cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7873328
title: Suppl.Data5_16S.Root.z.score.txt from Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes

description: Cyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics and agricultural practices: more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes or those uninfected by nematodes. Based on a network analysis of potential microbe–microbe associations, we further found that several fungal taxa potentially preying on nematodes (<i>Dactylellina</i> (Orbiliales), <i>Rhizophydium</i> (Rhizophydiales), <i>Clonostachys</i> (Hypocreales), <i>Pochonia</i> (Hypocreales) and <i>Purpureocillium</i> (Hypocreales)) co-occurred in the soybean rhizosphere at a small spatial scale. This study suggests how ‘consortia’ of anti-nematode microbes can derive from indigenous (resident) microbiomes, providing basic information for managing anti-nematode microbial communities in agroecosystems.
DOI: 10.6084/m9.figshare.7873331.v1
title: Suppl.Data4_ITS.Root_1.txt from Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes

description: Cyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics and agricultural practices: more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes or those uninfected by nematodes. Based on a network analysis of potential microbe–microbe associations, we further found that several fungal taxa potentially preying on nematodes (<i>Dactylellina</i> (Orbiliales), <i>Rhizophydium</i> (Rhizophydiales), <i>Clonostachys</i> (Hypocreales), <i>Pochonia</i> (Hypocreales) and <i>Purpureocillium</i> (Hypocreales)) co-occurred in the soybean rhizosphere at a small spatial scale. This study suggests how ‘consortia’ of anti-nematode microbes can derive from indigenous (resident) microbiomes, providing basic information for managing anti-nematode microbial communities in agroecosystems.
DOI: 10.6084/m9.figshare.7873322
title: Suppl.Data4_16S.Soil_1.txt from Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes

description: Cyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics and agricultural practices: more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes or those uninfected by nematodes. Based on a network analysis of potential microbe–microbe associations, we further found that several fungal taxa potentially preying on nematodes (<i>Dactylellina</i> (Orbiliales), <i>Rhizophydium</i> (Rhizophydiales), <i>Clonostachys</i> (Hypocreales), <i>Pochonia</i> (Hypocreales) and <i>Purpureocillium</i> (Hypocreales)) co-occurred in the soybean rhizosphere at a small spatial scale. This study suggests how ‘consortia’ of anti-nematode microbes can derive from indigenous (resident) microbiomes, providing basic information for managing anti-nematode microbial communities in agroecosystems.
DOI: 10.6084/m9.figshare.7873325
title: Suppl.Data5_16S.Soil.P.value.txt from Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes

description: Cyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics and agricultural practices: more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes or those uninfected by nematodes. Based on a network analysis of potential microbe–microbe associations, we further found that several fungal taxa potentially preying on nematodes (<i>Dactylellina</i> (Orbiliales), <i>Rhizophydium</i> (Rhizophydiales), <i>Clonostachys</i> (Hypocreales), <i>Pochonia</i> (Hypocreales) and <i>Purpureocillium</i> (Hypocreales)) co-occurred in the soybean rhizosphere at a small spatial scale. This study suggests how ‘consortia’ of anti-nematode microbes can derive from indigenous (resident) microbiomes, providing basic information for managing anti-nematode microbial communities in agroecosystems.
DOI: 10.6084/m9.figshare.7873328.v1
title: Suppl.Data5_16S.Root.z.score.txt from Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes

description: Cyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics and agricultural practices: more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes or those uninfected by nematodes. Based on a network analysis of potential microbe–microbe associations, we further found that several fungal taxa potentially preying on nematodes (<i>Dactylellina</i> (Orbiliales), <i>Rhizophydium</i> (Rhizophydiales), <i>Clonostachys</i> (Hypocreales), <i>Pochonia</i> (Hypocreales) and <i>Purpureocillium</i> (Hypocreales)) co-occurred in the soybean rhizosphere at a small spatial scale. This study suggests how ‘consortia’ of anti-nematode microbes can derive from indigenous (resident) microbiomes, providing basic information for managing anti-nematode microbial communities in agroecosystems.
DOI: 10.6084/m9.figshare.7873337.v1
title: Suppl.Data4_ITS.Soil_1.txt from Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes

description: Cyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics and agricultural practices: more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes or those uninfected by nematodes. Based on a network analysis of potential microbe–microbe associations, we further found that several fungal taxa potentially preying on nematodes (<i>Dactylellina</i> (Orbiliales), <i>Rhizophydium</i> (Rhizophydiales), <i>Clonostachys</i> (Hypocreales), <i>Pochonia</i> (Hypocreales) and <i>Purpureocillium</i> (Hypocreales)) co-occurred in the soybean rhizosphere at a small spatial scale. This study suggests how ‘consortia’ of anti-nematode microbes can derive from indigenous (resident) microbiomes, providing basic information for managing anti-nematode microbial communities in agroecosystems.
DOI: 10.6084/m9.figshare.7873289
title: Database of all genes in Bacillus subtilis 168 that do not have recognition sequence of NdeI and BamHI

