cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5001896
title: Dataset for: Structural features of Aspergillus niger β-galactosidase define its activity against glycoside linkages

description: β-galactosidases are biotechnologically interesting enzymes that catalyze the hydrolysis or transgalactosylation of β-galactosides. Among them, the Aspergillus niger β-galactosidase (AnβGal) belongs to the glycoside hydrolase family 35 (GH35) and is widely used in the industry due to its high hydrolytic activity degrading lactose. We present here its three-dimensional structure in complex with different oligosaccharides, to illustrate the structural determinants of the broad specificity of the enzyme against different glycoside linkages. Remarkably, the residues Phe264, Tyr304 and Trp806 make a dynamic hydrophobic platform that accommodates the sugar at subsite +1 suggesting a main role on the recognition of structurally different substrates. Moreover, complexes with the trisaccharides show two potential subsites +2 depending on the substrate type. This feature and the peculiar shape of its wide cavity suggest that AnβGal might accommodate branched substrates from the complex net of polysaccharides composing the plant material in its natural environment. Relevant residues were selected and mutagenesis analyses were performed to evaluate their role in the catalytic performance and the hydrolase/transferase ratio of AnβGal. Thus, we generated mutants with improved transgalactosylation activity. In particular, the variant Y304F/Y355H/N357G/W806F displays a higher level of galacto-oligosaccharides (GOS) production than the Aspergillus oryzae β-galactosidase, which is the preferred enzyme in the industry owing to its high transferase activity. Our results provide new knowledge on the determinants modulating specificity and the catalytic performance of fungal GH35 β-galactosidases. In turn, this fundamental background gives novel tools for the future improvement of these enzymes, which represent an interesting target for rational design.
DOI: 10.6084/m9.figshare.5001902.v1
title: Dataset for: Quantum chemical modeling of the reaction path of chorismate mutase based on the experimental substrate/product complex

description: Chorismate mutase is a well-known model enzyme, catalyzing the Claisen rearrangement of chorismate to prephenate. Recent high-resolution crystal structures along the reaction coordinate of this enzyme enable computational analyses at unprecedented detail. Using quantum chemical simulations, we have investigated how the catalytic reaction mechanism is affected by electrostatic and hydrogen bond interactions. Our calculations showed that the transition state was mainly stabilized electrostatically, with Arg90 playing the leading role. The effect was augmented by selective hydrogen bond formation to the transition state in the wild-type enzyme, facilitated by a small-scale local induced fit. We further identified a previously underappreciated water molecule, which separates the negative charges during the reaction. The analysis includes the wild-type enzyme and a non-natural enzyme variant, where the catalytic arginine was replaced with an isosteric citrulline residue.
DOI: 10.6084/m9.figshare.5001920.v2
title: Dedicated Cardiac Rehabilitation Wearable Sensor and Its Clinical Potential

description: We introduce our developed wearable sensor for cardiac rehabilitation (CR) exercise. For an efficient guide for CR exercise, the dedicated CR wearable sensor (DCRW) automatically recommends the exercise intensity to a patient by comparing the real-time measured heart rate (HR) with a predefined target heart rate zone (THZ) during exercise.
DOI: 10.6084/m9.figshare.5001896.v1
title: Dataset for: Structural features of Aspergillus niger β-galactosidase define its activity against glycoside linkages

description: β-galactosidases are biotechnologically interesting enzymes that catalyze the hydrolysis or transgalactosylation of β-galactosides. Among them, the Aspergillus niger β-galactosidase (AnβGal) belongs to the glycoside hydrolase family 35 (GH35) and is widely used in the industry due to its high hydrolytic activity degrading lactose. We present here its three-dimensional structure in complex with different oligosaccharides, to illustrate the structural determinants of the broad specificity of the enzyme against different glycoside linkages. Remarkably, the residues Phe264, Tyr304 and Trp806 make a dynamic hydrophobic platform that accommodates the sugar at subsite +1 suggesting a main role on the recognition of structurally different substrates. Moreover, complexes with the trisaccharides show two potential subsites +2 depending on the substrate type. This feature and the peculiar shape of its wide cavity suggest that AnβGal might accommodate branched substrates from the complex net of polysaccharides composing the plant material in its natural environment. Relevant residues were selected and mutagenesis analyses were performed to evaluate their role in the catalytic performance and the hydrolase/transferase ratio of AnβGal. Thus, we generated mutants with improved transgalactosylation activity. In particular, the variant Y304F/Y355H/N357G/W806F displays a higher level of galacto-oligosaccharides (GOS) production than the Aspergillus oryzae β-galactosidase, which is the preferred enzyme in the industry owing to its high transferase activity. Our results provide new knowledge on the determinants modulating specificity and the catalytic performance of fungal GH35 β-galactosidases. In turn, this fundamental background gives novel tools for the future improvement of these enzymes, which represent an interesting target for rational design.
DOI: 10.6084/m9.figshare.5001869
title: Dataset for: Detecting the Significant Flux Backbone of <i>Escherichia coli </i>metabolism

