cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6803183.v1
title: Supplementary Material for: The Extended C-Terminal α-Helix of the HypC Chaperone Restricts Recognition of Large Subunit Precursors by the Hyp-Scaffold Machinery during [NiFe]-Hydrogenase Maturation in <b><i>Escherichia coli</i></b>

description: Members of the HypC protein family are chaperone-like proteins that play a central role in the maturation of [NiFe]-hydrogenases (Hyd). <i>Escherichia coli</i> has a second copy of HypC, called HybG, and, as a component of the HypDEF maturation scaffold, these proteins help synthesize the NiFe-cofactor and guide the scaffold to its designated hydrogenase large subunit precursor. HypC is required to synthesize active Hyd-1 and Hyd-3, while HybG facilitates Hyd-2 and Hyd-1 synthesis. To identify determinants on HypC that allow it to discriminate against Hyd-2, we made amino acid exchanges in 3 variable regions, termed VR1, VR2, and VR3, of HypC, that make it more similar to HybG. Region VR3 includes a HypC-specific C-terminal α-helical extension, and this proved particularly important in preventing the maturation of Hyd-2 by HypC. Truncation of this extension on HypC increased Hyd-2 activity in the absence of HybG, while retaining maturation of Hyd-3 and Hyd-1. Combining this truncation with amino acid exchanges in VR1 and VR2 of HypC negatively affected the synthesis of active Hyd-1. The C-terminus of <i>E. coli</i> HypC is thus a key determinant in hindering Hyd-2 maturation, while VR1 and VR2 appear more important for Hyd-1 matu­ration.
DOI: 10.6084/m9.figshare.6803147.v1
title: <i>In silico</i> design of chiral dimers to direct the synthesis of a chiral zeolite

description: We have applied <i>in silico</i> materials design in an effort to design chiral organic structure directing agents (OSDAs) for the synthesis of enantiomerically enriched STW zeolite. To do so, we have used both exhaustive virtual screening of a limited set of symmetrical imidazolium dimers and a multi-objective genetic algorithm to effectively search a larger virtual combinatorial chemistry space that is too vast for an exhaustive approach.
DOI: 10.6084/m9.figshare.6802826
title: Additional file 9: of The evolutionary signal in metagenome phyletic profiles predicts many gene functions

description: Number of COG and NOG gene families that are assigned to GO terms, considering the known GO function annotations from Uniprot-GOA dated either December 2013 or November 2016, and for COGs/NOGs from either the eggNOG database v3 or eggNOG v4. (XLSX 140 kb)
DOI: 10.6084/m9.figshare.6802826.v1
title: Additional file 9: of The evolutionary signal in metagenome phyletic profiles predicts many gene functions

description: Number of COG and NOG gene families that are assigned to GO terms, considering the known GO function annotations from Uniprot-GOA dated either December 2013 or November 2016, and for COGs/NOGs from either the eggNOG database v3 or eggNOG v4. (XLSX 140 kb)
DOI: 10.6084/m9.figshare.6802817
title: Additional file 8: of The evolutionary signal in metagenome phyletic profiles predicts many gene functions

description: Gene family function annotations predicted by MPP-H, by MPP-O, by MPP-I, by MPP-16S, by PP (matched with MPP-H), by PP (matched with MPP-O) and by PP (matched with MPP-I and MPP-16S), all provided in separate table files. In each table, rows are gene families (first column lists the COG or NOG ID), columns are GO functions (the header row lists GO ID) and values are the precision (Pr) thresholds at which a GO term was assigned to a COG or a NOG. Values of Pr
DOI: 10.6084/m9.figshare.6802817.v1
title: Additional file 8: of The evolutionary signal in metagenome phyletic profiles predicts many gene functions

description: Gene family function annotations predicted by MPP-H, by MPP-O, by MPP-I, by MPP-16S, by PP (matched with MPP-H), by PP (matched with MPP-O) and by PP (matched with MPP-I and MPP-16S), all provided in separate table files. In each table, rows are gene families (first column lists the COG or NOG ID), columns are GO functions (the header row lists GO ID) and values are the precision (Pr) thresholds at which a GO term was assigned to a COG or a NOG. Values of Pr
DOI: 10.6084/m9.figshare.6802811
title: Additional file 7: of The evolutionary signal in metagenome phyletic profiles predicts many gene functions

