cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.825552.v1
title: An siRNA designing tool with a unique functional off-target filtering approach

description: Investigations have revealed that silencing unwanted transcripts or off-targeting can induce false positive phenotype during RNA interference (RNAi)-based gene function study. But still the standard computational approaches towards small interfering RNA (siRNA) off-target minimization fall short in terms of addressing this false positive phenotype issue. Some of these off-targets may interfere with the biochemical pathway being investigated. It may also inadvertently target cell’s metabolic pathways with unquantifiable consequences on the processes of user’s interest. Here, we report the development of a siRNA selection tool that, for the first time, implements a functional off-target filtering that aims to minimize false positive phenotypes arising from inadvertent targets that are functionally similar or related to the direct target gene, along with a multi-parametric classifier (support vector machine) for optimized selection of potent siRNAs. The functional off-target filtering minimizes the number of off-target genes which are functionally related to the direct target gene, i.e. involved in a common biological process and may have similar phenotype. A text-mining algorithm is used to find related biological processes associated with the direct target and each off-target transcript by comparison of the biological processes associated with these genes. It also gives the user a choice to select one or more off-targets that may be potentially more harmful, from a predicted off-target gene list to be filtered out. Testing with huge set of biologically validated siRNAs from three different sources showed consistent good performance of our tool in terms of effective siRNA selection. It outperformed four potent siRNA selection algorithms of present day in terms of specificity in the selection of highly efficient siRNAs when compared on a common test set. A genome wide testing with potent siRNAs used in high-content screening confirmed validation of 2767 designed siRNAs in terms of phenotypic output. This tool presently supports siRNA designs for human genes and is freely available at http://gyanxet-beta.com.
DOI: 10.6084/m9.figshare.825547
title: The GABAergic-like system in the cyprid of <i>Balanus amphitrite (=Amphibalanus amphitrite)</i> (Cirripedia, Crustacea)

description: In the present study, biochemical and immunochemical methods were used to investigate the presence and distribution of GABA, glutamate decarboxylase (GAD), GABA<sub>B</sub>R1 and GABA<sub>A</sub> γ2 subunit receptors and the vesicular GABA transporter (vGAT) in the cyprid of <i>Balanus amphitrite (=Amphibalanus amphitrite)</i>. GAD<sub>65/67</sub> immunoreactive neuron cell bodies and nerve fibers were detected in the central nervous system. Paired GAD<sub>65/67</sub> immunoreactive nerves running from the posterior ganglion to the body and limb muscles were detected. Thin GABA-immunoreactive nerve terminals were present on striated muscular fibers and in the antennules. Furthermore, GABA, GAD<sub>65/67</sub>, GABA<sub>B</sub>R1 and GABA<sub>A</sub>γ2 subunit receptors and vGAT were observed in the lateral compound eyes, and GABA<sub>A</sub>γ2 subunit receptor immunoreactivity was seen in the naupliar eye. These results suggest a neurotransmitter/neuromodulatory role for GABA in thoracic muscle contraction and regulatory functions in compound eyes and antennules of <i>B. amphitrite</i> cyprids.
DOI: 10.6084/m9.figshare.825548
title: Using enzymes to remove biofilms of bacterial isolates sampled in the food-industry

description: The aim of this study was to analyze the cleaning efficiency of polysaccharidases and proteolytic enzymes against biofilms of bacterial species found in food industry processing lines and to study enzyme effects on the composition of extracellular polymeric substances (EPS) and biofilm removal in a Clean-in-Place (CIP) procedure. The screening of 7 proteases and polysaccharidases for removal of biofilms of 16 bacterial species was first evaluated using a microtiter plate assay. The alkaline pH buffer removed more biofilm biomass as well as affecting a larger range of bacterial species. The two serine proteases and α-amylase were the most efficient enzymes. Proteolytic enzymes promoted biofilm removal of a larger range of bacterial species than polysaccharidases. Using three isolates derived from two bacterial species widely found in food processing lines (<i>Pseudomonas fluorescens</i> and the <i>Bacillus cereus</i> group), biofilms were developed on stainless steel slides and enzymatic solutions were used to remove the biofilms using CIP procedure. Serine proteases were more efficient in removing cells of <i>Bacillus</i> biofilms than polysaccharidases. However, polysaccharidases were more efficient in removing <i>P. fluorescens</i> biofilms than serine proteases. Solubilization of enzymes with a buffer containing surfactants, and dispersing and chelating agents enhanced the efficiency of polysaccharidases and proteases respectively in removing biofilms of <i>Bacillus</i> and <i>P. fluorescens</i>. A combination of enzymes targeting several components of EPS, surfactants, dispersing and chelating agents would be an efficient alternative to chemical cleaning agents.
DOI: 10.6084/m9.figshare.825547.v1
title: The GABAergic-like system in the cyprid of <i>Balanus amphitrite (=Amphibalanus amphitrite)</i> (Cirripedia, Crustacea)