description: The heterogeneity of computationally predicted reaction fluxes in metabolic networks within a single flux state can be exploited to detect their significant flux backbone. Here, we disclose the backbone of <i>Escherichia coli</i>, and compare it with the backbones of other bacteria. We find that, in general, the core of the backbones is mainly composed of reactions in energy metabolism corresponding to ancient pathways. In <i>E. coli</i>, the synthesis of nucleotides and the metabolism of lipids form smaller cores which rely critically on energy metabolism. Moreover, the consideration of different media leads to the identification of pathways sensitive to environmental changes. The metabolic backbone of an organism is thus useful to trace simultaneously both its evolution and adaptation fingerprints.
DOI: 10.6084/m9.figshare.5001866
title: Bird species richness and densities in relation to sulphur dioxide gradients and environmental variables

description: The expansion of coal-fired power stations in South Africa has resulted in growing environmental concerns as they are the largest emitters of sulphur dioxide (SO<sub>2</sub>). Sulphur dioxide emissions from power plants pose a potential threat to avian populations. However, the effect of SO<sub>2</sub> pollution on bird communities is poorly understood. Using point counts we investigated the relationships of bird species richness and species-specific density with SO<sub>2</sub> concentrations around Matimba power station. Environmental parameters were derived from remotely sensed data and data reduction was performed using principal component analysis. Generalised linear mixed models were then used to infer the relationships of bird species richness and species-specific densities with SO<sub>2</sub> concentrations and the environmental variables. Our results revealed that SO<sub>2</sub>-polluted air had no influence on bird species richness and densities in our study sites, but SO<sub>2</sub> levels were below annual national ambient air quality standards. Vegetation productivity was found to have a greater influence on species densities than SO<sub>2</sub> pollution. Monitoring of bird population changes around Matimba power station once neighbouring Medupi power station is fully operational is recommended, as SO<sub>2</sub> content of the air will increase significantly, and species may be sensitive to this increase in SO<sub>2</sub> levels.
DOI: 10.6084/m9.figshare.5001869.v1
title: Dataset for: Detecting the Significant Flux Backbone of <i>Escherichia coli </i>metabolism

description: The heterogeneity of computationally predicted reaction fluxes in metabolic networks within a single flux state can be exploited to detect their significant flux backbone. Here, we disclose the backbone of <i>Escherichia coli</i>, and compare it with the backbones of other bacteria. We find that, in general, the core of the backbones is mainly composed of reactions in energy metabolism corresponding to ancient pathways. In <i>E. coli</i>, the synthesis of nucleotides and the metabolism of lipids form smaller cores which rely critically on energy metabolism. Moreover, the consideration of different media leads to the identification of pathways sensitive to environmental changes. The metabolic backbone of an organism is thus useful to trace simultaneously both its evolution and adaptation fingerprints.
DOI: 10.6084/m9.figshare.5001920.v3
title: Dedicated Cardiac Rehabilitation Wearable Sensor and Its Clinical Potential

description: We introduce our developed wearable sensor for cardiac rehabilitation (CR) exercise. For an efficient guide for CR exercise, the dedicated CR wearable sensor (DCRW) automatically recommends the exercise intensity to a patient by comparing the real-time measured heart rate (HR) with a predefined target heart rate zone (THZ) during exercise.
DOI: 10.6084/m9.figshare.5001857
title: Identification of candidate proteins interacted with ovalbumin during the early phase of embryonic development

