The natriuretic peptide/helokinestatin precursor from Mexican beaded lizard (Heloderma horridum) venom: Amino acid sequence deduced from cloned cDNA and identification of two novel encoded helokinestatins

Natriuretic peptides are common components of reptile venoms and molecular cloning of their biosynthetic precursors has revealed that in snakes, they co-encode bradykinin-potentiating peptides and in venomous lizards, some co-encode bradykinin inhibitory peptides such as the helokinestatins. The common natriuretic peptide/helokinestatin precursor of the Gila Monster, Heloderma suspectum, encodes five helokinestatins of differing primary structures. Here we report the molecular cloning of a natriuretic peptide/helokinestatin precursor cDNA from a venom-derived cDNA library of the Mexican beaded lizard (Heloderma horridum). Deduction of the primary structure of the encoded precursor protein from this cloned cDNA template revealed that it consisted of 196 amino acid residues encoding a single natriuretic peptide and five helokinestatins. While the natriuretic peptide was of identical primary structure to its Gila Monster (H. suspectum) homolog, the encoded helokinestatins were not, with this region of the common precursor displaying some significant differences to its H. suspectum homolog. The helokinestatin-encoding region contained a single copy of helokinestatin-1, 2 copies of helokinestatin-3 and single copies of 2 novel peptides, (Phe)(5)-helokinestatin-2 (VPPAFVPLVPR) and helokinestatin-6 (GPPFNPPPFVDYEPR). All predicted peptides were found in reverse phase HPLC fractions of the same venom. Synthetic replicates of both novel helokinestatins were found to antagonize the relaxing effect of bradykinin on rat tail artery smooth muscle. Thus lizard venom continues to provide a source of novel biologically active peptides. (C) 2011 Published by Elsevier Inc.

Approaches to the Implementation of the Water Framework Directive: Targeting Mitigation Measures at Critical Source Areas of Diffuse Phosphorus in Irish Catchments

The Water Framework Directive (WFD) has initiated a shift towards a targeted approach to implementation through its focus on river basin districts as management units and the natural ecological characteristics of waterbodies. Due to its role in eutrophication, phosphorus (P) has received considerable attention, resulting in a significant body of research, which now forms the evidence base for the programme of measures (POMs) adopted in WFD River Basin Management Plans (RBMP). Targeting POMs at critical sources areas (CSAs) of P could significantly improve environmental efficiency and cost effectiveness of proposed mitigation strategies. This paper summarises the progress made towards targeting mitigation measures at CSAs in Irish catchments. A review of current research highlights that knowledge related to P export at field scale is relatively comprehensive however; the availability of site-specific data and tools limits widespread identification of CSA at this scale. Increasing complexity of hydrological processes at larger scales limits accurate identification of CSA at catchment scale. Implementation of a tiered approach, using catchment scale tools in conjunction with field-by-field surveys could decrease uncertainty and provide a more practical and cost effective method of delineating CSA in a range of catchments. Despite scientific and practical uncertainties, development of a tiered CSA-based approach to assist in the development of supplementary measures would provide a means of developing catchment-specific and cost-effective programmes of measures for diffuse P. The paper presents a conceptual framework for such an approach, which would have particular relevance for the development of supplementary measures in High Status Waterbodies (HSW). The cost and resources necessary for implementation are justified based on HSWs��� value as undisturbed reference condition ecosystems.

The identification of potential alternative biomarkers of nitrofurazone abuse in animal derived food products

Semicarbazide (SEM) was considered to be a characteristic protein-bound side-chain metabolite of the banned veterinary drug nitrofurazone and used as a marker of nitrofurazone abuse. It was recently discovered that SEM can arise in food from sources other than nitrofurazone. This uncertainty over the source of SEM may be overcome if alternative markers specific to tissue-bound nitrofurazone residues can be determined. The structure of nitrofurazone metabolites in vivo and particular proteins to which they are bound are not known. These proteins with altered structure due to the presence of the drug metabolites can be considered as potential alternative biomarkers of nitrofurazone abuse. The proteins implicated in the in vivo binding of nitrofurazone were separated and identified. A crude mixture of proteins extracted from the liver of a rat treated with the drug was separated using a series of different techniques such as preparative isoelectric focusing and size exclusion HPLC. Multiple fractions were assayed by LC-MS/MS to detect the presence of SEM. The proteins containing SEM residues were identified by peptide mass mapping using trypsin digestion and MALDI-TOF. The first protein identified as containing high concentration of SEM was albumin. It was also shown that low molecular weight species within a protein mixture whose main constituent was glutathione S-transferase contained a high concentration of SEM. The chemical composition of these components is under investigation. Preliminary data suggest the SEM forms part of a nitrofurazone metabolite conjugated to glutathione. (C) 2008 Elsevier Ltd. All rights reserved.