description: In the present study, biochemical and immunochemical methods were used to investigate the presence and distribution of GABA, glutamate decarboxylase (GAD), GABA<sub>B</sub>R1 and GABA<sub>A</sub> γ2 subunit receptors and the vesicular GABA transporter (vGAT) in the cyprid of <i>Balanus amphitrite (=Amphibalanus amphitrite)</i>. GAD<sub>65/67</sub> immunoreactive neuron cell bodies and nerve fibers were detected in the central nervous system. Paired GAD<sub>65/67</sub> immunoreactive nerves running from the posterior ganglion to the body and limb muscles were detected. Thin GABA-immunoreactive nerve terminals were present on striated muscular fibers and in the antennules. Furthermore, GABA, GAD<sub>65/67</sub>, GABA<sub>B</sub>R1 and GABA<sub>A</sub>γ2 subunit receptors and vGAT were observed in the lateral compound eyes, and GABA<sub>A</sub>γ2 subunit receptor immunoreactivity was seen in the naupliar eye. These results suggest a neurotransmitter/neuromodulatory role for GABA in thoracic muscle contraction and regulatory functions in compound eyes and antennules of <i>B. amphitrite</i> cyprids.
DOI: 10.6084/m9.figshare.825548.v1
title: Using enzymes to remove biofilms of bacterial isolates sampled in the food-industry

description: The aim of this study was to analyze the cleaning efficiency of polysaccharidases and proteolytic enzymes against biofilms of bacterial species found in food industry processing lines and to study enzyme effects on the composition of extracellular polymeric substances (EPS) and biofilm removal in a Clean-in-Place (CIP) procedure. The screening of 7 proteases and polysaccharidases for removal of biofilms of 16 bacterial species was first evaluated using a microtiter plate assay. The alkaline pH buffer removed more biofilm biomass as well as affecting a larger range of bacterial species. The two serine proteases and α-amylase were the most efficient enzymes. Proteolytic enzymes promoted biofilm removal of a larger range of bacterial species than polysaccharidases. Using three isolates derived from two bacterial species widely found in food processing lines (<i>Pseudomonas fluorescens</i> and the <i>Bacillus cereus</i> group), biofilms were developed on stainless steel slides and enzymatic solutions were used to remove the biofilms using CIP procedure. Serine proteases were more efficient in removing cells of <i>Bacillus</i> biofilms than polysaccharidases. However, polysaccharidases were more efficient in removing <i>P. fluorescens</i> biofilms than serine proteases. Solubilization of enzymes with a buffer containing surfactants, and dispersing and chelating agents enhanced the efficiency of polysaccharidases and proteases respectively in removing biofilms of <i>Bacillus</i> and <i>P. fluorescens</i>. A combination of enzymes targeting several components of EPS, surfactants, dispersing and chelating agents would be an efficient alternative to chemical cleaning agents.
DOI: 10.6084/m9.figshare.825541
title: Bacterial attachment on sub-nanometrically smooth titanium substrata

