growth parameters and fifteen AA deposition in muscle. A two-phase fuzzy methodology was used to obtain Pareto-optimal replacement levels for each fish. The results demonstrated that FM replacement levels were 7.63% and 36.79% respectively for L. rohita and M. vittatus when only four growth parameters were considered. However, based on the FM replacement level that maximized deposition of 15 amino acids and growth parameters, it was found that 12.23% and 40.02% replacement of FM by the WFAPB was ideal respectively for L. rohita and M. vittatus. The results revealed that only a fraction of both essential and non-essential amino acids absorbed in plasma could be converted into protein and deposited as bound amino acids in the muscle. It is concluded that fermentation by whey is an inexpensive, easily available, and environmentally sustainable technique to recycle animal protein in the formulation of feed for fish, and the stomach-bearing carnivorous fish are more efficient in utilizing fermented animal protein blend than the stomach-less carps.

Impact of dietary piperine on growth performance, immune response, antioxidant status, and immune-related gene expression in pathogen-aggravated Cyprinus carpio.

This study investigated the effects of dietary piperine (PIP) on growth performance, digestive enzymes, serum biochemical parameters, antioxidant and immune responses, and gene expression in Cyprinus carpio challenged with Aeromonas hydrophila. Six diets were prepared with PIP doses of 0, 0.5, 1.0, 2.0, 3.0, and 4.0 g/kg, corresponding with the control, PR50, PR100, PR200, PR300, and PR400, respectively. Fish were challenged with Aeromonas hydrophila after 8 weeks of feeding with the respective diets. Weight gain (PWG) and specific growth rate (SGR) were significantly enhanced, whereas feed conversion ratio (FCR) was lowered in PR200. The cumulative post-challenge survival was improved to 68.43% in the PR200 group compared with 28.08% in the control. Serum total protein and albumin levels were significantly enhanced in the PR200 group compared to the control. However, dietary PIP up to 3 g/kg had no significant effect on serum glucose, cortisol, aspartate aminotransferase, or alkaline phosphatase activities; however, the alanine aminotransferase level was lower (P < 0.05) in the PR200 group than in the control. Intestinal amylase, lipase, and protease activities increased in PR300, and intestinal amylase and lipase increased in the PR100 group (P < 0.05). The serum immunological indices (lysozyme, alternative complement pathway, phagocytic activity, and respiratory burst activity) were higher (P < 0.05) in the PR200 group than in the control group. Serum superoxide dismutase (SOD), glutathione peroxidase (GPx), and catalase (CAT) activities were significantly intensified in PR200-PR300 than in the control group, with the highest activity observed in the PR200 group. Malondialdehyde was significantly lower in the PR200 group than in the control group. Furthermore, SOD, CAT, and Nrf2 expression was strongly upregulated in the liver tissue of the PR200 and PR300 groups compared to that in the control. The transcript levels of pro-inflammatory cytokines viz. IL-1ß and TNF-α were significantly upregulated in the kidneys of the PR100 and PR200 post-challenged. In contrast, the anti-inflammatory cytokine IL-10 was significantly downregulated in the kidneys of PR200. The expression of HSP70 was upregulated only in the PR400. Quadratic regression analysis showed that the optimal dietary PIP level was estimated as 2.07-2.13 g/kg to maximize growth performance. Overall, these results indicate that dietary PIP at an appropriate level can improve immunity, cytokine gene expression, and disease resistance in C. carpio.

Dietary Syzygium cumini leaf extract influences growth performance, immunological responses and gene expression in pathogen-challenged Cyprinus carpio.