description: In the present study, protein complexes emerged in high molecular weight (MW) region (95–170 kDa) were observed in fertilised chicken egg white after 7 days of incubation. Investigations were performed to reveal the possible proteins involved in these complexes. The emerged 10 protein bands from SDS-PAGE gel were confirmed to be ovalbumin through matrix-assisted laser desorption/ionisation time-of-flight tandem mass spectrometry (MALDI-TOF MS/MS) followed by Western blot analysis. To reveal the possible interactions among ovalbumin and other egg white proteins, LC connected to LTQ-Orbitrap mass spectrometer was used. Besides ovalbumin, 11 egg white proteins were identified including ovotransferrin, lysozyme, ovalbumin-related protein X, ovalbumin-related protein Y, hep21, alpha-enolase, ovoinhibitor, and a protein similar to ryanodine receptor 1. These results indicated widespread thermal-induced protein interactions among ovalbumin and other egg white proteins.
DOI: 10.6084/m9.figshare.5001866.v2
title: Bird species richness and densities in relation to sulphur dioxide gradients and environmental variables

description: The expansion of coal-fired power stations in South Africa has resulted in growing environmental concerns as they are the largest emitters of sulphur dioxide (SO<sub>2</sub>). Sulphur dioxide emissions from power plants pose a potential threat to avian populations. However, the effect of SO<sub>2</sub> pollution on bird communities is poorly understood. Using point counts we investigated the relationships of bird species richness and species-specific density with SO<sub>2</sub> concentrations around Matimba power station. Environmental parameters were derived from remotely sensed data and data reduction was performed using principal component analysis. Generalised linear mixed models were then used to infer the relationships of bird species richness and species-specific densities with SO<sub>2</sub> concentrations and the environmental variables. Our results revealed that SO<sub>2</sub>-polluted air had no influence on bird species richness and densities in our study sites, but SO<sub>2</sub> levels were below annual national ambient air quality standards. Vegetation productivity was found to have a greater influence on species densities than SO<sub>2</sub> pollution. Monitoring of bird population changes around Matimba power station once neighbouring Medupi power station is fully operational is recommended, as SO<sub>2</sub> content of the air will increase significantly, and species may be sensitive to this increase in SO<sub>2</sub> levels.
DOI: 10.6084/m9.figshare.5001857.v1
title: Identification of candidate proteins interacted with ovalbumin during the early phase of embryonic development

description: In the present study, protein complexes emerged in high molecular weight (MW) region (95–170 kDa) were observed in fertilised chicken egg white after 7 days of incubation. Investigations were performed to reveal the possible proteins involved in these complexes. The emerged 10 protein bands from SDS-PAGE gel were confirmed to be ovalbumin through matrix-assisted laser desorption/ionisation time-of-flight tandem mass spectrometry (MALDI-TOF MS/MS) followed by Western blot analysis. To reveal the possible interactions among ovalbumin and other egg white proteins, LC connected to LTQ-Orbitrap mass spectrometer was used. Besides ovalbumin, 11 egg white proteins were identified including ovotransferrin, lysozyme, ovalbumin-related protein X, ovalbumin-related protein Y, hep21, alpha-enolase, ovoinhibitor, and a protein similar to ryanodine receptor 1. These results indicated widespread thermal-induced protein interactions among ovalbumin and other egg white proteins.
DOI: 10.6084/m9.figshare.5001854
title: Dataset for: The Hfq regulon of <i>Neisseria meningitidis</i>

