cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3978606
title: Genome shuffling of <i>Lactobacillus plantarum</i> C88 improves adhesion

description: Genome shuffling is an important method for rapid improvement in microbial strains for desired phenotypes. In this study, ultraviolet irradiation and nitrosoguanidine were used as mutagens to enhance the adhesion of the wild-type <i>Lactobacillus plantarum</i> C88. Four strains with better property were screened after mutagenesis to develop a library of parent strains for three rounds of genome shuffling. Fusants F3-1, F3-2, F3-3, and F3-4 were screened as the improved strains. The <i>in vivo</i> and <i>in vitro</i> tests results indicated that the population after three rounds of genome shuffling exhibited improved adhesive property. Random Amplified Polymorphic DNA results showed significant differences between the parent strain and recombinant strains at DNA level. These results suggest that the adhesive property of <i>L. plantarum</i> C88 can be significantly improved by genome shuffling. Improvement in the adhesive property of bacterial cells by genome shuffling enhances the colonization of probiotic strains which further benefits to exist probiotic function. RAPD analysis of <i>L. plantarum</i> C88 and fusants F3-1, F3-2, F3-3, and F3-4. Primers Z3, Z4, Z5, Z6, Z7, Z8, Z9, Coc, and OPA-3 were used in this test.
DOI: 10.7910/dvn/v1rjpf/uhlogt
title: snk20160614_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3978606.v1
title: Genome shuffling of <i>Lactobacillus plantarum</i> C88 improves adhesion

description: Genome shuffling is an important method for rapid improvement in microbial strains for desired phenotypes. In this study, ultraviolet irradiation and nitrosoguanidine were used as mutagens to enhance the adhesion of the wild-type <i>Lactobacillus plantarum</i> C88. Four strains with better property were screened after mutagenesis to develop a library of parent strains for three rounds of genome shuffling. Fusants F3-1, F3-2, F3-3, and F3-4 were screened as the improved strains. The <i>in vivo</i> and <i>in vitro</i> tests results indicated that the population after three rounds of genome shuffling exhibited improved adhesive property. Random Amplified Polymorphic DNA results showed significant differences between the parent strain and recombinant strains at DNA level. These results suggest that the adhesive property of <i>L. plantarum</i> C88 can be significantly improved by genome shuffling. Improvement in the adhesive property of bacterial cells by genome shuffling enhances the colonization of probiotic strains which further benefits to exist probiotic function. RAPD analysis of <i>L. plantarum</i> C88 and fusants F3-1, F3-2, F3-3, and F3-4. Primers Z3, Z4, Z5, Z6, Z7, Z8, Z9, Coc, and OPA-3 were used in this test.
DOI: 10.7910/dvn/v1rjpf/fyd1y6
title: snk20160906_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/wa1m7m
title: snk20160912_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3978603
title: High production of a class III lantipeptide AmfS in <i>Streptomyces griseus</i>

description: AmfS, a class III lantipeptide serves as a morphogen in <i>Streptomyces griseus</i>. Here, we constructed a high production system of AmfS in <i>S. griseus</i>. We isolated <i>S. griseus</i> Grd1 strain defective in glucose repression of aerial mycelium formation and found it suitable for the overproduction of AmfS. Two expression vectors carrying the strong and constitutive <i>ermE2</i> promoter were constructed using a multicopy number plasmid, pIJ702. The use of the Grd1 strain combined with the expression vectors enabled high production of AmfS by <i>S. griseus</i> into its culture broth. The expression system was also effective for the generation of abundant AmfS derived from <i>Streptomyces avermitilis</i>. In addition, site-directed mutagenesis revealed the amino acid residues essential for the morphogen activity of AmfS. These results indicate that the constructed system enables efficient production of class III lantipeptides by <i>Streptomyces</i>. High production of a class III lantipeptide AmfS in <i>Streptomyces griseus</i>.
DOI: 10.6084/m9.figshare.3978603.v1
title: High production of a class III lantipeptide AmfS in <i>Streptomyces griseus</i>

