Find research datasets worth reusing

Data from: A single microphone noise reduction algorithm based on the detection and reconstruction of spectro-temporal features

Animals throughout the animal kingdom excel at extracting individual sounds from competing background sounds, yet current state-of-the-art signal processing algorithms struggle to process speech in the presence of even modest background noise. Recent psychophysical experiments in humans and electrophysiological recordings in animal models suggest that the brain is adapted to process sounds within the restricted domain of spectro-temporal modulations found in natural sounds. Here, we describe a novel single microphone noise reduction algorithm called spectro-temporal detection–reconstruction (STDR) that relies on an artificial neural network trained to detect, extract and reconstruct the spectro-temporal features found in speech. STDR can significantly reduce the level of the background noise while preserving the foreground speech quality and improving estimates of speech intelligibility. In addition, by leveraging the strong temporal correlations present in speech, the STDR algorithm can also operate on predictions of upcoming speech features, retaining similar performance levels while minimizing inherent throughput delays. STDR performs better than a competing state-of-the-art algorithm for a wide range of signal-to-noise ratios and has the potential for real-time applications such as hearing aids and automatic speech recognition.

Data from: Experimental reduction of intromittent organ length reduces male reproductive success in a bug

It is now clear in many species that male and female genital evolution has been shaped by sexual selection. However, it has historically been difficult to confirm correlations between morphology and fitness, as genital traits are complex and manipulation tends to impair function significantly. In this study, we investigate the functional morphology of the elongate male intromittent organ (or processus) of the seed bug Lygaeus simulans, in two ways. We first use micro-computed tomography (micro-CT) and flash-freezing to reconstruct in high resolution the interaction between the male intromittent organ and the female internal reproductive anatomy during mating. We successfully trace the path of the male processus inside the female reproductive tract. We then confirm that male processus length influences sperm transfer by experimental ablation and show that males with shortened processi have significantly reduced post-copulatory reproductive success. Importantly, male insemination function is not affected by this manipulation per se. We thus present rare, direct experimental evidence that an internal genital trait functions to increase reproductive success and show that, with appropriate staining, micro-CT is an excellent tool for investigating the functional morphology of insect genitalia during copulation.

Data from: Quantitative comparison of commercial and non-commercial metal artifact reduction techniques in computed tomography

Objectives: Typical streak artifacts known as metal artifacts occur in the presence of strongly attenuating materials in computed tomography (CT). Recently, vendors have started offering metal artifact reduction (MAR) techniques. In addition, a MAR technique called the metal deletion technique (MDT) is freely available and able to reduce metal artifacts using reconstructed images. Although a comparison of the MDT to other MAR techniques exists, a comparison of commercially available MAR techniques is lacking. The aim of this study was therefore to quantify the difference in effectiveness of the currently available MAR techniques of different scanners and the MDT technique. Materials and Methods: Three vendors were asked to use their preferential CT scanner for applying their MAR techniques. The scans were performed on a Philips Brilliance ICT 256 (S1), a GE Discovery CT 750 HD (S2) and a Siemens Somatom Definition AS Open (S3). The scans were made using an anthropomorphic head and neck phantom (Kyoto Kagaku, Japan). Three amalgam dental implants were constructed and inserted between the phantom's teeth. The average absolute error (AAE) was calculated for all reconstructions in the proximity of the amalgam implants. Results: The commercial techniques reduced the AAE by 22.0±1.6%, 16.2±2.6% and 3.3±0.7% for S1 to S3 respectively. After applying the MDT to uncorrected scans of each scanner the AAE was reduced by 26.1±2.3%, 27.9±1.0% and 28.8±0.5% respectively. The difference in efficiency between the commercial techniques and the MDT was statistically significant for S2 (p=0.004) and S3 (p<0.001), but not for S1 (p=0.63). Conclusions: The effectiveness of MAR differs between vendors. S1 performed slightly better than S2 and both performed better than S3. Furthermore, for our phantom and outcome measure the MDT was more effective than the commercial MAR technique on all scanners.

opencc-zeroAug 2019View details →

Data from: Scalable, semi-automated fluorescence reduction neutralization assay for qualitative assessment of Ebola virus-neutralizing antibodies in human clinical samples