This study evaluated the effects of jamun leaf extract (JLE) as a feed supplement on growth performance, haemato-immunological, oxidative stress-related parameters, and cytokine gene expression in Cyprinus carpio challenged with Aeromonas hydrophila.. Diets containing four different JLE concentrations, that is, 0 (basal diet), 5 (JLE5), 10 (JLE10), and 15 g kg-1 (JLE15), were fed to carp (6.17 ± 0.43 g) for eight weeks. Growth performance was significantly higher in JLE10. Haemato-immunological and antioxidant parameters were determined in fish at 48 h post-challenge with A. hydrohila. The cumulative survival was highest in JLE10 (69.69%) 14 days post-challenge. Serum protein (2.18 ± 0.06 g dL-1), lysozyme (32.38 ± 1.2 U mL-1), alternative complement pathway (70.43 ± 1.61 U mL-1), phagocytic activity (21.18 ± 0.48%), respiratory burst activity (0.289 ± 0.09 OD630nm), and immunoglobulin levels (6.67 ± 0.36 U mg mL-1) were significantly higher in JLE10 than in the control. Serum alanine aminotransferase (44.06 ± 1.62 Unit mL-1), aspartate aminotransferase (31.58 ± 1.82 Unit mL-1), and malondialdehyde (2.57 ± 0.26 nmol mL-1) levels were lower in JLE10 than in the control (p < 0.05), whereas myeloperoxidase activity was significantly higher in JLE5 and JLE10 than in the control. Superoxide dismutase levels in the serum were higher (p < 0.05) in JLE5 and JLE10 than in the other groups. Gene expression analysis revealed that the mRNA expression of pro-inflammatory cytokines TNF-α and IL-1ß was upregulated (p < 0.05) in the liver, head-kidney, and intestine of challenged carp in JLE10. The signalling molecule NF-κB p65 was upregulated in lymphoid organs in JLE10 but not in the liver. The anti-inflammatory cytokine IL-10 was significantly downregulated in challenged carp in JLE10 compared with that in the control. Quadratic regression analysis showed that optimal dietary JLE was estimated to be 9.03-10.15 g kg-1 to maximize the growth performance. Results of the present study revealed that dietary JLE at 10 g kg-1 can significantly improve the immunity and disease resistance of C. carpio. Thus, JLE is a promising food additive for carp aquaculture.

Transfer of chromium from environment to fish in East Kolkata wetlands - evaluation by structural equation modeling.

Chromium (Cr) is a significant pollutant in the effluents from leather industries and domestic city sewage. Cr was determined in water, sediment, and different tissues (gill, muscle, intestine, liver, and kidney) of Nile tilapia, Oreochromis niloticus harvested from wastewater-fed aquaculture (WFA) situated at Bamonghata, Bantala, Chowbaga and Chingrighata of East Kolkata Wetlands (EKW), a Ramsar site in West Bengal, India. The results showed that Cr concentration in surface water ranged between 0.05 to 0.15 mg/L, while Cr was detected at high concentration (100-300 mg/kg) in the sediment soil of the first three WFAs and in moderate concentration (50-110 mg/kg) in Chingrighata WFA. Average Cr concentrations in the tissues were ranked in the following sequence: kidney>liver>intestine>gill>muscle. However, the extent of accumulation of Cr in different tissues varied between the WFAs. We used Structural Equation Modeling (SEM) to determine the route of Cr transfer. The fitness of the model was evaluated by the performance measures. Cr accumulation pathways varied between the sites depending upon the level of Cr in water or sediment. Except for Bamonghata WFA, sediment was found as the principal source of accumulation of Cr in different tissues of O. niloticus. Cr refluxed from sediment into overlying water and accumulated in fish either through the food chain or through direct accumulation from water. In Bamonghata WFA, the role of sediment in the transfer of Cr could not be established due to the high water depth or biological non-availability of Cr in the sediment. It is concluded from this study that fish reared in the WFAs of EKW are still not hazardous in respect to Cr but require proper management to avoid the influx of Cr-containing effluents into the WFAs.

Prevalence and attributes of traumatic dental injuries to anterior teeth among school going children of Kolkata, India.

Background: Traumatic Dental Injuries (TDI) have emerged as a very significant public health and social problem, especially among children and adolescents. The aim of this study was to investigate the prevalence and associated risk factors of traumatic dental injuries to permanent anterior teeth in school going children of Kolkata aged 7-14 years. Method: A cross-sectional study was conducted among 3762 school going children attending various private and public schools of Kolkata aged 7-14 years. A multistage random clustering sampling technique was adopted to select the children.Type of trauma using Ellis and Davey classification of fractures along with Andresen's Epidemiological Classification of Traumatic Injuries to Anterior Teeth, including WHO codes, was used. All values were considered statistically significant at P < 0.05. Results: Prevalence of TDI to anterior teeth was found to be 9.89%. The mean age of children who presented with TDI was 11.06 ± 1.99.years. The most common place of occurrence of TDI was home. Falls were the most common causes of trauma. Children belonging to higher socioeconomic status were observed to have an increased prevalence of TDIs.The highest potential risk factor for the occurrence of trauma was a past history of trauma. Conclusion: Present study found a prevalence of 9.89%, and a very low percentage of children had received treatment.

A robust and stable gene selection algorithm based on graph theory and machine learning.