description: AmfS, a class III lantipeptide serves as a morphogen in <i>Streptomyces griseus</i>. Here, we constructed a high production system of AmfS in <i>S. griseus</i>. We isolated <i>S. griseus</i> Grd1 strain defective in glucose repression of aerial mycelium formation and found it suitable for the overproduction of AmfS. Two expression vectors carrying the strong and constitutive <i>ermE2</i> promoter were constructed using a multicopy number plasmid, pIJ702. The use of the Grd1 strain combined with the expression vectors enabled high production of AmfS by <i>S. griseus</i> into its culture broth. The expression system was also effective for the generation of abundant AmfS derived from <i>Streptomyces avermitilis</i>. In addition, site-directed mutagenesis revealed the amino acid residues essential for the morphogen activity of AmfS. These results indicate that the constructed system enables efficient production of class III lantipeptides by <i>Streptomyces</i>. High production of a class III lantipeptide AmfS in <i>Streptomyces griseus</i>.
DOI: 10.7910/dvn/v1rjpf/9nsbra
title: snk20150901_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/kpybtj
title: snk20150422_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/7rk6es
title: snk20150829_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/etlvpy
title: snk20150902_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3978588
title: The role of mafic microgranular enclaves in the generation of Early Cretaceous granitic rocks of SE China: evidence from zircon U–Pb geochronology, geochemistry, and Hf isotopic data for the Liangnong pluton, eastern Zhejiang Province

description: In order to constrain the timing and petrogenesis of both the hosting rocks and the inner mafic microgranular enclaves (MMEs) of the Liangnong pluton, SE China, we have performed a series of bulk-rock geochemistry, zircon U–Pb, and Hf isotopic analysis, respectively. Zircon laser ablation–inductively coupled plasma–mass spectrometry U–Pb isotopic analysis yielded ages of 106.3 ± 1.1 Ma for the granodiorite and 103.9 ± 1.6 to 105 ± 1.8 Ma for monzogranite phases within the hosting pluton, as well as an age of 104.7 ± 0.8 Ma for the associated MMEs. The host rocks are metaluminous, have A/CNK values of 0.91–1.09, contain relatively high concentrations of SiO<sub>2</sub> and K<sub>2</sub>O, are enriched in Rb, Th, Ba, Zr, and Hf, are depleted of Sr, P, Ti, Nd, and Ta, contain high concentrations of the rare earth elements (REE) and the light REE, and have moderately negative Eu anomalies (Eu*/Eu = 0.6–0.8). In comparison, the MMEs contain high concentrations of Al<sub>2</sub>O<sub>3</sub>, FeO, MgO, and TiO<sub>2</sub>, are relatively enriched in Ba, U, and Sr, and are depleted in Th, Nd, and Zr. They have lower total REE concentrations and higher Eu*/Eu values than the hosting granites. The zircons within the hosting granites have Hf crustal model ages (T<sub>DM</sub><sup>C</sup>) that show a peak at 1.29–1.85 Ga. Zircons within the MMEs have different εHf(t) values (–3.7 to +4.9) than the zircons within the hosting granites (–10.8 to –1.9). The results indicate that the MMEs and the hosting granites crystallized from magmas with different sources, thereby showing that the Early Cretaceous magmatism in the coastal areas of SE China was generated by the widespread injection of mantle-derived magmas caused by rollback of the subducting palaeo-Pacific Plate.
DOI: 10.7910/dvn/v1rjpf/8calvf
title: snk20150831_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/pfzx2u
title: snk20151021_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ejdjda
title: snk20151030_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/9wksk4
title: snk20160114_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3978570
title: The Neoproterozoic continental rift magmatism of the eastern Jiangnan orogen: new evidence from the mafic sheets in northern Zhejiang Province, South China

