Bayesian adaptation and adaptively trained systems

As the use of found data increases, more systems are being built using adaptive training. Here transforms are used to represent unwanted acoustic variability, e.g. speaker and acoustic environment changes, allowing a canonical model that models only the "pure" variability of speech to be trained. Adaptive training may be described within a Bayesian framework. By using complexity control approaches to ensure robust parameter estimates, the standard point estimate adaptive training can be justified within this Bayesian framework. However during recognition there is usually no control over the amount of data available. It is therefore preferable to be able to use a full Bayesian approach to applying transforms during recognition rather than the standard point estimates. This paper discusses various approximations to Bayesian approaches including a new variational Bayes approximation. The application of these approaches to state-of-the-art adaptively trained systems using both CAT and MLLR transforms is then described and evaluated on a large vocabulary speech recognition task. © 2005 IEEE.

Trade of live brooders of the black tiger shrimp, Penaeus Monodon Fabricius 1978, at Visakhapatnam, Andhra Pradesh

The demand for brooders of Penaeus monodon by the hatcheries, which are solely dependant on wild brooders for their seed production, has resulted in a vigorous fishery and trade for this species, especially along the Visakhapatnam coast. More than three hundred brooders are brought in per day for trading during the peak landing season from December to March every year. The price of gravid brooders has been declining over the years but on an average is about Rs. 30,000 per brooder. The total length of male brooders ranged from 190 to 246 mm during the three years under study and for females it varied between 210 and 330 mm. A specialized methodology for transportation, storage and trade of P. monodon brooders has been evolved over the years at Visakhapatnam Fishing Harbour. Concentrated exploitation of brooders from the wild and presence of pathogens in them makes a strong case for development of specific pathogen free brooders and conservation of wild stock.

Origination and evolution of a human-specific transmembrane protein gene, c1orf37-dup

A transmembrane protein gene, c1orf37-dup, was identified as a young gene specific to humans. It was derived from the conserved c1orf37 gene through retroposition after the divergence of human and chimpanzee. This gene has evolved rapidly driven by positi

Project neptune: Improved operation of water distribution networks

Water service providers (WSPs) in the UK have statutory obligations to supply drinking water to all customers that complies with increasingly stringent water quality regulations and minimum flow and pressure criteria. At the same time, the industry is required by regulators and investors to demonstrate increasing operational efficiency and to meet a wide range of performance criteria that are expected to improve year-on-year. Most WSPs have an ideal for improving the operation of their water supply systems based on increased knowledge and understanding of their assets and a shift to proactive management followed by steadily increasing degrees of system monitoring, automation and optimisation. The fundamental mission is, however, to ensure security of supply, with no interruptions and water quality of the highest standard at the tap. Unfortunately, advanced technologies required to fully understand, manage and automate water supply system operation either do not yet exist, are only partially evolved, or have not yet been reliably proven for live water distribution systems. It is this deficiency that the project NEPTUNE seeks to address by carrying out research into 3 main areas; these are: data and knowledge management; pressure management (including energy management); and the associated complex decision support systems on which to base interventions. The 3-year project started in April of 2007 and has already resulted in a number of research findings under the three main research priority areas (RPA). The paper summarises in greater detail the overall project objectives, the RPA activities and the areas of research innovation that are being undertaken in this major, UK collaborative study. Copyright 2009 ASCE.

VISUALIZATION OF THE CHROMOSOME SCAFFOLD IN A PRIMITIVE EUKARYOTE DINOFLAGELLATE CRYPTHECOAINIUM-COHNII

The chromosome scaffolds in higher eukaryotic nuclei have been described elsewhere. But it is unknown when they evolved. The dinoflagellates are the primitive organisms that may be the intermediate between prokaryotes and eukaryotes. Combining chromosome scaffold preparation methods with embedment-free section microscopy, we demonstrate that the dinoflagellate Crypthecodinium cohnii chromosome retains a protein scaffold after the depletion of DNA and soluble proteins. This scaffold preserves the morphology characteristic of the chromosome. Two-dimensional electrophoreses show that the chromosome scaffolds are mainly composed of acidic proteins. Our results suggest that a framework similar to the chromosome scaffold in the mammalian cell appeared in the primitive eukaryote. We propose that the chromosome scaffold possibly originated from the early stages of eukaryote evolution.