Antibody titers against a viral pathogen are typically measured using an antigen binding assay, such as an enzyme-linked immunosorbent assay (ELISA), which only measures the ability of antibodies to identify a viral antigen of interest. Neutralization assays measure the presence of virus-neutralizing antibodies in a sample. Traditional neutralization assays, such as the plaque reduction neutralization test (PRNT), are often difficult to use on a large scale due to being both labor and resource intensive. Here we describe an Ebola virus fluorescence reduction neutralization assay (FRNA), which tests for neutralizing antibodies, that requires only a small volume of sample in a 96-well format and is easy to automate. The readout of the FRNA is the percentage of Ebola virus-infected cells measured with an optical reader or overall chemiluminescence that can be generated by multiple reading platforms and the readout is compatible with lytic and non-lytic viruses. Using blinded human clinical samples (EVD survivors or contacts) obtained in Liberia during the 2013–2016 Ebola virus disease outbreak, we demonstrate that FRNA-measured antibody titers are highly correlated with those measured by the Filovirus Animal Non-clinical Group (FANG) ELISA - the current standard for anti-EBOV antibody measurement with the important distinction of providing information on the neutralizing capabilities of the antibodies.

opencc-zeroDec 2017View details →

Data from: Reduction of baseline corticosterone secretion correlates with climate warming and drying across wild lizard populations

1. Climate change should lead to massive loss of biodiversity in most taxa but the detailed physiological mechanisms underlying population extinction remain largely elusive so far. In vertebrates, baseline levels of hormones such as glucocorticoids (GCs) may be indicators of population state since their secretion to chronic stress can impair survival and reproduction. However, the relationship between GC secretion, climate change and population extinction risk remains unclear. 2. In this study we investigated whether levels of baseline corticosterone (the main GCs in reptiles) correlate with environmental conditions and associated extinction risk across wild populations of the common lizard Zootoca vivipara. 3. First, we performed a cross-sectional comparison of baseline corticosterone levels along an altitudinal gradient among 14 populations. Then, we used a longitudinal study in 8 populations to examine the changes in corticosterone levels following the exposure to a heat wave period. 4. Unexpectedly, baseline corticosterone decreased with increasing thermal conditions at rest in females, and was not correlated with extinction risk. In addition, baseline corticosterone levels decreased after exposure to an extreme heat wave period. This seasonal corticosterone decrease was more pronounced in populations without access to standing water. 5. We suggest that low basal secretion of corticosterone may entail down-regulating activity levels and limit exposure to adverse climatic conditions, especially to reduce water loss. These new insights suggest that rapid population decline might be preceded by a down-regulation of the corticosterone secretion.

Data from: Evolution of drug-tolerant nematode populations in response to density reduction

Resistance to xenobiotics remains a pressing issue in parasite treatment and global agriculture. Multiple factors may affect the evolution of resistance, including interactions between life-history traits and the strength of selection imposed by different drug-doses. We experimentally created replicate selection lines of free-living Caenorhabditis remanei exposed to Ivermectin at high and low doses to assess whether survivorship of lines selected in drug-treated environments increased, and if this varied with dose. Additionally, we maintained lines where mortality was imposed randomly to control for differences in density between drug-treatments and to distinguish between the evolutionary consequences of drug-treatment vs ecological processes due to changes in density-dependent feedback. After 10 generations we exposed all of the selected lines to high-dose, low-dose and drug-free environments to evaluate evolutionary changes in survivorship as well as any costs to adaptation. Both adult and juvenile survival was measured to explore relationships between life-history stage, selection regime and survival. Intriguingly, both drug-selected and random-mortality lines showed an increase in survivorship when challenged with Ivermectin; the magnitude of this increase varied with the intensity of selection and life-history stage. Our results suggest that interactions between density-dependent processes and life-history may mediate evolved changes in susceptibility to control measures.

opencc-zeroDec 2017View details →

Data from: Functional redundancy in bird community decreases with riparian forest width reduction