description: Despite the volume of work that has been conducted on the topic, the role of surface topography in mediating bacterial cell adhesion is not well understood. The primary reason for this lack of understanding is the relatively limited extent of topographical characterisation employed in many studies. In the present study, the topographies of three sub-nanometrically smooth titanium (Ti) surfaces were comprehensively characterised, using nine individual parameters that together describe the height, shape and distribution of their surface features. This topographical analysis was then correlated with the adhesion behaviour of the pathogenic bacteria <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i>, in an effort to understand the role played by each aspect of surface architecture in influencing bacterial attachment. While <i>P. aeruginosa</i> was largely unable to adhere to any of the three sub-nanometrically smooth Ti surfaces, the extent of <i>S. aureus</i> cell attachment was found to be greater on surfaces with higher average, RMS and maximum roughness and higher surface areas. The cells also attached in greater numbers to surfaces that had shorter autocorrelation lengths and skewness values that approached zero, indicating a preference for less ordered surfaces with peak heights and valley depths evenly distributed around the mean plane. Across the sub-nanometrically smooth range of surfaces tested, it was shown that <i>S. aureus</i> more easily attached to surfaces with larger features that were evenly distributed between peaks and valleys, with higher levels of randomness. This study demonstrated that the traditionally employed amplitudinal roughness parameters are not the only determinants of bacterial adhesion, and that spatial parameters can also be used to predict the extent of attachment.
DOI: 10.6084/m9.figshare.825541.v1
title: Bacterial attachment on sub-nanometrically smooth titanium substrata

description: Despite the volume of work that has been conducted on the topic, the role of surface topography in mediating bacterial cell adhesion is not well understood. The primary reason for this lack of understanding is the relatively limited extent of topographical characterisation employed in many studies. In the present study, the topographies of three sub-nanometrically smooth titanium (Ti) surfaces were comprehensively characterised, using nine individual parameters that together describe the height, shape and distribution of their surface features. This topographical analysis was then correlated with the adhesion behaviour of the pathogenic bacteria <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i>, in an effort to understand the role played by each aspect of surface architecture in influencing bacterial attachment. While <i>P. aeruginosa</i> was largely unable to adhere to any of the three sub-nanometrically smooth Ti surfaces, the extent of <i>S. aureus</i> cell attachment was found to be greater on surfaces with higher average, RMS and maximum roughness and higher surface areas. The cells also attached in greater numbers to surfaces that had shorter autocorrelation lengths and skewness values that approached zero, indicating a preference for less ordered surfaces with peak heights and valley depths evenly distributed around the mean plane. Across the sub-nanometrically smooth range of surfaces tested, it was shown that <i>S. aureus</i> more easily attached to surfaces with larger features that were evenly distributed between peaks and valleys, with higher levels of randomness. This study demonstrated that the traditionally employed amplitudinal roughness parameters are not the only determinants of bacterial adhesion, and that spatial parameters can also be used to predict the extent of attachment.
DOI: 10.6084/m9.figshare.825535
title: Biofilm development and the dynamics of preferential flow paths in porous media

description: A two-dimensional pore-scale numerical model was developed to evaluate the dynamics of preferential flow paths in porous media caused by bioclogging. The liquid flow and solute transport through the pore network were coupled with a biofilm model including biomass attachment, growth, decay, lysis, and detachment. Blocking of all but one flow path was obtained under constant liquid inlet flow rate and biomass detachment caused by shear forces only. The stable flow path formed when biofilm detachment balances growth, even with biomass weakened by decay. However, shear forces combined with biomass lysis upon starvation could produce an intermittently shifting location of flow channels. Dynamic flow pathways may also occur when combined liquid shear and pressure forces act on the biofilm. In spite of repeated clogging and unclogging of interconnected pore spaces, the average permeability reached a quasi-constant value. Oscillations in the medium permeability were more pronounced for weaker biofilms.
DOI: 10.6084/m9.figshare.825535.v1
title: Biofilm development and the dynamics of preferential flow paths in porous media

description: A two-dimensional pore-scale numerical model was developed to evaluate the dynamics of preferential flow paths in porous media caused by bioclogging. The liquid flow and solute transport through the pore network were coupled with a biofilm model including biomass attachment, growth, decay, lysis, and detachment. Blocking of all but one flow path was obtained under constant liquid inlet flow rate and biomass detachment caused by shear forces only. The stable flow path formed when biofilm detachment balances growth, even with biomass weakened by decay. However, shear forces combined with biomass lysis upon starvation could produce an intermittently shifting location of flow channels. Dynamic flow pathways may also occur when combined liquid shear and pressure forces act on the biofilm. In spite of repeated clogging and unclogging of interconnected pore spaces, the average permeability reached a quasi-constant value. Oscillations in the medium permeability were more pronounced for weaker biofilms.
DOI: 10.6084/m9.figshare.825529
title: Long-range periodic sequence of the cement/silk protein of <i>Stenopsyche marmorata</i>: purification and biochemical characterisation