description: Known GO annotations downloaded from the Uniprot-GOA database of (i) December 2013 and assigned to eggNOG v3 COG/NOGs, (ii) December 2013 and assigned to eggNOG v4 COG/NOGs, and (iii) November 2016 and assigned to eggNOG v4 COG/NOGs; in all cases using the 50% rule for propagating GO functions across genes within a COG or a NOG. (7Z 391 kb)
DOI: 10.6084/m9.figshare.6802811.v1
title: Additional file 7: of The evolutionary signal in metagenome phyletic profiles predicts many gene functions

description: Known GO annotations downloaded from the Uniprot-GOA database of (i) December 2013 and assigned to eggNOG v3 COG/NOGs, (ii) December 2013 and assigned to eggNOG v4 COG/NOGs, and (iii) November 2016 and assigned to eggNOG v4 COG/NOGs; in all cases using the 50% rule for propagating GO functions across genes within a COG or a NOG. (7Z 391 kb)
DOI: 10.6084/m9.figshare.6802802
title: Additional file 6: of The evolutionary signal in metagenome phyletic profiles predicts many gene functions

description: MPP-I, MPP-H and MPP-O predictions for genes of nine example microbes, given in separate directories in the archive, which are named after the NCBI Taxonomy ID of the selected strain. Two files in each directory contain predictions at a permissive threshold of Pr ≥ 0.1, where one file contains all predictions and the other only predictions that correspond to previously known annotations in the Uniprot-GOA database (December 2013). In the files, columns represent: gene name or synonym, COG/NOG or COGs/NOGs mapped to the gene, and the remaining columns are GO terms (header contains GO ID) that had received at least one prediction at Pr ≥ 0.1 (other GO terms are omitted from the table); cells contain the exact Pr scores at which each prediction was made. (7Z 6989 kb)
DOI: 10.6084/m9.figshare.6802802.v1
title: Additional file 6: of The evolutionary signal in metagenome phyletic profiles predicts many gene functions

description: MPP-I, MPP-H and MPP-O predictions for genes of nine example microbes, given in separate directories in the archive, which are named after the NCBI Taxonomy ID of the selected strain. Two files in each directory contain predictions at a permissive threshold of Pr ≥ 0.1, where one file contains all predictions and the other only predictions that correspond to previously known annotations in the Uniprot-GOA database (December 2013). In the files, columns represent: gene name or synonym, COG/NOG or COGs/NOGs mapped to the gene, and the remaining columns are GO terms (header contains GO ID) that had received at least one prediction at Pr ≥ 0.1 (other GO terms are omitted from the table); cells contain the exact Pr scores at which each prediction was made. (7Z 6989 kb)
DOI: 10.6084/m9.figshare.6802796
title: Additional file 5: of The evolutionary signal in metagenome phyletic profiles predicts many gene functions

description: Table S5. MPP-I vs. matched PP predictions that validated on CAFA 2 Escherichia coli and Pseudomonas aeruginosa benchmarks. Tables contain annotations with precision scores Pr ≥ 0.5 assigned by MPP-I and their matched PP to benchmark genes and the experimentally verified annotations from the benchmarks. Rows are clustered using the R package Seriation (column “Order”). (XLSX 152 kb)
DOI: 10.6084/m9.figshare.6802796.v1
title: Additional file 5: of The evolutionary signal in metagenome phyletic profiles predicts many gene functions

description: Table S5. MPP-I vs. matched PP predictions that validated on CAFA 2 Escherichia coli and Pseudomonas aeruginosa benchmarks. Tables contain annotations with precision scores Pr ≥ 0.5 assigned by MPP-I and their matched PP to benchmark genes and the experimentally verified annotations from the benchmarks. Rows are clustered using the R package Seriation (column “Order”). (XLSX 152 kb)
DOI: 10.6084/m9.figshare.6802781
title: Additional file 4: of The evolutionary signal in metagenome phyletic profiles predicts many gene functions