BACKGROUND: Nowadays we are observing an explosion of gene expression data with phenotypes. It enables us to accurately identify genes responsible for certain medical condition as well as classify them for drug target. Like any other phenotype data in medical domain, gene expression data with phenotypes also suffer from being a very underdetermined system. In a very large set of features but a very small sample size domain (e.g. DNA microarray, RNA-seq data, GWAS data, etc.), it is often reported that several contrasting feature subsets may yield near equally optimal results. This phenomenon is known as instability. Considering these facts, we have developed a robust and stable supervised gene selection algorithm to select a set of robust and stable genes having a better prediction ability from the gene expression datasets with phenotypes. Stability and robustness is ensured by class and instance level perturbations, respectively. RESULTS: We have performed rigorous experimental evaluations using 10 real gene expression microarray datasets with phenotypes. They reveal that our algorithm outperforms the state-of-the-art algorithms with respect to stability and classification accuracy. We have also performed biological enrichment analysis based on gene ontology-biological processes (GO-BP) terms, disease ontology (DO) terms, and biological pathways. CONCLUSIONS: It is indisputable from the results of the performance evaluations that our proposed method is indeed an effective and efficient supervised gene selection algorithm.

MSC: a metagenomic sequence classification algorithm.

MOTIVATION: Metagenomics is the study of genetic materials directly sampled from natural habitats. It has the potential to reveal previously hidden diversity of microscopic life largely due to the existence of highly parallel and low-cost next-generation sequencing technology. Conventional approaches align metagenomic reads onto known reference genomes to identify microbes in the sample. Since such a collection of reference genomes is very large, the approach often needs high-end computing machines with large memory which is not often available to researchers. Alternative approaches follow an alignment-free methodology where the presence of a microbe is predicted using the information about the unique k-mers present in the microbial genomes. However, such approaches suffer from high false positives due to trading off the value of k with the computational resources. In this article, we propose a highly efficient metagenomic sequence classification (MSC) algorithm that is a hybrid of both approaches. Instead of aligning reads to the full genomes, MSC aligns reads onto a set of carefully chosen, shorter and highly discriminating model sequences built from the unique k-mers of each of the reference sequences. RESULTS: Microbiome researchers are generally interested in two objectives of a taxonomic classifier: (i) to detect prevalence, i.e. the taxa present in a sample, and (ii) to estimate their relative abundances. MSC is primarily designed to detect prevalence and experimental results show that MSC is indeed a more effective and efficient algorithm compared to the other state-of-the-art algorithms in terms of accuracy, memory and runtime. Moreover, MSC outputs an approximate estimate of the abundances. AVAILABILITY AND IMPLEMENTATION: The implementations are freely available for non-commercial purposes. They can be downloaded from https://drive.google.com/open?id=1XirkAamkQ3ltWvI1W1igYQFusp9DHtVl.

Smart Glycopolymeric Nanoparticles for Multivalent Lectin Binding and Stimuli-Controlled Guest Release.

The synthesis and self-assembly of a polymer featuring a self-complementary supramolecular binding motif guanidiniocarbonyl pyrrole carboxylate zwitterion (GCP-zwitterion) bearing lactose moieties are reported. The GCP-zwitterion acts as a cross-linker to facilitate self-assembly of the polymeric chain into nanoparticles (NPs) at neutral pH in an aqueous medium. The formation of polymeric NPs can be controlled by addition of external stimuli (acid or base), which disfavors self-assembly of the GCP-zwitterion because of protonation or deprotonation of the GCP units in the polymer chain. The small-sized (<40 nm) NPs have a hydrophobic cavity and accessible lactose units on the outer shell for multivalent lectin binding. The multivalent interaction between NPs and the lectin peanut agglutinin was confirmed by agglutination experiments. In addition, the stimuli-responsive property of NPs was exploited for the uptake and release of a hydrophobic guest Nile red. Furthermore, the selectivity toward different cell lines (HEK 296T, HeLa, and Hep2G) was tested, and a cellular uptake of cargo-loaded NPs was found for Hep2G cells bearing the lactose-specific asialogylcoprotein receptor, whereas all other cells showed no NP interaction.

Multi Criteria Decision Making for the Multi-Satellite Image Acquisition Scheduling Problem.