description: Molecular cloning is a critical tool for heterologous gene expression in metabolic engineering or synthetic biology applications. Since its discovery in the 1970s, restriction enzyme digestion remains an important enabling tool in molecular cloning through facilitating the insertion of specific gene fragment in the correct orientation into the expression vector. To do this, the first requirement is that the gene of interest does not contain recognition sequence of the restriction enzymes used in molecular cloning. In this contribution, a database of genes in<i> Bacillus subtilis</i> 168 (Genbank accession number: NC_000964.3) that do not contain the recognition sequence of restriction enzymes NdeI and BamHI was obtained using an in-house MATLAB software. Specifically, identity of the gene and its sequence were catalogued together with a logical value of 0 or 1 where 1 indicates that the recognition sequence of NdeI or BamHI was present in the gene. Overall, the database should find use in enabling the verification of whether specific genes of interest in<i> B. subtilis</i> 168 contain the recognition sequence of NdeI and BamHI in molecular cloning or plasmid construction applications.<br>
DOI: 10.6084/m9.figshare.7873289.v1
title: Database of all genes in Bacillus subtilis 168 that do not have recognition sequence of NdeI and BamHI

description: Molecular cloning is a critical tool for heterologous gene expression in metabolic engineering or synthetic biology applications. Since its discovery in the 1970s, restriction enzyme digestion remains an important enabling tool in molecular cloning through facilitating the insertion of specific gene fragment in the correct orientation into the expression vector. To do this, the first requirement is that the gene of interest does not contain recognition sequence of the restriction enzymes used in molecular cloning. In this contribution, a database of genes in<i> Bacillus subtilis</i> 168 (Genbank accession number: NC_000964.3) that do not contain the recognition sequence of restriction enzymes NdeI and BamHI was obtained using an in-house MATLAB software. Specifically, identity of the gene and its sequence were catalogued together with a logical value of 0 or 1 where 1 indicates that the recognition sequence of NdeI or BamHI was present in the gene. Overall, the database should find use in enabling the verification of whether specific genes of interest in<i> B. subtilis</i> 168 contain the recognition sequence of NdeI and BamHI in molecular cloning or plasmid construction applications.<br>
DOI: 10.6084/m9.figshare.7873322.v1
title: Suppl.Data4_16S.Soil_1.txt from Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes

description: Cyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics and agricultural practices: more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes or those uninfected by nematodes. Based on a network analysis of potential microbe–microbe associations, we further found that several fungal taxa potentially preying on nematodes (<i>Dactylellina</i> (Orbiliales), <i>Rhizophydium</i> (Rhizophydiales), <i>Clonostachys</i> (Hypocreales), <i>Pochonia</i> (Hypocreales) and <i>Purpureocillium</i> (Hypocreales)) co-occurred in the soybean rhizosphere at a small spatial scale. This study suggests how ‘consortia’ of anti-nematode microbes can derive from indigenous (resident) microbiomes, providing basic information for managing anti-nematode microbial communities in agroecosystems.
DOI: 10.6084/m9.figshare.7873325.v1
title: Suppl.Data5_16S.Soil.P.value.txt from Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes

description: Cyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics and agricultural practices: more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes or those uninfected by nematodes. Based on a network analysis of potential microbe–microbe associations, we further found that several fungal taxa potentially preying on nematodes (<i>Dactylellina</i> (Orbiliales), <i>Rhizophydium</i> (Rhizophydiales), <i>Clonostachys</i> (Hypocreales), <i>Pochonia</i> (Hypocreales) and <i>Purpureocillium</i> (Hypocreales)) co-occurred in the soybean rhizosphere at a small spatial scale. This study suggests how ‘consortia’ of anti-nematode microbes can derive from indigenous (resident) microbiomes, providing basic information for managing anti-nematode microbial communities in agroecosystems.
DOI: 10.6084/m9.figshare.7873247
title: Regional patterns of anthropogenic influences on streams and rivers in the conterminous United States, from the early 1970s to 2012

description: This paper introduces a dataset containing consistent time-series measurements of anthropogenic activities potentially affecting stream quality across the conterminous United States and summarizes the most noteworthy trends from 61 variables in 16 categories. Data include measures of atmospheric deposition, agricultural production, livestock, urbanization, irrigation, land use, nutrients from fertilizer, dams/reservoirs, and pesticide use, among others. The trend periods range from 10 to 40 years, beginning as early as 1970 and ending in 2012. Detailed summaries are provided for 1992-2012. Key results include: increase of urbanization and ‘exurbanization’, particularly in the South, Southwest, and Mid-Atlantic; increases in crop production and fertilizer use in much of the Midwest; increases in the concentration of livestock, particularly of hogs/pigs; increases in irrigation, dams, and reservoirs in the Lower Mississippi and Lower Missouri watersheds, widespread increase in the use of the pesticide glyphosate; and widespread decrease in atmospheric deposition of sulfate. These results and others provide a framework for evaluating potential causes of water-quality changes over the past four decades.
DOI: 10.6084/m9.figshare.7873256
title: Substituted naphthalene reaction rates with peroxy-acid treatment: prediction of reactivity using PEST