1. Riparian ecosystems are suffering anthropogenic threats that reduce biodiversity and undermine ecosystem services. However, there is a great deal of uncertainty about the way species composition of assemblages is related to ecosystem function, especially in a landscape fragmentation context. 2. Here we assess the impact of habitat loss and disturbance on Functional Diversity (FD) components Functional Redundancy (FRed), Functional Evenness (FEve) and Functional Richness (FRic) of riparian forest bird assemblages to evaluate (1) how FD components respond to riparian forest width reduction and vegetation disturbance; (2) the existence of thresholds within these relationships; (3) which of the main birds diet guild (frugivores, insectivores and omnivores) respond to such thresholds. We predict that FD components will be affected negatively and non-linearly by riparian changes. However, guilds could have different responses due to differences of species sensitivity to fragmentation and disturbance. We expect to find thresholds in FD responses, because fragmentation and disturbance drive loss of specific FD components. 3. Our results show that FRed and FEve were linearly affected by width and disturbance of riparian habitats, respectively. FRed was significantly lower in riparian forests assemblages below 400 m wide and FEve was significantly higher above 60% disturbance. These responses of FD were also followed to the decline in insectivores and frugivores richness in riparian forests most affected by these changes. 4. Consequently, our study suggests communities do not tolerate reduction in riparian forest width or disturbance intensification without negative impact on FD, and this becomes more critical for riparian area less than 400 m wide or with more than 60% disturbance. This minimum riparian width required to maintain FRed is greater than the minimum width required for riparian forests by Brazilian law. Thus, is important to consider mechanisms to expand riparian habitats and reduce the disturbance intensity in riparian forests so that riparian bird community FD may be effectively conserved.

opencc-zeroDec 2018View details →

Data from: Extensive reduction of the nuclear pore complex in nucleomorphs

The nuclear pore complex (NPC) is a large macromolecular assembly situated within the pores of the nuclear envelope. Through interactions between its subcomplexes and import proteins, the NPC mediates the transport of molecules into and out of the nucleus and facilitates dynamic chromatin regulation and gene expression. Accordingly, the NPC constitutes a highly integrated nuclear component that is ubiquitous and conserved amongst eukaryotes. Potential exceptions to this are nucleomorphs: highly reduced, relict nuclei that were derived from green and red algae following their endosymbiotic integration into two lineages, the chlorarachniophytes and the cryptophyceans. A previous investigation failed to identify NPC genes in nucleomorph genomes suggesting that these genes have either been relocated to the host nucleus or lost. Here we sought to investigate the composition of the NPC in nucleomorphs by using genomic and transcriptomic data to identify and phylogenetically classify NPC proteins in nucleomorph-containing algae. Although we found NPC proteins in all examined lineages, most of those found in chlorarachniophytes and cryptophyceans were single copy, host-related proteins that lacked signal peptides. Two exceptions were Nup98 and Rae1, which had clear nucleomorph-derived homologues. However, these proteins alone are likely insufficient to structure a canonical NPC and previous reports revealed that Nup98 and Rae1 have other nuclear functions. Ultimately, these data indicate that nucleomorphs represent eukaryotic nuclei without a canonical NPC, raising fundamental questions about their structure and function.

Data from: Distributed cognition and social brains: reductions in mushroom body investment accompanied the origins of sociality in wasps (Hymenoptera: Vespidae)

The social brain hypothesis assumes the evolution of social behaviour changes animals' ecological environments, and predicts evolutionary shifts in social structure will be associated with changes in brain investment. Most social brain models to date assume social behaviour imposes additional cognitive challenges to animals, favouring the evolution of increased brain investment. Here, we present a modification of social brain models, which we term the distributed cognition hypothesis. Distributed cognition models assume group members can rely on social communication instead of individual cognition; these models predict reduced brain investment in social species. To test this hypothesis, we compared brain investment among 29 species of wasps (Vespidae family), including solitary species and social species with a wide range of social attributes (i.e. differences in colony size, mode of colony founding and degree of queen/worker caste differentiation). We compared species means of relative size of mushroom body (MB) calyces and the antennal to optic lobe ratio, as measures of brain investment in central processing and peripheral sensory processing, respectively. In support of distributed cognition predictions, and in contrast to patterns seen among vertebrates, MB investment decreased from solitary to social species. Among social species, differences in colony founding, colony size and caste differentiation were not associated with brain investment differences. Peripheral lobe investment did not covary with social structure. These patterns suggest the strongest changes in brain investment—a reduction in central processing brain regions—accompanied the evolutionary origins of eusociality in Vespidae.