The multi-satellite image acquisition scheduling problem is traditionally seen as a complex optimization problem containing a generic objective function that represents the priority structure of the satellite operator. However, the majority of literature neglect the collective and contemporary effect of factors associated with the operational goal in the objective function, i.e., uncertainty in cloud cover, customer priority, image quality criteria, etc. Consequently, the focus of the article is to integrate a real-time scoring approach of imaging attempts that considers these aspects. This is accomplished in a multi-satellite planning environment, through the utilization of the multi-criteria decision making (MCDM) models, Elimination and Choice Expressing Reality (ELECTRE-III) and the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS), and the formulation of a binary linear programming model. The two scoring approaches belong to different model classes of MCDM, respectively an outranking approach and a distance to ideal point approach, and they are compared with a naive approach. Numerical experiments are conducted to validate the models and illustrate the importance of criteria neglected in previous studies. The results demonstrate the customized behaviour allowed by MCDM methods, especially the ELECTRE-III approach.

Fermented mulberry leaf meal as fishmeal replacer in the formulation of feed for carp Labeo rohita and catfish Heteropneustes fossilis-optimization by mathematical programming.

Search for cost-effective, eco-friendly and sustainable plant resources as potential feedstuff to replace fishmeal in the formulation of feed for fish has been in the forefront of aquaculture researches since the last few years. In this study, experiments were conducted to evaluate if replacement of fishmeal by the fermented leaf meal of mulberry (Morus indica) was viable in the formulation of feed for carp fish Labeo rohita and catfish Heteropneustes fossilis. Four iso-proteinous, iso-lipidic and iso-energetic experimental feed were formulated by replacing 0, 25, 50 and 75% of fishmeal by the fermented mulberry leaf meal (FMLM), and both species were grown on these feeds for 8 weeks. Since the results revealed differences in response to fishmeal replacement level between parameters, we determined optimum fishmeal replacement level (OFRL) for each parameter from the polynomial curve equation. While maximum weight gain and specific growth rate and minimum feed conversion ratio was found at 30-32% OFRL for L. rohita and at 52-53% OFRL for H. fossilis, other parameters responded differently in both fish. Therefore, we applied a two-phase fuzzy goal programming technique using all parameters, which showed overall OFRL for L. rohita and H. fossilis as 30.95% and 52%, respectively. We also applied the concept of 'decision tree' to identify the key factor behind utilization of FMLM. It was concluded that activity of amylase and subsequent utilization of carbohydrate was the key factor in utilizing FMLM. Interestingly, H. fossilis was found more efficient in utilizing carbohydrate of FMLM than L. rohita.

Efficient algorithms for polyploid haplotype phasing.

BACKGROUND: Inference of haplotypes, or the sequence of alleles along the same chromosomes, is a fundamental problem in genetics and is a key component for many analyses including admixture mapping, identifying regions of identity by descent and imputation. Haplotype phasing based on sequencing reads has attracted lots of attentions. Diploid haplotype phasing where the two haplotypes are complimentary have been studied extensively. In this work, we focused on Polyploid haplotype phasing where we aim to phase more than two haplotypes at the same time from sequencing data. The problem is much more complicated as the search space becomes much larger and the haplotypes do not need to be complimentary any more. RESULTS: We proposed two algorithms, (1) Poly-Harsh, a Gibbs Sampling based algorithm which alternatively samples haplotypes and the read assignments to minimize the mismatches between the reads and the phased haplotypes, (2) An efficient algorithm to concatenate haplotype blocks into contiguous haplotypes. CONCLUSIONS: Our experiments showed that our method is able to improve the quality of the phased haplotypes over the state-of-the-art methods. To our knowledge, our algorithm for haplotype blocks concatenation is the first algorithm that leverages the shared information across multiple individuals to construct contiguous haplotypes. Our experiments showed that it is both efficient and effective.

Selective Encapsulation of Disaccharide Xylobiose by an Aromatic Foldamer Helical Capsule.

Xylobiose sequestration in a helical aromatic oligoamide capsule was evidenced by circular dichroism, NMR spectroscopy, and crystallography. The preparation of the 5 kDa oligoamide sequence was made possible by the transient use of acid-labile dimethoxybenzyl tertiary amide substituents that disrupt helical folding and prevent double helix formation. Binding of other disaccharides was not detected. Crystallographic data revealed a complex composed of a d-xylobiose α anomer and two water molecules accommodated in the right-handed helix. The disaccharide was found to adopt an unusual all-axial compact conformation. A dense network of 18 hydrogen bonds forms between the guest, the cavity wall, and the two water molecules.

Authors' response to 'Comment on: ERGC: An efficient Referential Genome Compression Algorithm'.