Identification of low inorganic and total grain arsenic rice cultivars from Bangladesh

For the world's population, rice consumption is a major source of inorganic arsenic (As), a nonthreshold class 1 carcinogen. Reducing the amount of total and inorganic As within the rice grain would reduce the exposure risk. In this study, grain As was measured in 76 cultivars consisting of Bangladeshi landraces, improved Bangladesh Rice Research Institute (BRRI) cultivars, and parents of permanent mapping populations grown in two field sites in Bangladesh, Faridpur and Sonargaon, irrigated with As-contaminated tubewell water. Grain As ranged from 0.16 to 0.74 mg kg(-1) at Faridpur and from 0.07 to 0.28 mg kg(-1) at Sonargaon. Highly significant cultivar differences were detected and a significant correlation (r = 0.802) in the grain As between the two field sites was observed, indicating stable genetic differences in As accumulation. The cultivars with the highest concentration of grain As were the Bangladeshi landraces. Landraces with red bran had significantly more grain As than the cultivars with brown bran. The percent of inorganic As decreased linearly with increasing total As, but genetic variation within this trend was identified. A number of local cultivars with low grain As were identified. Some tropical japonica cultivars with low grain As have the potential to be used in breeding programs and genetic studies aiming to identify genes which decrease grain As.

Identification of genetically and oceanographically distinct blooms of jellyfish

Reports of nuisance jellyfish blooms have increased worldwide during the last half-century, but the possible causes remain unclear.Apersistent difficulty lies in identifying whether blooms occur owing to local or regional processes. This issue can be resolved, in part, by establishing the geographical scales of connectivity among locations, which may be addressed using genetic analyses and oceanographic modelling. We used landscape genetics and Lagrangian modelling of oceanographic dispersal to explore patterns of connectivity in the scyphozoan jellyfish Rhizostoma octopus, which occurs en masse at locations in the Irish Sea and northeastern Atlantic. We found significant genetic structure distinguishing three populations, with both consistencies and inconsistencies with prevailing physical oceanographic patterns. Our analyses identify locations where blooms occur in apparently geographically isolated populations, locations where blooms may be the source or result of migrants, and a location where blooms do not occur consistently and jellyfish are mostly immigrant. Our interdisciplinary approach thus provides a means to ascertain the geographical origins of jellyfish in outbreaks, which may have wide utility as increased international efforts investigate jellyfish blooms. �� 2013 The Authors.

Predicting critical source areas of sediment in headwater catchments

Mitigation of diffuse nutrient and sediment delivery to streams requires successful identification andmanagement of critical source areas within catchments. Approaches to predicting high risk areas forsediment loss have typically relied on structural drivers of connectivity and risk, with little considera-tion given to process driven water quality responses. To assess the applicability of structural metrics topredict critical source areas, geochemical tracing of land use sources was conducted in three headwateragricultural catchments in Co. Down and Co. Louth, Ireland, within a Monte Carlo framework. Outputswere applied to the inverse optimisation of a connectivity model, based on LiDAR DEM data, to assess theefficacy of land use risk weightings to predict sediment source contributions over the 18 month studyperiod in the Louth Upper, Louth Lower and Down catchments. Results of the study indicated sedimentproportions over the study period varied from 6 to 10%, 84 to 87%, 4%, and 2 to 3% for the Down Catch-ment, 79 to 85%, 9 to 17%, 1 to 3% and 2 to 3% in the Louth Upper and 2 to 3%, 79 to 85%, 10 to 17%and 2 to 3% in the Louth Lower for arable, channel bank, grassland, and woodland sources, respectively.Optimised land use risk weightings for each sampling period showed that at the larger catchment scale,no variation in median land use weightings were required to predict land use contributions. However,for the two smaller study catchments, variation in median risk weightings was considerable, which mayindicate the importance of functional connectivity processes at this spatial scale. In all instances, arableland consistently generated the highest risk of sediment loss across all catchments and sampling times.This study documents some of the first data on sediment provenance in Ireland and indicates the needfor cautious consideration of land use as a tool to predict critical source areas at the headwater scale

Identification and Functional Analysis of a Novel Tryptophyllin Peptide from the Skin of the Red-eye Leaf Frog, Agalychnis callidryas