description: Massive mafic sheets were recently recognized intruding the Neoproterozoic strata in Fuyang area, eastern Jiangnan orogen. Geochronological, geochemical, and isotopic studies were carried out to understand their mantle source, crust–mantle interaction, and tectonic setting. LA-ICP-MS U-Pb zircon data indicate that the sheets were generated at 808 ± 7 Ma. The mafic sheets consist of two groups: high Ti and low Ti. They are enriched in light rare earth elements (LREE; 3.3–5.3 ppm) and show negligible Eu anomalies (<i>δ</i>Eu = 0.77–1.12). They also have strong large-ion lithophile element (LILE; Sr, K, Rb, Ba) enrichment, moderately strong high-field-strength element (HFSE) enrichment (except for Nb-Ta depletion), and positive <i>ε</i>Nd(<i>t</i>) (5.1–9.1). Geochemical and isotopic data indicate that the mafic sheets were generated from a depleted asthenospheric mantle source. The high-Ti mafic sheets have higher HFSE contents and less Nb-Ta depletion than the low Ti series, indicating a lower degree of partial melting and crustal contamination. The mafic sheets grew in a within-plate setting, concurrent with the ~820–750 Ma rifting events in the eastern Jiangnan orogen. They are likely related to the breakup of the Rodinia supercontinent.
DOI: 10.6084/m9.figshare.3978570.v1
title: The Neoproterozoic continental rift magmatism of the eastern Jiangnan orogen: new evidence from the mafic sheets in northern Zhejiang Province, South China

description: Massive mafic sheets were recently recognized intruding the Neoproterozoic strata in Fuyang area, eastern Jiangnan orogen. Geochronological, geochemical, and isotopic studies were carried out to understand their mantle source, crust–mantle interaction, and tectonic setting. LA-ICP-MS U-Pb zircon data indicate that the sheets were generated at 808 ± 7 Ma. The mafic sheets consist of two groups: high Ti and low Ti. They are enriched in light rare earth elements (LREE; 3.3–5.3 ppm) and show negligible Eu anomalies (<i>δ</i>Eu = 0.77–1.12). They also have strong large-ion lithophile element (LILE; Sr, K, Rb, Ba) enrichment, moderately strong high-field-strength element (HFSE) enrichment (except for Nb-Ta depletion), and positive <i>ε</i>Nd(<i>t</i>) (5.1–9.1). Geochemical and isotopic data indicate that the mafic sheets were generated from a depleted asthenospheric mantle source. The high-Ti mafic sheets have higher HFSE contents and less Nb-Ta depletion than the low Ti series, indicating a lower degree of partial melting and crustal contamination. The mafic sheets grew in a within-plate setting, concurrent with the ~820–750 Ma rifting events in the eastern Jiangnan orogen. They are likely related to the breakup of the Rodinia supercontinent.
DOI: 10.7910/dvn/v1rjpf/jles32
title: snk20160220_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/qvib4p
title: snk20161228_03.txt.gz

description: :unav
DOI: 10.21227/6yps-xr84
title: Tryout of submission (with sample_submission.csv from data.zip).

description: Tryout of submission (with sample_submission.csv from data.zip).
DOI: 10.6084/m9.figshare.3978528
title: Poly(γ-glutamic acid) modulates the properties of poly(ethylene glycol) hydrogel for biomedical applications

description: In this paper, a series of copolymer hydrogels were fabricated from methacrylated poly(γ-glutamic acid) (mPGA) and poly(ethylene glycol) diacrylate (PEGDA). The effect of ionic strength and pH on the swelling behavior and mechanical properties of these hydrogels were studied in detail. Release of Rhodamine B as a model drug from the hydrogel was evaluated under varied pH. <i>In vitro</i> photoencapsulation of bovine cartilage chondrocytes was performed to assess the cytotoxicity of this copolymer hydrogel. The results revealed that the copolymer hydrogel is ionic- and pH-sensitive, and does not exhibit acute cytotoxicity; this copolymer hydrogel may have promising application as matrix for controlled drug release and scaffolding material in tissue engineering.
DOI: 10.7910/dvn/v1rjpf/2emjk6
title: snk20160706_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3978528.v1
title: Poly(γ-glutamic acid) modulates the properties of poly(ethylene glycol) hydrogel for biomedical applications

description: In this paper, a series of copolymer hydrogels were fabricated from methacrylated poly(γ-glutamic acid) (mPGA) and poly(ethylene glycol) diacrylate (PEGDA). The effect of ionic strength and pH on the swelling behavior and mechanical properties of these hydrogels were studied in detail. Release of Rhodamine B as a model drug from the hydrogel was evaluated under varied pH. <i>In vitro</i> photoencapsulation of bovine cartilage chondrocytes was performed to assess the cytotoxicity of this copolymer hydrogel. The results revealed that the copolymer hydrogel is ionic- and pH-sensitive, and does not exhibit acute cytotoxicity; this copolymer hydrogel may have promising application as matrix for controlled drug release and scaffolding material in tissue engineering.
DOI: 10.7910/dvn/v1rjpf/bwsuny
title: snk20160212_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/4oaeyw
title: snk20150320_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/jtvuji
title: snk20151024_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/t9blzr
title: snk20150825_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3978516.v1
title: IJCSET16-07-09-001 (2).pdf