description: The conserved RNA-binding protein Hfq has multiple regulatory roles within the prokaryotic cell, including promoting stable duplex formation between small RNAs and mRNAs, and thus <i>hfq</i> deletion mutants have pleiotropic phenotypes. Previous proteome and transcriptome studies of <i>Neisseria meningitidis</i> have generated limited insight into differential gene expression due to Hfq loss. In this study, reversed-phase liquid chromatography combined with data-independent alternate scanning mass spectrometry (LC-MS<sup>E</sup>) was utilized for rapid high-resolution quantitative proteomic analysis to further elucidate the differentially expressed proteome of a meningococcal <i>hfq</i> deletion mutant. Whole cell lysates of <i>N. meningitidis</i> serogroup B H44/76 wild type (wt) and H44/76Δ<i>hfq</i> (Δ<i>hfq</i>) grown in liquid growth medium were subjected to tryptic digestion. The resulting peptide mixtures were separated by LC prior to analysis by MS<sup>E</sup>. Differential expression was analyzed by Student’s <i>t</i>-Test with control for false discovery rate (FDR). Reliable quantification of relative expression comparing wt and Δ<i>hfq</i> was achieved with 506 proteins (20%). Upon FDR control at <i>q</i> ≤ 0.05, 48 up- and 59 downregulated proteins were identified. From these, 81 were identified as novel Hfq-regulated candidates, while 15 proteins were previously found by SDS-PAGE/MS and 24 with microarray analyses. Thus, using LC-MS<sup>E</sup> we have expanded the repertoire of Hfq regulated proteins. In conjunction with previous studies, a comprehensive network of Hfq regulated proteins was constructed and differentially expressed proteins were found to be involved in a large variety of cellular processes. The results and comparisons with other Gram-negative model systems, suggest still unidentified sRNA analogues in <i>N. meningitidis</i>.
DOI: 10.6084/m9.figshare.5001848
title: Computation of ultimate SAR amplification factors for radiofrequency hyperthermia in non-uniform body models: impact of frequency and tumour location

description: <b>Purpose:</b> We introduce a method for calculation of the ultimate specific absorption rate (SAR) amplification factors (uSAF) in non-uniform body models. The uSAF is the greatest possible SAF achievable by any hyperthermia (HT) phased array for a given frequency, body model and target heating volume. <b>Methods:</b> First, we generate a basis-set of solutions to Maxwell’s equations inside the body model. We place a large number of electric and magnetic dipoles around the body model and excite them with random amplitudes and phases. We then compute the electric fields created in the body model by these excitations using an ultra-fast volume integral solver called MARIE. We express the field pattern that maximises the SAF in the target tumour as a linear combination of these basis fields and optimise the combination weights so as to maximise SAF (concave problem). We compute the uSAFs in the Duke body models at 10 frequencies in the 20–900 MHz range and for twelve 3 cm-diameter tumours located at various depths in the head and neck. <b>Results:</b> For both shallow and deep tumours, the frequency yielding the greatest uSAF was ∼900 MHz. Since this is the greatest frequency that we simulated, we hypothesise that the globally optimal frequency is actually greater. <b>Conclusions:</b> The uSAFs computed in this work are very large (40–100 for shallow tumours and 4–17 for deep tumours), indicating that there is a large room for improvement of the current state-of-the-art head and neck HT devices.
DOI: 10.6084/m9.figshare.5001848.v1
title: Computation of ultimate SAR amplification factors for radiofrequency hyperthermia in non-uniform body models: impact of frequency and tumour location

description: <b>Purpose:</b> We introduce a method for calculation of the ultimate specific absorption rate (SAR) amplification factors (uSAF) in non-uniform body models. The uSAF is the greatest possible SAF achievable by any hyperthermia (HT) phased array for a given frequency, body model and target heating volume. <b>Methods:</b> First, we generate a basis-set of solutions to Maxwell’s equations inside the body model. We place a large number of electric and magnetic dipoles around the body model and excite them with random amplitudes and phases. We then compute the electric fields created in the body model by these excitations using an ultra-fast volume integral solver called MARIE. We express the field pattern that maximises the SAF in the target tumour as a linear combination of these basis fields and optimise the combination weights so as to maximise SAF (concave problem). We compute the uSAFs in the Duke body models at 10 frequencies in the 20–900 MHz range and for twelve 3 cm-diameter tumours located at various depths in the head and neck. <b>Results:</b> For both shallow and deep tumours, the frequency yielding the greatest uSAF was ∼900 MHz. Since this is the greatest frequency that we simulated, we hypothesise that the globally optimal frequency is actually greater. <b>Conclusions:</b> The uSAFs computed in this work are very large (40–100 for shallow tumours and 4–17 for deep tumours), indicating that there is a large room for improvement of the current state-of-the-art head and neck HT devices.
DOI: 10.6084/m9.figshare.5001362
title: Importance of ultrasonography re-evaluation for referred patients diagnosed with thyroid cancer

description: <b>raw data</b>
DOI: 10.6084/m9.figshare.5001359
title: The Intestinal TORC2 Signaling Pathway contributes to Associative Learning in Caenorhabditis elegans

description: These are raw data of the paper titled "The Intestinal TORC2 Signaling Pathway contributes to Associative Learning in Caenorhabditis elegans".<br><br>
DOI: 10.6084/m9.figshare.5001353
title: Fish acoustics in China