CONTACT: subrata.saha@engr.uconn.edu or rajasek@engr.uconn.edu.

NRGC: a novel referential genome compression algorithm.

MOTIVATION: Next-generation sequencing techniques produce millions to billions of short reads. The procedure is not only very cost effective but also can be done in laboratory environment. The state-of-the-art sequence assemblers then construct the whole genomic sequence from these reads. Current cutting edge computing technology makes it possible to build genomic sequences from the billions of reads within a minimal cost and time. As a consequence, we see an explosion of biological sequences in recent times. In turn, the cost of storing the sequences in physical memory or transmitting them over the internet is becoming a major bottleneck for research and future medical applications. Data compression techniques are one of the most important remedies in this context. We are in need of suitable data compression algorithms that can exploit the inherent structure of biological sequences. Although standard data compression algorithms are prevalent, they are not suitable to compress biological sequencing data effectively. In this article, we propose a novel referential genome compression algorithm (NRGC) to effectively and efficiently compress the genomic sequences. RESULTS: We have done rigorous experiments to evaluate NRGC by taking a set of real human genomes. The simulation results show that our algorithm is indeed an effective genome compression algorithm that performs better than the best-known algorithms in most of the cases. Compression and decompression times are also very impressive. AVAILABILITY AND IMPLEMENTATION: The implementations are freely available for non-commercial purposes. They can be downloaded from: http://www.engr.uconn.edu/~rajasek/NRGC.zip CONTACT: rajasek@engr.uconn.edu.

Polyamide-Polyamine Cryptand as Dicarboxylate Receptor: Dianion Binding Studies in the Solid State, in Solution, and in the Gas Phase.

Polyamide-polyamine hybrid macrobicycle L is explored with respect to its ability to bind α,ω-dicarboxylate anions. Potentiometric studies of protonated L with the series of dianions from succinate (suc2-) through glutarate (glu2-), α-ketoglutarate (kglu2-), adipate (adi2-), pimelate (pim2-), suberate (sub2-), to azelate (aze2-) have shown adipate preference with association constant value of K = 4900 M-1 in a H2O/DMSO (50:50 v/v) binary solvent mixture. The binding constant increases from glu2- to adi2- and then continuously decreases with the length of the anion chain. Further, potentiometric studies suggest that hydrogen bonding between the guest anions and the amide/ammonium protons of the receptor also contributes to the stability of the associations along with electrostatic interactions. Negative-mode electrospray ionization of aqueous solutions of host-guest complexes shows clear evidence for the selective formation of 1:1 complexes. Single-crystal X-ray structures of complexes of the receptor with glutaric acid, α-ketoglutaric acid, adipic acid, pimelic acid, suberic acid, and azelaic acid assist to understand the observed binding preferences. The solid-state structures reveal a size/shape complementarity between the host and the dicarboxylate anions, which is nicely reflected in the solution state binding studies.

ERGC: an efficient referential genome compression algorithm.

MOTIVATION: Genome sequencing has become faster and more affordable. Consequently, the number of available complete genomic sequences is increasing rapidly. As a result, the cost to store, process, analyze and transmit the data is becoming a bottleneck for research and future medical applications. So, the need for devising efficient data compression and data reduction techniques for biological sequencing data is growing by the day. Although there exists a number of standard data compression algorithms, they are not efficient in compressing biological data. These generic algorithms do not exploit some inherent properties of the sequencing data while compressing. To exploit statistical and information-theoretic properties of genomic sequences, we need specialized compression algorithms. Five different next-generation sequencing data compression problems have been identified and studied in the literature. We propose a novel algorithm for one of these problems known as reference-based genome compression. RESULTS: We have done extensive experiments using five real sequencing datasets. The results on real genomes show that our proposed algorithm is indeed competitive and performs better than the best known algorithms for this problem. It achieves compression ratios that are better than those of the currently best performing algorithms. The time to compress and decompress the whole genome is also very promising. AVAILABILITY AND IMPLEMENTATION: The implementations are freely available for non-commercial purposes. They can be downloaded from http://engr.uconn.edu/∼rajasek/ERGC.zip. CONTACT: rajasek@engr.uconn.edu.

Kinetics of Deposition, Acute Toxicity and Bioaccumulation of Copper in some Freshwater Organisms.