opencc-zeroDec 2017View details →

Data from: Effects of breathing movement on the reduction of postural sway during postural-cognitive dual tasking

An execution of cognitive processing interferes with postural sway during quiet standing. It reduces sway variability in young adults, but the mechanism is not clear. To elucidate the mechanisms, we focused on breathing in the present study. The purpose of this study was to clarify whether a decrease in postural sway amplitude during a postural-cognitive task is related to the change in breathing movement. The center of pressure (COP) was recorded via a force plate and the motion of leg joints (ankle, knee, and hip), and breathing movements were measured with a 3D motion capture system in quiet standing and standing with cognitive (mental arithmetic) task conditions. The change ratios of each variable from the quiet standing condition to the cognitive task were also calculated. In the results, the breathing rate was faster and the amplitude of breathing movement smaller when subjects performed the cognitive task. A significant positive correlation (r = 0.75, p < 0.01) was found between the change ratio of breathing amplitude and the COP amplitude. The present results suggest that reduced standing postural sway during a cognitive task is related, at least in part, to a decrease in breathing amplitude.

Data from: Conditional reduction of predation risk associated with a facultative symbiont in an insect

Symbionts are widespread among eukaryotes and their impacts on the ecology and evolution of their hosts are meaningful. Most insects harbour obligate and facultative symbiotic bacteria that can influence their phenotype. In the pea aphid Acyrthosiphon pisum, an astounding symbiotic-mediated phenotype has been recently observed: when infected with the symbiotic bacteria Rickettsiella viridis, young red aphid larvae become greener at adulthood and even darker green when co-infected with Rickettsiella viridis and Hamiltonella defensa. As body colour affects the susceptibility towards natural enemies in aphids, the influence of the colour change due to these facultative symbionts on the host survival in presence of predators was tested. Our results suggested that the Rickettsiella viridis infection may impact positively host survival by reducing predation risk. Due to results from uninfected aphids (i.e., more green ones attacked), the main assumption is that this symbiotic infection would deter the predatory ladybird feeding by reducing the profitability of their hosts rather than decreasing host detection through body colour change. Aphids co-infected with Rickettsiella viridis and Hamiltonella defensa were, however, more exposed to predation suggesting an ecological cost associated with multiple infections. The underlying mechanisms and ecological consequences of these symbiotic effects are discussed.

Data from: Impact of genetic reduction of NMNAT2 on chemotherapy-induced losses in cell viability in vitro and peripheral neuropathy in vivo

Nicotinamide mononucleotide adenylyl transferases (NMNATs) are essential neuronal maintenance factors postulated to preserve neuronal function and protect against axonal degeneration in various neurodegenerative disease states. We used in vitro and in vivo approaches to assess the impact of NMNAT2 reduction on cellular and physiological functions induced by treatment with a vinca alkaloid (vincristine) and a taxane-based (paclitaxel) chemotherapeutic agent. NMNAT2 null (NMNAT2-/-) mutant mice die at birth and cannot be used to probe functions of NMNAT2 in adult animals. Nonetheless, primary cortical cultures derived from NMNAT2-/- embryos showed reduced cell viability in response to either vincristine or paclitaxel treatment whereas those derived from NMNAT2 heterozygous (NMNAT2+/-) mice were preferentially sensitive to vincristine-induced degeneration. Adult NMNAT2+/- mice, which survive to adulthood, exhibited a 50% reduction of NMNAT2 protein levels in dorsal root ganglia relative to wildtype (WT) mice with no change in levels of other NMNAT isoforms (NMNAT1 or NMNAT3), NMNAT enzyme activity (i.e. NAD/NADH levels) or microtubule associated protein-2 (MAP2) or neurofilament protein levels. We therefore compared the impact of NMNAT2 knockdown on the development and maintenance of chemotherapy-induced peripheral neuropathy induced by vincristine and paclitaxel treatment using NMNAT2+/- and WT mice. NMNAT2+/- did not differ from WT mice in either the development or maintenance of either mechanical or cold allodynia induced by either vincristine or paclitaxel treatment. Intradermal injection of capsaicin, the pungent ingredient in hot chili peppers, produced equivalent hypersensitivity in NMNAT2+/- and WT mice receiving vehicle in lieu of paclitaxel. Capsaicin-evoked hypersensitivity was enhanced by prior paclitaxel treatment but did not differ in either NMNAT2+/- or WT mice. Thus, capsaicin failed to unmask differences in nociceptive behaviors in either paclitaxel-treated or paclitaxel-untreated NMNAT2+/- and WT mice. Moreover, no differences in motor behavior were detected between genotypes in the rotarod test. Our studies do not preclude the possibility that complete knockout of NMNAT2 in a conditional knockout animal could unmask a role for NMNAT2 in protection against detrimental effects of chemotherapeutic treatment.