Amphibian skin has proved repeatedly to be a largely untapped source of bioactive peptides and this is especially true of members of the Phyllomedusinae subfamily of frogs native to South and Central America. Tryptophyllins are a group of peptides mainly found in the skin of members of this genus. In this study, a novel tryptophyllin (TPH) type 3 peptide, named AcT-3, has been isolated and structurally-characterised from the skin secretion and lyophilised skin extract of the red-eye leaf frog, Agalychnis callidryas. The peptide was identified in and purified from the skin secretion by reverse-phase HPLC. MALDI-TOF mass spectrometry and MS/MS fragmentation sequencing established its primary structure as: pGlu-Gly-Lys-Pro-Tyr-Trp-Pro-Pro-Pro-Phe-Leu-Pro-Glu, with a non-protonated molecular mass of 1538.19Da. The mature peptide possessed the canonical N-terminal pGlu residue that arises from post-translational modification of a Gln residue. The deduced open-reading frame consisted of 63 amino acid residues encoding a highly-conserved signal peptide of approximately 22 amino acid residues, an intervening acidic spacer peptide domain, a single AcT-3 encoding domain and a C terminal processing site. A synthetic replicate of AcT-3 was found to antagonise the effect of BK on rat tail artery smooth muscle and to contract the intestinal smooth muscle preparations. It was also found that AcT-3 could dose-dependently inhibit the proliferation of human prostate cancer cell lines after 72h incubation.

Musicologist-driven writer identification in early music manuscripts

Recent renewed interest in computational writer identification has resulted in an increased number of publications. In relation to historical musicology its application has so far been limited. One of the obstacles seems to be that the clarity of the images from the scans available for computational analysis is often not sufficient. In this paper, the use of the Hinge feature is proposed to avoid segmentation and staff-line removal for effective feature extraction from low quality scans. The use of an auto encoder in Hinge feature space is suggested as an alternative to staff-line removal by image processing, and their performance is compared. The result of the experiment shows an accuracy of 87 % for the dataset containing 84 writers��� samples, and superiority of our segmentation and staff-line removal free approach. Practical analysis on Bach���s autograph manuscript of the Well-Tempered Clavier II (Additional MS. 35021 in the British Library, London) is also presented and the extensive applicability of our approach is demonstrated.

Material Identification of Loose Particles in Sealed Electronic Devices Using PCA and SVM

The existence of loose particles left inside the sealed electronic devices is one of the main factors affecting the reliability of the whole system. It is important to identify the particle material for analyzing their source. The conventional material identification algorithms mainly rely on time, frequency and wavelet domain features. However, these features are usually overlapped and redundant, resulting in unsatisfactory material identification accuracy. The main objective of this paper is to improve the accuracy of material identification. First, the principal component analysis (PCA) is employed to reselect the nine features extracted from time and frequency domains, leading to six less correlated principal components. And then the reselected principal components are used for material identification using a support vector machine (SVM). Finally, the experimental results show that this new method can effectively distinguish the type of materials including wire, aluminum and tin particles.

Recurrent Convolutional Network for Video-based Person Re-Identification

In this paper we propose a novel recurrent neural networkarchitecture for video-based person re-identification.Given the video sequence of a person, features are extracted from each frame using a convolutional neural network that incorporates a recurrent final layer, which allows information to flow between time-steps. The features from all time steps are then combined using temporal pooling to give an overall appearance feature for the complete sequence. The convolutional network, recurrent layer, and temporal pooling layer, are jointly trained to act as a feature extractor for video-based re-identification using a Siamese network architecture.Our approach makes use of colour and optical flow information in order to capture appearance and motion information which is useful for video re-identification. Experiments are conduced on the iLIDS-VID and PRID-2011 datasets to show that this approach outperforms existing methods of video-based re-identification.<br/><br/>https://github.com/niallmcl/Recurrent-Convolutional-Video-ReID<br/>Project Source Code

Role of Automated Open Source Systems in the Intelligence Analysis of a High-Level Domain Expert

Brewer's spent grain from different types of malt: Evaluation of the antioxidant activity and identification of the major phenolic compounds

The antioxidant activity and phenolic composition of brewer's spent grain (BSG) extracts obtained by microwave-assisted extraction from twomalt types (light and darkmalts) were investigated. The total phenolic content (TPC) and antioxidant activity among the light BSG extracts (pilsen, melano, melano 80 and carared)were significantly different (p b 0.05) compared to dark extracts (chocolate and black types), with the pilsen BSG showing higher TPC (20 �� 1 mgGAE/g dry BSG). In addition, the antioxidant activity assessed by 2,2-diphenyl- 1-picrylhydrazyl, 2,2���-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) and deoxyribose assays decreased as a result of increasing kilning temperatures in the following order: pilsen N melano N melano 80 N carared N chocolate N black. HPLC-DAD/ESI-MS/MS analysis indicated the presence of phenolic acids, such as ferulic, p-coumaric and syringic acids, as well as several isomeric ferulate dehydrodimers and one dehydrotrimer. Chocolate and black extracts, obtained frommalts submitted to the highest kilning temperatures, showed the lowest levels of ferulic and p-coumaric acids. These results suggested that BSG extracts from pilsen malt might be used as an inexpensive and good natural source of antioxidants with potential interest for the food, pharmaceutical and/or cosmetic industries after purification.