Experiments with environmentally relevant concentrations of Cu in glass aquaria revealed that Cu was quickly removed from water. Cubic regression of Cu concentration against time showed that maximum rate of removal was around 69.34-72.11 h irrespective of treatment. The 96 h LC50 value of Cu was respectively 0.18, 0.19 and 0.35 mg/L for fish Cyprinus carpio, crustacean Diaptomus forbesi and worm Branchiura sowerbyi. Normalizing the lethal values and plotting them against time it was observed that there was sharp differences in mortality over time between the organisms and 96 h lethal values could misrepresent susceptibility of the organisms to Cu. Treatment of 0.1 mg/L of Cu in water resulted in accumulation of 10.57, 4.38, 1.46 and 2.44 µg/g of Cu, respectively in sediment, worm, crustacean zooplankton and whole body of fish. But, Cu deposited in high concentrations in gut and liver of fish indicating that Cu was principally accumulated through food.

EC: an efficient error correction algorithm for short reads.

BACKGROUND: In highly parallel next-generation sequencing (NGS) techniques millions to billions of short reads are produced from a genomic sequence in a single run. Due to the limitation of the NGS technologies, there could be errors in the reads. The error rate of the reads can be reduced with trimming and by correcting the erroneous bases of the reads. It helps to achieve high quality data and the computational complexity of many biological applications will be greatly reduced if the reads are first corrected. We have developed a novel error correction algorithm called EC and compared it with four other state-of-the-art algorithms using both real and simulated sequencing reads. RESULTS: We have done extensive and rigorous experiments that reveal that EC is indeed an effective, scalable, and efficient error correction tool. Real reads that we have employed in our performance evaluation are Illumina-generated short reads of various lengths. Six experimental datasets we have utilized are taken from sequence and read archive (SRA) at NCBI. The simulated reads are obtained by picking substrings from random positions of reference genomes. To introduce errors, some of the bases of the simulated reads are changed to other bases with some probabilities. CONCLUSIONS: Error correction is a vital problem in biology especially for NGS data. In this paper we present a novel algorithm, called Error Corrector (EC), for correcting substitution errors in biological sequencing reads. We plan to investigate the possibility of employing the techniques introduced in this research paper to handle insertion and deletion errors also. SOFTWARE AVAILABILITY: The implementation is freely available for non-commercial purposes. It can be downloaded from: http://engr.uconn.edu/~rajasek/EC.zip.

Formation and Transmetalation Mechanisms of Homo- and Heterometallic (Fe/Zn) Trinuclear Triple-Stranded Side-by-Side Helicates.

A novel linear hybrid tris-bidentate neutral ligand having 2,2'-bipyridine and two terminal triazolylpyridine coordination sites (L) was efficiently synthesized and explored in the synthesis of trinuclear triple-stranded homometallic side-by-side helicates L3Fe3(OTf)6 (1) and L3Zn3(OTf)6 (2), in which the three metal centers display alternating Λ and Δ configurations. Selective formation of the analogous heterometallic side-by-side helicate L3Fe2Zn(OTf)6 (3) was achieved from a mixture of L, Fe(CH3CN)2(OTf)2, and Zn(OTf)2 (1:1:1) in acetonitrile at room temperature. Various analytical techniques, i.e., single-crystal X-ray diffraction and NMR and UV/vis spectroscopy, were used to elucidate the sequence of the metal atoms within the heterometallic helicate, with the Zn(2+) at the central position. The formation of 3 was also achieved starting from either L3Zn3(OTf)6 or L3Fe3(OTf)6 by adding Fe(CH3CN)2(OTf)2 or Zn(OTf)2, respectively. ESI-MS and (1)H NMR studies elucidated different transmetalation mechanisms for the two cases: While a Zn(2+)-to-Fe(2+) transmetalation occurs by the stepwise exchange of single ions on the helicate L3Zn3(OTf)6 at room temperature, this mechanism is almost inoperative for the Fe(2+)-to-Zn(2+) transmetalation in L3Fe3(OTf)6, which is kinetically trapped at room temperature. In contrast, dissociation of L3Fe3(OTf)6 at higher temperature is required, followed by reassembly to give L3Fe2Zn(OTf)6. The reassembly follows an interesting mechanistic pathway when an excess of Zn(OTf)2 is present in solution: First, L3Zn3(OTf)6 forms as the high-temperature thermodynamic product, which is then slowly converted into the thermodynamic heterometallic L3Fe2Zn(OTf)6 product at room temperature. The temperature-dependent equilibrium shift is traced back to significant entropy differences resulting from an enhancement of the thermal motion of the ligands at high temperature, which destabilize the octahedral iron terminal complex and select zinc in a more stable tetrahedral geometry.