description: Analyzed data for the 66 fish call types
DOI: 10.6084/m9.figshare.5001359.v1
title: The Intestinal TORC2 Signaling Pathway contributes to Associative Learning in Caenorhabditis elegans

description: These are raw data of the paper titled "The Intestinal TORC2 Signaling Pathway contributes to Associative Learning in Caenorhabditis elegans".<br><br>
DOI: 10.6084/m9.figshare.5001314
title: Microbial Biogeography Study - Meyer et al. 2018 ISME-J

description: The V3 and V4 region of the 16S rRNA gene of the DNA and cDNA amplified using the primers 319F and 806R. Data are demultiplexed, quality-filtered, trimmed fasta files with primers removed. <br>OTU tables are from 2 community inference methods: DNA- based and RNA (cDNA)- based. OTU tables also differ by similarity threshold, i.e. 95, 97, 99, and 100% sequence similarity. None of these tables have been rarefied or normalized, thus differences in sequencing depth (i.e. sampling extent) across samples will vary. Naming convention is as follows: 'otu_table_rabi_uparse_{OTU sequence similarity threshold}_{community inference method}.txt'. Only OTU tables at 97% cutoff have taxonomic assignments. <br>'Rabi_geodist_matrix.txt' is a matrix of pairwise geographic distance (in meters) between samples. <br>'soil_chemical_data_pared.txt' is a table with soil chemical attributes as columns and samples as rows. <br>'Sampling_effort_DD.R' is an R function that performs a single rarefaction of a community matrix, calculates the slope of the distance-decay relationship of that community, then repeats iteratively.<br>Please cite: Meyer et al. 2018 ISME-J, DOI: 10.1038/s41396-018-0103-3
DOI: 10.6084/m9.figshare.5001317
title: Supplementary datasets for "On the relative importance of thermal and chemical buoyancy in regular and impact-induced melting in a Mars-like planet" by Ruedas & Breuer (2017)

description: Datasets displayed in Figures 2, 3, 4, 6, 7, 8, and A.1 of the main text.
DOI: 10.6084/m9.figshare.5001317.v1
title: Supplementary datasets for "On the relative importance of thermal and chemical buoyancy in regular and impact-induced melting in a Mars-like planet" by Ruedas & Breuer (2017)

description: Datasets displayed in Figures 2, 3, 4, 6, 7, 8, and A.1 of the main text.
DOI: 10.6084/m9.figshare.5001305
title: Optimal Interim Decision Rules Based on a Binary Surrogate Outcome for Adaptive Biomarker-Based Trials in Oncology

description: Adaptive enrichment designs represent a promising approach to evaluate targeted therapies, for example, in oncology. They allow selection of the most promising target population in an interim analysis and then combination of the data from the two trial stages for the final proof of efficacy. Application of these designs is motivated by the assumption that there might be a biomarker-defined subgroup of patients with an increased treatment benefit as compared to the total patient population. If the primary outcome is a time-to-event variable and the respective event takes a relatively long time to be observed, it could be beneficial to select the most promising patient population based on an earlier available binary surrogate, for example, response, to save time and costs. We propose an adaptive enrichment design which allows us to implement such a trial setting. For this design, optimal decision rules are derived minimizing the expected loss incurred due to a false interim decision. These rules are compared to ad hoc rules in terms of selection probability and power within a simulation study which is motivated by a clinical trial example. Furthermore, the impact of the correlation between surrogate and primary outcome on power is investigated. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5001302
title: Increased placental sFlt-1 but unchanged PlGF expression in late-onset preeclampsia

description: <i>Objective</i>: To investigate whether differences between late-onset preeclampsia (PE) and intrauterine growth restriction (IUGR) can be explained by differential placental expression patters of sFlt-1, Flt-1, and placental growth factor (PlGF). <i>Methods</i>: Placental tissues and maternal blood samples from seven patients with PE, five IUGR, and seven age-matched controls were studied for mRNA and protein levels as well as protein localization and expression intensity. <i>Results</i>: Placental PlGF mRNA and protein expression were not altered by placental dysfunction while placental villous trophoblast expression intensity of PlGF was increased. <i>Conclusion</i>: High sFlt-1 concentrations may account for diminished maternal serum PlGF levels.