Data from: State-space reduction and equivalence class sampling for a molecular self-assembly model

Direct simulation of a model with a large state space will generate enormous volumes of data, much of which is not relevant to the questions under study. In this paper, we consider a molecular self-assembly model as a typical example of a large state-space model, and present a method for selectively retrieving 'target information' from this model. This method partitions the state space into equivalence classes, as identified by an appropriate equivalence relation. The set of equivalence classes H, which serves as a reduced state space, contains none of the superfluous information of the original model. After construction and characterization of a Markov chain with state space H, the target information is efficiently retrieved via Markov chain Monte Carlo sampling. This approach represents a new breed of simulation techniques which are highly optimized for studying molecular self-assembly and, moreover, serves as a valuable guideline for analysis of other large state-space models.

opencc-zeroAug 2016View details →

Data file for the paper "Mechanistic Insights into the Oxygen Reduction Reaction on Metal--N--C Electrocatalysts under Fuel Cell Conditions", ChemElectroChem , 2016, DOI: 10.1002/celc.201600354

Dataset for the above paper.

opencc-zeroAug 2016View details →

Data file for the paper "Mechanistic Insights into the Oxygen Reduction Reaction on Metal--N--C Electrocatalysts under Fuel Cell Conditions", ChemElectroChem , 2016, DOI: 10.1002/celc.201600354

Dataset for the above paper

opencc-by-4.0Apr 2024View details →

Measurement Data for "LIRPA: Parallelized List Reductions for Language Agnostic Test Case Reducers"

Open the record for dataset details and reuse information.

opencc-zeroJul 2022View details →

Raw data of: Changes in magnetic properties of magnetite nanoparticles upon microbial iron reduction

The magnetic signals of magnetite nanoparticles (NPs) preserved in rocks, soils, and sediments are effective index for paleoenvironmental reconstruction. It has been demonstrated that magnetite NPs can serve as a terminal electron sink for the microbial respiration (i.e., microbial iron reduction). The magnetic properties of magnetite NPs may be altered by microbial iron reduction, which is a critical but often overlooked process in paleomagnetism. In this study, three magnetite NPs with different particle sizes were reduced by a dissimilatory iron-reducing bacterium (Shewanella oneidensis MR-1) under a non-growth condition mimicking that of the early Earth and modern oligotrophic environment. The changes in magnetic, chemical as well as crystallographic properties of the magnetite NPs during the microbial reduction process were examined. Our results showed that the bioreduction rate of magnetite NPs was mainly controlled by their particle size and redox state. In addition, the microbial iron reduction could affect both the crystallographic and magnetic properties of three types of magnetite NPs used herein. After bioreduction, the crystal lattice parameters and magnetic susceptibility of the magnetite NPs increased, while their remanence recording capability and coercivity decreased (i.e., "softer" magnetism). Furthermore, bioreduced magnetite NPs had a larger remanence loss near the Verwey transition region with low-temperature magnetic analysis. These results indicate that the microbial reduction of magnetite NPs deserves attention when sedimentary magnetites are used in paleoenvironment reconstruction.

opencc-by-4.0May 2024View details →

Data and code for synergistic reductions

Open the record for dataset details and reuse information.

opencc-by-4.0Jun 2024View details →

Comparison of dimensional reduction methods in Raman spectral data of mouse uterus and placenta tissues

Open the record for dataset details and reuse information.