description: K-Means algorithm is the most commonly chosen technique for color image segmentation task.Although this algorithm is famous for its low complexity and easy implementation, but usually it is seen thatthe segmentation results are suffering from noises and over-segmentation, which mislead the final imageanalysis process. This is because of the inappropriate selection of the number of clusters in K-Means. Also,choosing a proper distance metric for this algorithm is very important as it impacts on the final segmentationresults. This paper deals with these problems and presents a novel approach to solving the same. As per colorimage segmentation concerned, so choosing a suitable color space is the first mandatory condition. HSVcolor space is selected for the proposed research work. The input RGB image is first converted to HSV one.Here, the number of clusters is determined from the input image beforehand. For this, it is considered thatnumber of regions in an image is equivalent to the number of clusters that can be formed through clusteringthe pixels of the image. The number of regions of an image is determined with Meyer’s Watershed algorithmwith a proper preprocessing technique. Generally, mere applying Watershed algorithm results in oversegmentation. So, we have introduced an improved Sobel filter based on multiple directional edge detection todeal with this problem. The V channel of the HSV converted image is filtered by the proposed improved Sobelfilter first and then the filtered image is sent as input to the watershed algorithm. The watershed algorithmanalyses the regions of the image through local minima calculations and the total number of regions herebyfound is assigned to K. Then with the predetermined K, the pixels of the HSV converted image are clusteredwith K-Means Algorithm. “Cosine Distance Metric” is chosen for the distance based calculations involved inthe K-Means algorithm. By properly labeling the different clusters, the final segmented image is obtained.The experimental results proved the better performance of the proposed approach in comparison to K-Meansalgorithm. Also, when applied to satellite color images, it is found that the proposed approach succeeds toform clear and distinct segments of the same and hence establishes a good framework for satellite colorimage segmentation.
DOI: 10.7910/dvn/v1rjpf/fzcmo5
title: snk20150724_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/395cgy
title: snk20151224_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3978384
title: Virtual reference logs: Lincoln University library July 2016 - June 2017

description: Anonymised chat logs from AskLive, the virtual reference service at Lincoln University Library, Teaching and Learning, between 1 July 2016 and 30 June 2017. AskLive uses the LibraryH3lp platform.<br><br>Columns include:<br>* Conversation ID - unique for each transaction<br>* Guest ID - unique for each individual user<br>* Date/Time - timestamp of beginning of conversation - in New Zealand time<br>* Duration - in seconds from first contact to last line of transcript<br>* Location - manually coded based on IP address, where known<br>* Referring URL - webpage the user was on when they initiated the chat, where known<br>* Main topic / subtopic - manually coded based on transcript. May be blank where the conversation is a continuation of a previous one (see next column) or where the contact was unanswered and a topic couldn't be determined.<br>* Continuation/unanswered - "Continuation of previous" is noted where a conversation window was closed by the user and then they contacted us again continuing the conversation. To identify 'the previous' conversation, sort by date/time or conversation ID and double-check against guest ID. "Unanswered" is noted where the user contacted us but no staff answered the contact.<br>
DOI: 10.6084/m9.figshare.3978384.v1
title: Virtual reference logs: Lincoln University library July 2016 - June 2017