description: Table S3. Associations between 725 GO terms and 7 environments. Each row in the table represents an association. The 168 associations highlighted in the text are at the top of the table and the selected environment is given in the “EA-Environment” column. (XLSX 117 kb)
DOI: 10.6084/m9.figshare.6802784
title: Additional file 4: of Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

description: Table S3. Relative abundance of functional gene categories related to motility and chemotaxis at subsystem level 3 (SEED database). The highest value for each one has been highlighted in red. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6802781.v1
title: Additional file 4: of The evolutionary signal in metagenome phyletic profiles predicts many gene functions

description: Table S3. Associations between 725 GO terms and 7 environments. Each row in the table represents an association. The 168 associations highlighted in the text are at the top of the table and the selected environment is given in the “EA-Environment” column. (XLSX 117 kb)
DOI: 10.6084/m9.figshare.6802784.v1
title: Additional file 4: of Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

description: Table S3. Relative abundance of functional gene categories related to motility and chemotaxis at subsystem level 3 (SEED database). The highest value for each one has been highlighted in red. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6802766
title: Additional file 3: of The evolutionary signal in metagenome phyletic profiles predicts many gene functions

description: Statistics of overlap between MPP-H and MPP-O predictions made for genes of nine example microbes, tallying assignments of GO terms at confidence of Pr ≥ 50% for the set of GO terms that can be simultaneously predicted by both MPP-H and MPP-O. These statistics reflect only predictions that match known annotations in the Uniprot-GOA database version Dec-2013. (ZIP 18 kb)
DOI: 10.6084/m9.figshare.6802769
title: Additional file 3: of Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

description: Table S2. Summary statistics of the reconstructed genomes obtained from metagenomes. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.6802769.v1
title: Additional file 3: of Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

description: Table S2. Summary statistics of the reconstructed genomes obtained from metagenomes. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.6802766.v1
title: Additional file 3: of The evolutionary signal in metagenome phyletic profiles predicts many gene functions

description: Statistics of overlap between MPP-H and MPP-O predictions made for genes of nine example microbes, tallying assignments of GO terms at confidence of Pr ≥ 50% for the set of GO terms that can be simultaneously predicted by both MPP-H and MPP-O. These statistics reflect only predictions that match known annotations in the Uniprot-GOA database version Dec-2013. (ZIP 18 kb)
DOI: 10.6084/m9.figshare.6802751
title: Additional file 2: of Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

description: Table S1. Relative abundance of 16S rRNA reads. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.6802748
title: Additional file 2: of The evolutionary signal in metagenome phyletic profiles predicts many gene functions

description: Accuracy of MPP-H, MPP-O, and MPP-I classification models, as the AUPRC score (using out-of-bag estimates provided by Random Forest) for individual GO terms. Next to each AUPRC score, the table lists the number of COG/NOG gene families for which that GO term is predicted at Pr thresholds of ≥ 10% (least stringent), ≥ 30%, ≥ 50%, ≥ 70% and ≥ 90% (most stringent). (XLSX 298 kb)
DOI: 10.6084/m9.figshare.6802748.v1
title: Additional file 2: of The evolutionary signal in metagenome phyletic profiles predicts many gene functions

description: Accuracy of MPP-H, MPP-O, and MPP-I classification models, as the AUPRC score (using out-of-bag estimates provided by Random Forest) for individual GO terms. Next to each AUPRC score, the table lists the number of COG/NOG gene families for which that GO term is predicted at Pr thresholds of ≥ 10% (least stringent), ≥ 30%, ≥ 50%, ≥ 70% and ≥ 90% (most stringent). (XLSX 298 kb)
DOI: 10.6084/m9.figshare.6802751.v1
title: Additional file 2: of Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

description: Table S1. Relative abundance of 16S rRNA reads. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.6802544
title: Some relationships between Biology’s autonomy and the emergence of its didactics: considerations about the complexity of teaching a complex science