Disease identification based on ambulatory drugs dispensation and in-hospital ICD-10 diagnoses: a comparison.

BACKGROUND: Pharmacy-based case mix measures are an alternative source of information to the relatively scarce outpatient diagnoses data. But most published tools use national drug nomenclatures and offer no head-to-head comparisons between drugs-related and diagnoses-based categories. The objective of the study was to test the accuracy of drugs-based morbidity groups derived from the World Health Organization Anatomical Therapeutic Chemical Classification of drugs by checking them against diagnoses-based groups. METHODS: We compared drugs-based categories with their diagnoses-based analogues using anonymous data on 108,915 individuals insured with one of four companies. They were followed throughout 2005 and 2006 and hospitalized at least once during this period. The agreement between the two approaches was measured by weighted kappa coefficients. The reproducibility of the drugs-based morbidity measure over the 2��years was assessed for all enrollees. RESULTS: Eighty percent used a drug associated with at least one of the 60 morbidity categories derived from drugs dispensation. After accounting for inpatient under-coding, fifteen conditions agreed sufficiently with their diagnoses-based counterparts to be considered alternative strategies to diagnoses. In addition, they exhibited good reproducibility and allowed prevalence estimates in accordance with national estimates. For 22 conditions, drugs-based information identified accurately a subset of the population defined by diagnoses. CONCLUSIONS: Most categories provide insurers with health status information that could be exploited for healthcare expenditure prediction or ambulatory cost control, especially when ambulatory diagnoses are not available. However, due to insufficient concordance with their diagnoses-based analogues, their use for morbidity indicators is limited.

Identification of pyridine analogs as new predator-derived kairomones.

In the wild, animals have developed survival strategies relying on their senses. The individual ability to identify threatening situations is crucial and leads to increase in the overall fitness of the species. Rodents, for example have developed in their nasal cavities specialized olfactory neurons implicated in the detection of volatile cues encoding for impending danger such as predator scents or alarm pheromones. In particular, the neurons of the Grueneberg ganglion (GG), an olfactory subsystem, are implicated in the detection of danger cues sharing a similar chemical signature, a heterocyclic sulfur- or nitrogen-containing motif. Here we used a "from the wild to the lab" approach to identify new molecules that are involuntarily emitted by predators and that initiate fear-related responses in the recipient animal, the putative prey. We collected urines from carnivores as sources of predator scents and first verified their impact on the blood pressure of the mice. With this approach, the urine of the mountain lion emerged as the most potent source of chemical stress. We then identified in this biological fluid, new volatile cues with characteristic GG-related fingerprints, in particular the methylated pyridine structures, 2,4-lutidine and its analogs. We finally verified their encoded danger quality and demonstrated their ability to mimic the effects of the predator urine on GG neurons, on mice blood pressure and in behavioral experiments. In summary, we were able to identify here, with the use of an integrative approach, new relevant molecules, the pyridine analogs, implicated in interspecies danger communication.

The identification and characterization of inter- and intra-species genetic diversity derived from retrotransposons in humans

Retrotransposons, which used to be considered as ���junk DNA���, have begun to reveal their immense value to genome evolution and human biology due to recent studies. They consist of at least ~45% of the human genome and are more or less the same in other mammalian genomes. Retrotransposon elements (REs) are known to affect the human genome through many different mechanisms, such as generating insertion mutations, genomic instability, and alteration in gene expression. Previous studies have suggested several RE subfamilies, such as Alu, L1, SVA and LTR, are currently active in the human genome, and they are an important source of genetic diversity between human and other primates, as well as among humans. Although several groups had used Retrotransposon Insertion Polymorphisms (RIPs) as markers in studying primate evolutionary history, no study specifically focused on identifying Human-Specific Retrotransposon Element (HS-RE) and their roles in human genome evolution. In this study, by computationally comparing the human genome to 4 primate genomes, we identified a total of 18,860 HS-REs, among which are 11,664 Alus, 4,887 L1s, 1,526 SVAs and 783 LTRs (222 full length entries), representing the largest and most comprehensive list of HS-REs generated to date. Together, these HS-REs contributed a total of 14.2Mb sequence increase from the inserted REs and Target Site Duplications (TSDs), 71.6Kb increase from transductions, and 268.2 Kb sequence deletion of from insertion-mediated deletion, leading to a net increase of ~14 Mb sequences to the human genome. Furthermore, we observed for the first time that Y chromosome might be a hot target for new retrotransposon insertions in general and particularly for LTRs. The data also allowed for the first time the survey of frequency of TE insertions inside other TEs in comparison with TE insertion into none-TE regions. In summary, our data suggest that retrotransposon elements have played a significant role in the evolution of Homo sapiens.