description: The long-range periodic amino acid sequence of the bifunctional silk/cement protein from larvae of the caddisfly, <i>Stenopsyche marmorata</i>, is discussed in this study. The protein, named the <i>S. marmorata</i> silk protein (Smsp-1), was first purified to electrophoretic homogeneity. The results of Edman-based sequencing of Smsp-1 tryptic digests were consistent with the amino acid sequence deduced from a cDNA clone of the Smsp-1 gene. All undetected amino acids in the Edman-based sequencing were encoded as Ser, suggesting the presence of <i>O</i>-phospho-Ser. <sup>31</sup>P-NMR and an <i>O</i>-phospho-amino acid analysis successfully showed that the <i>O</i>-phospho-Ser residue occurred in a clustered manner, serving a cement function for Smsp-1. Two patterns of non-phosphorylated repeats, –SLGPYGDPRGDXLGPYGG– (X = V, G or D) and –GVGPYGDGLGPYGG–, were enriched in Smsp-1 compared with the <i>O</i>-phospho-Ser cluster, and have fibre-forming functions.
DOI: 10.6084/m9.figshare.825529.v1
title: Long-range periodic sequence of the cement/silk protein of <i>Stenopsyche marmorata</i>: purification and biochemical characterisation

description: The long-range periodic amino acid sequence of the bifunctional silk/cement protein from larvae of the caddisfly, <i>Stenopsyche marmorata</i>, is discussed in this study. The protein, named the <i>S. marmorata</i> silk protein (Smsp-1), was first purified to electrophoretic homogeneity. The results of Edman-based sequencing of Smsp-1 tryptic digests were consistent with the amino acid sequence deduced from a cDNA clone of the Smsp-1 gene. All undetected amino acids in the Edman-based sequencing were encoded as Ser, suggesting the presence of <i>O</i>-phospho-Ser. <sup>31</sup>P-NMR and an <i>O</i>-phospho-amino acid analysis successfully showed that the <i>O</i>-phospho-Ser residue occurred in a clustered manner, serving a cement function for Smsp-1. Two patterns of non-phosphorylated repeats, –SLGPYGDPRGDXLGPYGG– (X = V, G or D) and –GVGPYGDGLGPYGG–, were enriched in Smsp-1 compared with the <i>O</i>-phospho-Ser cluster, and have fibre-forming functions.
DOI: 10.6084/m9.figshare.825517
title: Holothuroidea of the Charlie Gibbs Fracture Zone area, northern Mid-Atlantic Ridge

description: Holothurians are among the most species-rich taxa in the megabenthos on the northern Mid-Atlantic Ridge at depths of 2200–3700 m. Extensive new collections of 32 holothurian species were made in 2007–2010 in the Charlie Gibbs Fracture Zone area as part of the ECOMAR project. New material includes samples taken using a trawl and the ROV <i>Isis</i>. Samples and <i>in situ</i> observations from the ROV were of particular value because the morphological details of a number of holothurian species could be clarified. Many of these species are gelatinous and fragile and were damaged in trawls. Three species of elasipodid holothurians are described as new to science. An annotated check-list of all species of deep-sea holothurians collected in the Charlie Gibbs Fracture Zone area is provided. The checklist includes synonyms, distribution data and morphological descriptions as well as photographs taken <i>in situ</i> and in vivo. Ecological remarks are given for some species.
DOI: 10.6084/m9.figshare.825521
title: Phthalates and food-contact materials: enforcing the 2008 European Union plastics legislation