description: Abstract: In this paper, we discuss some relations between the institutionalization of Biology as an autonomous science and the initial proposals that consider Biology’s didactics as a specific field of knowledge. We believe that Biology teaching shares many characteristics with the teaching of other sciences of nature, but those two didactics also differ in several respects. In this way, we claim that those specific features of Biology as science (like epistemological status of science of living things) have important implications in the field of Biology´s Didactics. In this regard, we appeal to some authors who have put in mind the necessity to recognize which those would be, and then, consider the qualities that make Biology as a different science to, for example, physics and chemistry. We have also taken up some ideas of certain authors who distinguish between Biology´s teaching from teaching of another natural sciences.
DOI: 10.6084/m9.figshare.6802544.v1
title: Some relationships between Biology’s autonomy and the emergence of its didactics: considerations about the complexity of teaching a complex science

description: Abstract: In this paper, we discuss some relations between the institutionalization of Biology as an autonomous science and the initial proposals that consider Biology’s didactics as a specific field of knowledge. We believe that Biology teaching shares many characteristics with the teaching of other sciences of nature, but those two didactics also differ in several respects. In this way, we claim that those specific features of Biology as science (like epistemological status of science of living things) have important implications in the field of Biology´s Didactics. In this regard, we appeal to some authors who have put in mind the necessity to recognize which those would be, and then, consider the qualities that make Biology as a different science to, for example, physics and chemistry. We have also taken up some ideas of certain authors who distinguish between Biology´s teaching from teaching of another natural sciences.
DOI: 10.6084/m9.figshare.6802541
title: Potential of natural repellents methylanthranilate and anthraquinone applied on maize seeds and seedlings against house sparrow (Passer domesticus) in captivity

description: Abstract Various bird pests caused severe economic losses to valuable crops and fruit orchards all over the world. Among the birds, house sparrow is also considered to cause heavy plunder, not only to seeds of crops but also seedlings especially in organic farming. In present study two bird repellents, methylanthranilate and anthraquinone tested against house sparrows on maize seeds and seedlings in aviary conditions. Trial group in aviary-I, the treated maize seeds and seedlings with different doses of both bird repellents, control group in aviary-II, untreated seeds and seedlings were provided for three hours in the early morning. In each aviary, two closed circuit cameras were also installed to monitor the behavioral responses against different concentrations of both chemical repellents. Statistical analysis showed that there existed highly significant (P&lt;0.01) variations among the trial and control groups for seeds and seedlings. By comparing both repellents, significant (P&lt;0.05) differences were detected and anthraquinone showed better efficacy when compared to methylanthranilate, but in maize seedlings both repellents equal repellent properties. Non-significant (P&gt;0.05) differences were observed in different grading of both natural chemical repellents for maize seeds while significant (P&lt;0.05) variations were noticed for maize seedlings when provided to sparrows. By videotaped behavior sparrows presented manifest head juddering and feather upsetting activities by consumption of treated seeds and seedlings with higher concentrations of both natural bird repellents.
DOI: 10.6084/m9.figshare.6802538
title: Structural insights into Plasmodium falciparum nicotinamide mononucleotide adenylyltransferase: oligomeric assembly

description: The biochemical pathways involved in nicotinamide adenine dinucleotide (NAD) biosynthesis converge at the enzymatic step catalysed by nicotinamide mononucleotide adenylyltransferase (NMNAT, EC: 2.7.7.1). The majority of NMNATs are assembled into homo-oligomeric states that comprise 2-6 subunits. Recently, the NMNAT of Plasmodium falciparum (PfNMNAT) has been identified as a pharmacological target. The enzymatic characterisation, cellular location, and tertiary structure of the PfNMNAT protein have been reported. Nonetheless, its quaternary structure remains to be explored. The present study describes the oligomeric assembly of the 6 x His-PfNMNAT recombinant protein using immobilised metal affinity chromatography coupled with size exclusion chromatography (SEC) and native protein electrophoresis combined with Ferguson plot graphing. These chromatographic approaches resulted in the elution of an active monomer from the SEC column, whereas the Ferguson plot indicated a dimeric assembly of the 6 x His-PfNMNAT protein.
DOI: 10.6084/m9.figshare.6802541.v1
title: Potential of natural repellents methylanthranilate and anthraquinone applied on maize seeds and seedlings against house sparrow (Passer domesticus) in captivity