description: Anonymised chat logs from AskLive, the virtual reference service at Lincoln University Library, Teaching and Learning, between 1 July 2016 and 30 June 2017. AskLive uses the LibraryH3lp platform.<br><br>Columns include:<br>* Conversation ID - unique for each transaction<br>* Guest ID - unique for each individual user<br>* Date/Time - timestamp of beginning of conversation - in New Zealand time<br>* Duration - in seconds from first contact to last line of transcript<br>* Location - manually coded based on IP address, where known<br>* Referring URL - webpage the user was on when they initiated the chat, where known<br>* Main topic / subtopic - manually coded based on transcript. May be blank where the conversation is a continuation of a previous one (see next column) or where the contact was unanswered and a topic couldn't be determined.<br>* Continuation/unanswered - "Continuation of previous" is noted where a conversation window was closed by the user and then they contacted us again continuing the conversation. To identify 'the previous' conversation, sort by date/time or conversation ID and double-check against guest ID. "Unanswered" is noted where the user contacted us but no staff answered the contact.<br>
DOI: 10.7910/dvn/v1rjpf/uu4oje
title: snk20151018_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/fuu4mf
title: snk20150816_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/al80dx
title: snk20161001_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/wmw67m
title: snk20151006_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3978300
title: Supplementary Tables

description: All Supplementary Tables from the published article. Contains a few updates of strain names. Excel file.<br><br>
DOI: 10.6084/m9.figshare.3978303
title: SNP calls for all 161 strains.

description: SNP calls for all 161 strains. In VCF format. Annotated with SnpEff. Called using GATK.<br>
DOI: 10.6084/m9.figshare.3978303.v1
title: SNP calls for all 161 strains.

description: SNP calls for all 161 strains. In VCF format. Annotated with SnpEff. Called using GATK.<br>
DOI: 10.7910/dvn/v1rjpf/dqsv6i
title: snk20150112_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/lwtcr2
title: snk20151026_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3978294
title: Spore viability and geographic distance data.

description: Data describing the spore viability from crosses and geographic distances between strain locations. <br>Details are in the published article methods.<br>
DOI: 10.6084/m9.figshare.3978279
title: SGA de novo assemblies of all wild strains

description: SGA de novo assemblies of all wild strains. In fasta format.
DOI: 10.6084/m9.figshare.3978294.v1
title: Spore viability and geographic distance data.

description: Data describing the spore viability from crosses and geographic distances between strain locations. <br>Details are in the published article methods.<br>
DOI: 10.6084/m9.figshare.3978279.v1
title: SGA de novo assemblies of all wild strains

description: SGA de novo assemblies of all wild strains. In fasta format.
DOI: 10.7910/dvn/v1rjpf/cgjdnx
title: snk20160922_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3978276
title: Indel calls.

description: Indel calls from the 57 non-clonal strains. Called with Cortex and GATK. In VCF format.<br>Unless you need to compare to the results in the Nature Genetics article, I would advise using the indel calls in the "fission yeast structural variation" project - as these are a newer, more comprehensive set.<br><br>
DOI: 10.6084/m9.figshare.3978276.v1
title: Indel calls.

description: Indel calls from the 57 non-clonal strains. Called with Cortex and GATK. In VCF format.<br>Unless you need to compare to the results in the Nature Genetics article, I would advise using the indel calls in the "fission yeast structural variation" project - as these are a newer, more comprehensive set.<br><br>
DOI: 10.7910/dvn/v1rjpf/loxmfg
title: snk20151215_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/bkna7x
title: snk20150704_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/azcfap
title: snk20160204_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/irjnsv
title: snk20161212_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3978246.v1
title: Inselect, informatics, and collections digitization at the Natural History Museum, London

description: Presentation given at The Smithsonian National Museum of Natural History on 2016-09-27.
DOI: 10.7910/dvn/v1rjpf/fcfuqy
title: snk20151217_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3978216
title: Effect of iron oxide on nitrification in two agricultural soils with different pH

description: Effect of iron oxide on nitrification in two agricultural soils with different pH
DOI: 10.7910/dvn/v1rjpf/5q1eyh
title: snk20160312_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3978168
title: Data.xlsx

description: Effect of iron oxide on nitrification in two agricultural soils with different pH
DOI: 10.6084/m9.figshare.3978216.v1
title: Effect of iron oxide on nitrification in two agricultural soils with different pH

description: Effect of iron oxide on nitrification in two agricultural soils with different pH
DOI: 10.6084/m9.figshare.3978168.v1
title: Data.xlsx

description: Effect of iron oxide on nitrification in two agricultural soils with different pH
DOI: 10.15156/bio/sh1281296.08fu
title: SH1281296.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.