Perspectives on the origin of microfilaments, microtubules, the relevant chaperonin system and cytoskeletal motors - a commentary on the spirochaete origin of flagella

The origin of cytoskeleton and the origin of relevant intracellular transportation system are big problems for understanding the emergence of eukaryotic cells. The present article summarized relevant information of evidences and molecular traces on the origin of actin, tubulin, the chaperonin system for folding them, myosins, kinesins, axonemal dyneins and cytoplasmic dyneins. On this basis the authors proposed a series of works, which should be done in the future, and indicated the ways for reaching the targets. These targets are mainly: 1) the reconstruction of evolutionary path from MreB protein of archaeal ancestor of eukaryotic cells to typical actin; 2) the finding of the MreB or MreB-related proteins in crenarchaea and using them to examine J. A. Lake's hypothesis on the origin of eukaryote from "eocytes" (crenarchaea); 3) the examinations of the existence and distribution of cytoskeleton made of MreB-related protein within coccoid archaea, especially in amoeboid archaeon Thermoplasm acidophilum; 4) using Thermoplasma as a model of archaeal ancestor of eukaryotic cells; 5) the searching for the homolog of ancestral dynein in present-day living archaea. During the writing of this article, Margulis' famous spirochaete hypothesis on the origin of flagella and cilia was unexpectedly involved and analyzed from aspects of tubulins, dyneins and spirochaetes. Actually, spirochaete cannot be reasonably assumed as the ectosymbiotic ancestor of eukaryotic flagella and cilia, since their swing depends upon large amount of bacterial flagella beneath the flexible outer wall, but not depends upon their intracellular tubules and the assumed dyneins. In this case, if they had "evolved" into cilia and lost their bacterial flagella, they would immediately become immobile! In fact, tubulin and dynein-like proteins have not been found in any spirochaete.

New symbiotic hypothesis on the origin of eukaryotic flagella

The origin of eukaryotic flagella has long been a mystery. Here we review the possibility that flagella sprouted evolutionarily from the eukaryotic cell proper seems very unlikely because it is hard to imagine what function and benefit in natural selection the flagella would have provided to the cells when they first emerged as simple buds. Lynn Margulis' 1970 spirochete hypothesis, though popular still, has never been confirmed. Moreover, the absence of tubulin and axonemal dynein in the spirochetes and the incapability of the bacterial and eukaryotic membranes' making a continuum now suggest that the hypothesis is outdated. Tubulin genes were recently identified in a new bacteria division, verrucomicrobia, and microtubules have also been found in one of these species, epixenosomes, the defensive ectosymbionts. On the basis of these data, we propose a new symbiotic hypothesis: that the mid-ancestor of eukaryotic cells obtained epixenosomelike verrucomicrobia as defensive ectosymbionts and the ectosymbionts later became endosymbiotic. They still, however, protruded from the surface of their host to play their role. Later, many genes were lost or incorporated into the host genome. Finally, the genome, the bacterial membrane, and the endosymbiotic vesicle membrane were totally lost, and fingerlike protrusions with microtubules formed. As the cells grew larger, the defensive function of the protrusions eventually weakened and then vanished. Some of the protrusions took on a new role in cell movement, which led them to evolve into flagella. The key step in this process was that the dynein obtained from the host evolved into axonemal dyneins, attaching onto the microtubules and forming motile axonemes. Our hypothesis is unproven, but it offers a possible explanation that is consistent with current scientific thought. We hope that our ideas will stimulate additional studies on the origin of eukaryotic flagella and on investigations of verrucomicrobia. Whether such studies confirm, refine, or replace our hypothesis, they should nevertheless further our understanding of the origin of eukaryotic cells.

Antihemostatic molecules from saliva of blood-feeding arthropods

The ability to feed on vertebrate blood has evolved many times in various arthropod clades. Consequently, saliva of blood-feeding arthropods has proven to be a rich source of antihemostatic molecules. A variety of platelet aggregation inhibitors antagonize platelet responses to wound-generated signals, including ADP, thrombin, and collagen. Anticoagulants disrupt elements of both the intrinsic and extrinsic pathways. Vasodilators include nitrophorins (nitric oxide storage and transport heme proteins), a variety of peptides that mimic endogenous vasodilatory neuropeptides, and proteins that catabolize or sequester endogenous vasoconstrictors. Multiple salivary proteins may be directed against each component of hemostasis, resulting in both redundancy and in some cases cooperative interactions between antihemostatic proteins. The complexity and redundancy of saliva ensures an efficient blood meal for the arthropod, but it also provides a diverse array of novel antihemostatic molecules for the pharmacologist.

Speaker and noise factorisation on the AURORA4 task

For many realistic scenarios, there are multiple factors that affect the clean speech signal. In this work approaches to handling two such factors, speaker and background noise differences, simultaneously are described. A new adaptation scheme is proposed. Here the acoustic models are first adapted to the target speaker via an MLLR transform. This is followed by adaptation to the target noise environment via model-based vector Taylor series (VTS) compensation. These speaker and noise transforms are jointly estimated, using maximum likelihood. Experiments on the AURORA4 task demonstrate that this adaptation scheme provides improved performance over VTS-based noise adaptation. In addition, this framework enables the speech and noise to be factorised, allowing the speaker transform estimated in one noise condition to be successfully used in a different noise condition. © 2011 IEEE.