description: Abstract Various bird pests caused severe economic losses to valuable crops and fruit orchards all over the world. Among the birds, house sparrow is also considered to cause heavy plunder, not only to seeds of crops but also seedlings especially in organic farming. In present study two bird repellents, methylanthranilate and anthraquinone tested against house sparrows on maize seeds and seedlings in aviary conditions. Trial group in aviary-I, the treated maize seeds and seedlings with different doses of both bird repellents, control group in aviary-II, untreated seeds and seedlings were provided for three hours in the early morning. In each aviary, two closed circuit cameras were also installed to monitor the behavioral responses against different concentrations of both chemical repellents. Statistical analysis showed that there existed highly significant (P&lt;0.01) variations among the trial and control groups for seeds and seedlings. By comparing both repellents, significant (P&lt;0.05) differences were detected and anthraquinone showed better efficacy when compared to methylanthranilate, but in maize seedlings both repellents equal repellent properties. Non-significant (P&gt;0.05) differences were observed in different grading of both natural chemical repellents for maize seeds while significant (P&lt;0.05) variations were noticed for maize seedlings when provided to sparrows. By videotaped behavior sparrows presented manifest head juddering and feather upsetting activities by consumption of treated seeds and seedlings with higher concentrations of both natural bird repellents.
DOI: 10.6084/m9.figshare.6802538.v1
title: Structural insights into Plasmodium falciparum nicotinamide mononucleotide adenylyltransferase: oligomeric assembly

description: The biochemical pathways involved in nicotinamide adenine dinucleotide (NAD) biosynthesis converge at the enzymatic step catalysed by nicotinamide mononucleotide adenylyltransferase (NMNAT, EC: 2.7.7.1). The majority of NMNATs are assembled into homo-oligomeric states that comprise 2-6 subunits. Recently, the NMNAT of Plasmodium falciparum (PfNMNAT) has been identified as a pharmacological target. The enzymatic characterisation, cellular location, and tertiary structure of the PfNMNAT protein have been reported. Nonetheless, its quaternary structure remains to be explored. The present study describes the oligomeric assembly of the 6 x His-PfNMNAT recombinant protein using immobilised metal affinity chromatography coupled with size exclusion chromatography (SEC) and native protein electrophoresis combined with Ferguson plot graphing. These chromatographic approaches resulted in the elution of an active monomer from the SEC column, whereas the Ferguson plot indicated a dimeric assembly of the 6 x His-PfNMNAT protein.
DOI: 10.6084/m9.figshare.6802532
title: Evaluating the Electrochemical Characteristics of Babassu Coconut Mesocarp Ethanol Produced to Be Used in Fuel Cells

description: The aim of the present study is to assess the potential of ethanol deriving from the mesocarp of babassu coconut to be used in fuel cells. Babassu ethanol was generated through hydrolysis and fermentation processes. The Pt, PtRh and PtRu electrodes were prepared in carbon Vulcan XC72R through the reduction method and applied as electrocatalysts in ethanol oxidation reaction. X-Ray diffraction (XRD), energy-dispersive X-ray (EDX), stripping CO, cyclic voltammetry, chronoamperometry, and online differential electrochemical mass spectrometry (DEMS) were used to characterize the synthesized eletrocatalysts. The electrocatalyst Pt80Ru20/C presented larger active area and higher catalytic activity than other studied materials. The current efficiency of CO2 production rated less than 1% in all studied electrocatalysts, thus showing that babassu ethanol oxidation produces less pollutants than the commercial ethanol.
DOI: 10.6084/m9.figshare.6802535
title: UnB's planning center: historical aspects, structural pathology mapping and intervention proposals

description: Abstract Durability is the ability of the structure to remain in full conditions of utilization, without presenting showing damage that could compromise partly or totally the use for which it was designed. The construction of SG-10 was based on precast walls in form of "U" and coverage of precast prestressed beams. Since its construction has no record of interventions that have been undertaken in order to prolong its service life. Based on this context, and knowing that the set of General Departments pavilions comprises representative buildings of UnB, this article aimed to assess the condition of the SG-10 concrete structure and map the deterioration levels of the elements and present intervention proposals. As an evaluation method was used the Inspections Guide that includes the GDE/UnB methodology as a basis for quantifying damage. After applying the methodology, it was found that the building needs to undergo an intervention process immediately, once recovery services need to be performed.