description: Persistent organic contaminants in the environment pose an environmental risk due to widespread occurrence and toxic properties. Advanced oxidation processes (AOPs) are treatment methods that have been used to successfully degrade organic contaminants in water, soil, sediments and sludge. Reaction rate constants (<i>k</i>) for peroxy acid treatment of 10 substituted naphthalene compounds were determined. The treatment method utilized acetic acid, hydrogen peroxide and a sulphuric acid catalyst to degrade the polyaromatic structures found in the compounds. Molecular structures of the selected compounds were derived at the B3LYP/6-31G* level of theory. Property-encoded surface translator (PEST) descriptors were calculated from B3LYP/6-31G* optimized structures and were found to have significant levels of correlation with <i>k</i>. Models using minimum local ionization potential (PIP.MIN) and a histogram [bin] of the gradient of the K electronic kinetic energy normal to the isosurface (DKN) were evaluated and found to agree within 10% of experimentally derived values of <i>k</i> in most instances. Results show that a combination of PEST descriptors could be used to predict reactivity by the peroxy-acid process. The PEST technology could prove to be a valuable asset for effective remediation design by predicting reaction outcomes for substituted naphthalene compounds and possibly other hydrophobic organic compounds (HOCs).
DOI: 10.6084/m9.figshare.7873274
title: Mtb and Msm PepNs share high degree of sequence identity.pdf

description: Mtb and Msm PepNs share high degree of sequence identity<br>
DOI: 10.6084/m9.figshare.7873256.v1
title: Substituted naphthalene reaction rates with peroxy-acid treatment: prediction of reactivity using PEST

description: Persistent organic contaminants in the environment pose an environmental risk due to widespread occurrence and toxic properties. Advanced oxidation processes (AOPs) are treatment methods that have been used to successfully degrade organic contaminants in water, soil, sediments and sludge. Reaction rate constants (<i>k</i>) for peroxy acid treatment of 10 substituted naphthalene compounds were determined. The treatment method utilized acetic acid, hydrogen peroxide and a sulphuric acid catalyst to degrade the polyaromatic structures found in the compounds. Molecular structures of the selected compounds were derived at the B3LYP/6-31G* level of theory. Property-encoded surface translator (PEST) descriptors were calculated from B3LYP/6-31G* optimized structures and were found to have significant levels of correlation with <i>k</i>. Models using minimum local ionization potential (PIP.MIN) and a histogram [bin] of the gradient of the K electronic kinetic energy normal to the isosurface (DKN) were evaluated and found to agree within 10% of experimentally derived values of <i>k</i> in most instances. Results show that a combination of PEST descriptors could be used to predict reactivity by the peroxy-acid process. The PEST technology could prove to be a valuable asset for effective remediation design by predicting reaction outcomes for substituted naphthalene compounds and possibly other hydrophobic organic compounds (HOCs).
DOI: 10.6084/m9.figshare.7873238
title: Supplementary Material for: Thiamine Substitution in Alcohol Use Disorder: A Narrative Review of Medical Guidelines

description: <b><i>Aims:</i></b> Patients with alcohol use disorder (AUD) frequently suffer from cognitive deficits ranging from mild symptoms to most severe forms. Wernicke encephalopathy (WE), caused by thiamine deficiency, is a potentially fatal syndrome characterized by the clinical triad of ophthalmoplegia, ataxia, and confusion. WE frequently presents in patients with AUD and, if left untreated, can progress to Wernicke-Korsakoff syndrome, which constitutes severe anterograde amnesia, confabulation, and behavioral abnormalities. Due to oftentimes indistinct clinical presentation, WE remains undiagnosed in up to 80% of cases. We conducted a review of current treatment guidelines for AUD in order to identify recommendations for the use of thiamine. <b><i>Methods:</i></b> Three different keyword combinations (“alcohol treatment guideline,” “alcohol withdrawal guideline,” and “alcohol treatment recommendation”) were entered in PubMed and Scopus, additional guidelines were searched screening the online sites of the respective agencies or societies. In total, 14 guidelines were included. <b><i>Results:</i></b> Thiamine was mentioned in all but one of the reviewed publications. Specifications on application modalities and indications varied considerably. While the majority of reviewed guidelines recommended parenteral thiamine only for patients at high risk for WE, some gave no information regarding the application form or dosage. <b><i>Conclusion:</i></b> Substitution of parenteral thiamine in individuals with suspected WE is a well-established treatment regimen. However, suggestions according to guidelines vary widely. Furthermore, hardly any evidence-based recommendations exist on a more general use of thiamine as a preventative intervention in individuals with AUD. Further research is of utmost importance to raise awareness for this potentially undervalued problem.