Shifting rice farming to fish culture in some selected areas of Mymensingh, Bangladesh: the process, conflicts and impacts

The evolutionary process of converting low-lying paddy fields into fish farms and its impact on agrarian communities in some selected areas of Mymensingh district were studied. This study was conducted through participatory rural appraisal (PRA) covering 12 villages from each of selected upazillas viz. Fulpur and Haluaghat of Mymensing [sic] district. A total of 12 PRA sessions were conducted where 90 farmers participated during 29 July to 26 August 2004. It is seen that the use of low-lying paddy fields was mostly confined to Broadcast Aman (B. Aman) rice production until 1960s. With the introduction of modern rice farming technology, the farmers started to produce Boro rice in Rabi season and B. Aman rice in Kharif season. With the passage of time, aquaculture technologies have been evolved and the farmers realized that fish farming is more profitable than rice cultivation, and then they started to utilize their paddy fields for alternate rice-fish farming and rice-cum-fish farming. Now a days, aquaculture based crop production system is in practice in more than 25% of the low-lying paddy fields. Conversion of rice fields in to fish ponds has brought up a change in the livelihood patterns of the rural farmers. The areas where the farmers involved themselves in the new production systems were fingerling collection, transportation and marketing of fry and fingerlings. During 1960s to 1970s, a few people used to culture fish in the permanent ponds for their own consumption, the species produced were rohu, catla, mrigal, ghainna, long whiskered catfish, freshwater shark (boal), snake head (shol) etc. Small fishes like climbing perch, stinging catfish, walking catfish, barb, minnows etc. were available in the rice fields during monsoon season. In 1980s to mid 1990s, some rice fields were converted into fish ponds and the people started to produce fish for commercial purposes. When rice-fish farming became profitable, a large number of people started converting their rice fields in to rice-fish culture ponds. Culture of some exotic fishes like silver carp, tilapia, grass carp, silver barb etc. also started in the paddy fields. Higher income from fish farming contributed positively in improving the housing, sanitation and education system in the study areas. It is seen that the medium and medium high lands were only used for alternate rice fish farming. The net income was high in any fish based cropping system that motivated the farmers to introduce fish based cropping system in the low-lying inland areas. As a result, the regional as well as communal income disparities occurred. However, the extraction of ground water became common during the dry period as the water was used for both rice and fish farming. Mass conversion of paddy fields into rice-fish culture ponds caused water logging in the study areas. In most cases, the participated farmers mentioned that they could be easily benefited by producing fish with T. Aman or only fish during the monsoon season. They agreed that this was an impressive technology to them and they could generate employment opportunities throughout the year. Finally, the social, economic and technical problems which are acting as constraints to rapid expansion of fish production system were reported from the interviewee.

FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition

The nuclear RNA binding protein, FCA, promotes Arabidopsis reproductive development. FCA contains a WW protein interaction domain that is essential for FCA function. We have identified FY as a protein partner for this domain. FY belongs to a highly conserved group of eukaryotic proteins represented in Saccharomyces cerevisiae by the RNA 3' end-processing factor, Pfs2p. FY regulates RNA 3' end processing in Arabidopsis as evidenced through its role in FCA regulation. FCA expression is autoregulated through the use of different polyadenylation sites within the FCA pre-mRNA, and the FCA/FY interaction is required for efficient selection of the promoter-proximal polyadenylation site. The FCA/FY interaction is also required for the downregulation of the floral repressor FLC. We propose that FCA controls 3' end formation of specific transcripts and that in higher eukaryotes, proteins homologous to FY may have evolved as sites of association for regulators of RNA 3' end processing.

Demonstration of some selected aquaculture technologies under farming system research in Jessore and Santahar, Bangladesh