description: The migration of phthalates into foodstuffs from food-contact materials (FCM) is a well-known source of food contamination. In 2005, the European Food Safety Authority finalized its risk assessment for several of the classical phthalate plasticizers. In their risk management procedure the European Commission transformed the tolerable daily intakes established by the Authority into legislative limits for phthalates in both plastic and food simulants, while taking exposure from other sources into consideration. These limits have been into force since 1 July 2008. A detailed interpretation of the regulation of these substances was agreed upon in the European network of FCM reference laboratories. This paper reports results from a Danish control campaign of samples collected by official food inspectors and analysed by a newly validated analytical method run under accreditation. Samples were from FCM producers, FCM importers and importers of packed foodstuffs from third-party countries. Products containing phthalates above the current limits were found in several categories of FCM: conveyor belts (six of six), lids from packed foodstuffs in glasses (eight of 28), tubes for liquid foodstuffs (four of five) and gloves (five of 14). More than 20% of the samples analysed contained dibutylphthalate (DBP) or di-(2-ethylhexyl)phthalate (DEHP) above the compositional limits of 0.05% and 0.1%, respectively. Analysis of residual phthalates in metal lid gaskets instead of analysis of phthalates in the food when controlling foodstuffs packed outside the European Union proved to be an efficient and simple control method. All findings of phthalates were associated with the use of plasticized polyvinylchloride (PVC).
DOI: 10.6084/m9.figshare.825516
title: Bioassays and field immersion tests: a comparison of the antifouling activity of copper-free poly(methacrylic)-based coatings containing tertiary amines and ammonium salt groups

description: This paper focuses on the activity spectrum of three dimethylalkyl tertiary amines as potential active molecules and the corresponding ammonium salt-based antifouling (AF) paints. Bioassays (using marine bacteria, microalgae and barnacles) and field tests were combined to assess the AF activity of coatings. Bioassay results demonstrated that the ammonium salt-based paints did not inhibit the growth of microorganisms (except the dimethyldodecylammonium-based coatings) and that the tertiary amines were potent towards bacteria, diatoms, and barnacle larvae at non-toxic concentrations (therapeutic ratio, LC<sub>50</sub>/EC<sub>50</sub>,
DOI: 10.6084/m9.figshare.825521.v1
title: Phthalates and food-contact materials: enforcing the 2008 European Union plastics legislation

description: The migration of phthalates into foodstuffs from food-contact materials (FCM) is a well-known source of food contamination. In 2005, the European Food Safety Authority finalized its risk assessment for several of the classical phthalate plasticizers. In their risk management procedure the European Commission transformed the tolerable daily intakes established by the Authority into legislative limits for phthalates in both plastic and food simulants, while taking exposure from other sources into consideration. These limits have been into force since 1 July 2008. A detailed interpretation of the regulation of these substances was agreed upon in the European network of FCM reference laboratories. This paper reports results from a Danish control campaign of samples collected by official food inspectors and analysed by a newly validated analytical method run under accreditation. Samples were from FCM producers, FCM importers and importers of packed foodstuffs from third-party countries. Products containing phthalates above the current limits were found in several categories of FCM: conveyor belts (six of six), lids from packed foodstuffs in glasses (eight of 28), tubes for liquid foodstuffs (four of five) and gloves (five of 14). More than 20% of the samples analysed contained dibutylphthalate (DBP) or di-(2-ethylhexyl)phthalate (DEHP) above the compositional limits of 0.05% and 0.1%, respectively. Analysis of residual phthalates in metal lid gaskets instead of analysis of phthalates in the food when controlling foodstuffs packed outside the European Union proved to be an efficient and simple control method. All findings of phthalates were associated with the use of plasticized polyvinylchloride (PVC).
DOI: 10.6084/m9.figshare.825516.v1
title: Bioassays and field immersion tests: a comparison of the antifouling activity of copper-free poly(methacrylic)-based coatings containing tertiary amines and ammonium salt groups

description: This paper focuses on the activity spectrum of three dimethylalkyl tertiary amines as potential active molecules and the corresponding ammonium salt-based antifouling (AF) paints. Bioassays (using marine bacteria, microalgae and barnacles) and field tests were combined to assess the AF activity of coatings. Bioassay results demonstrated that the ammonium salt-based paints did not inhibit the growth of microorganisms (except the dimethyldodecylammonium-based coatings) and that the tertiary amines were potent towards bacteria, diatoms, and barnacle larvae at non-toxic concentrations (therapeutic ratio, LC<sub>50</sub>/EC<sub>50</sub>,