BFRI evolved some selected aquaculture technologies viz. polyculture of carps in perennial ponds, monoculture of short cycled fish species (BFRI super strain) in seasonal ponds and prawn seed production through backyard hatchery system have been demonstrated under Farming System Research (FSR) component in Jessore and Santahar regions. Both polyculture of carps and monoculture of short cycled fish species technologies were tested in farmer's ponds in Kaium Kula village near Jessore town. In polyculture trials, seven species comprising of silver carp (Hypophthalmichthys molirrix), catla (Catla catla), rohu (Labeo rohita), grass carp (Ctenopharyngodon idellus), common carp (Cyprinus carpio), mrigal (Cirrhinus cirrhosus) and silver barb (Barbonymus gonionotus) were stocked @ 9,500 (ratio 6:2:4:2:1:5:5); 10,750 (ratio 6:2:4:2:1:5:5) and 12,000 (ratio 6:2:4:2:1:5:4) fish/ha respectively in ponds of T1, T2 and T3 having three replications of each. The mean highest fish production was 3,148 kg/ha in T3, followed by 2,899 kg/ha in T1 and 2,875 kg/ha in T2. Production of T3 was significantly different (P<0.05) than both T1 and T2, while there was no significant differences (P>0.05) between the production of T1 and T2. In case of trial of short cycled fish species, two treatments were tested: T1 (comprising of BFRI super strain of Nile tilapia, silver carp, common carp and silver barb; ratio 3:5:1:1) and T2 (having only BFRI super strain of Nile tilapia). Stocking density in both the treatments were same (20,000 fish/ha). In this trial average production was higher in T1 (2,743 kg/ha) than that of T2 (2,369 kg/ha) but the production figure in these two treatments was not significantly different (P>0.05). Demonstration of backyard prawn hatchery technology was tested at Santahar region of Bogra district, North-west part of Bangladesh. This hatchery consisted of three main components i) bio-filter, ii) rearing tank unit (chari) and iii) air blower/air pump unit. Plastic drum of 200-250 l capacity and cemented chari of 200-250 l capacity were used as bio-filter and larval rearing containers respectively. A 0.5 hp air blower with 6 aquarium air pump were used to operate the aeration system in the hatchery. Diluted sea water (10-12 ppt) made from brine solution (200-250 ppt) collected from salt-bed was used in the backyard hatchery system of hatching of eggs and rearing of larvae. Rearing of first stage zoea-larvae was reared in three rearing tanks following the stocking densities of 40, 50 and 60/l of water respectively. Production of post-larvae were 20±0.82, 22±1.12 and 28±1.63/liter of water in treatments I, II and III respectively in 38, 40 and 39 days rearing period.

Mitochondrial cytochrome b sequences variation of Protura and molecular systematics of Apterygota

Mitochondrial cytochrome b genes of about 450 bp fragments from 3 proturan species, 5 collembolan species and 2 dipluran species have been sequenced. The number of nucleotide substitutions and Kimura 2-parameter distances have also been calculated, and a series of molecular phylogenetic trees reconstructed by using parsimony and distance methods. The proturan, collembolan and dipluran species have evolved monophyletic groups. The results suggest that Protura and Collembola are sister groups, while Diplura is more or less demonstrating a closer phylogenetic relationship to the pterygotan insects. The phylogeny and their systematic position of protura and other groups are also discussed.

Structure analysis of CCR5 from human and primates

It is well known that the chemokine receptor CCR5 plays very important roles in HIV-1 virus infection. A three-dimensional molecular model of human CCR5 was generated by SYBYL, a distance geometry-based homologous modeling package, using the corresponding transmembrane domain of bacteriorhodopsin as the template. On the basis of human CCR5 model, we also built 18 3D molecular models of CCR5 in primates from Pongo pygmaeus, Pygathrix nemaeus, Macaca assameniss, Trachy-pithecus phayrei, T. francoisi, M. arotoides, Rhinopithecus roxellance, R, bieti, R. avunculus, Hylobates leucogenys, Pan troglodytes, Gorilla gorilla, Cercopithecus aethiops 1, C. aethiops 2, Papio hamadryas M. mulatta, M. fascicularis and M. nemestrina. Structural analyses and statistics results suggested that the main-chains of the primate CCR5 were similar to that of the human CCR5 and that the fit-RMS deviation values of these primate CCR5 were less than 0.1 Angstrom. Moreover, the structures of these CCR5 proteins, except those of the African green monkey 1 (C.aet1), do not have a remarkable difference. It is proved that the 14th residue is possibly very important in the inhibition infections by M-tropic HIV-1, and it is also demonstrated that the 13th residue of human CCR5 was changed from asparagine into aspartic acid in all these primates. It means that the primate CCR5 no longer depend on CD4 for efficient entry, but human CCR5 may have evolved subsequently due to the use of CD4 as a receptor, allowing the high-affinity chemokine receptor-binding site of HIV to be sequestered from host immune surveillance. (C) 2000 Elsevier Science B.V. All rights reserved.

Comparative efficiency of trawls made of nylon, polyethylene monofilament and tape twines

Results of comparative fishing operations conducted with three nets of identical design made of nylon, twisted polyethylene monofilament and high density polyethylene (HDPE) tape twines are presented in this communication. Since the tape net recorded the highest prawn and fish catch, monofilament and nylon following in order, it can be recommended to the fishing industry as one of the cheapest and effective fishing materials evolved for trawl fabrication.