The Semantic Web MIDI Tape: An Interface for Interlinking MIDI and Context Metadata

The Linked Data paradigm has been used to publish a large number of musical datasets and ontologies on the Semantic Web, such as MusicBrainz, AcousticBrainz, and the Music Ontology. Recently, the MIDI Linked Data Cloud has been added to these datasets, representing more than 300,000 pieces in MIDI format as Linked Data, opening up the possibility for linking fine-grained symbolic music representations to existing music metadata databases. Despite the dataset making MIDI resources available in Web data standard formats such as RDF and SPARQL, the important issue of finding meaningful links between these MIDI resources and relevant contextual metadata in other datasets remains. A fundamental barrier for the provision and generation of such links is the difficulty that users have at adding new MIDI performance data and metadata to the platform. In this paper, we propose the Semantic Web MIDI Tape, a set of tools and associated interface for interacting with the MIDI Linked Data Cloud by enabling users to record, enrich, and retrieve MIDI performance data and related metadata in native Web data standards. The goal of such interactions is to find meaningful links between published MIDI resources and their relevant contextual metadata. We evaluate the Semantic Web MIDI Tape in various use cases involving user-contributed content, MIDI similarity querying, and entity recognition methods, and discuss their potential for finding links between MIDI resources and metadata

BioTIME: A database of biodiversity time series for the Anthropocene.

MotivationThe BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.Main types of variables includedThe database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.Spatial location and grainBioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).Time period and grainBioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurementBioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.Software format.csv and .SQL

A systems serology approach to the investigation of infection-induced antibody responses and protection in trachoma.

BACKGROUND: Ocular infections with Chlamydia trachomatis serovars A-C cause the neglected tropical disease trachoma. As infection does not confer complete immunity, repeated infections are common, leading to long-term sequelae such as scarring and blindness. Here, we apply a systems serology approach to investigate whether systemic antibody features are associated with susceptibility to infection. METHODS: Sera from children in five trachoma endemic villages in the Gambia were assayed for 23 antibody features: IgG responses towards two C. trachomatis antigens and three serovars [elementary bodies and major outer membrane protein (MOMP), serovars A-C], IgG responses towards five MOMP peptides (serovars A-C), neutralization, and antibody-dependent phagocytosis. Participants were considered resistant if they subsequently developed infection only when over 70% of other children in the same compound were infected. RESULTS: The antibody features assayed were not associated with resistance to infection (false discovery rate < 0.05). Anti-MOMP SvA IgG and neutralization titer were higher in susceptible individuals (p < 0.05 before multiple testing adjustment). Classification using partial least squares performed only slightly better than chance in distinguishing between susceptible and resistant participants based on systemic antibody profile (specificity 71%, sensitivity 36%). CONCLUSIONS: Systemic infection-induced IgG and functional antibody responses do not appear to be protective against subsequent infection. Ocular responses, IgA, avidity, or cell-mediated responses may play a greater role in protective immunity than systemic IgG

Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA

Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. Here we present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world. Each sample represents fungal DNA extracted from 24 m3 of air. We applied a conservative bioinformatics pipeline that filtered out sequences that did not show strong evidence of representing a fungal species. The pipeline yielded 27,954 species-level operational taxonomic units (OTUs). Each OTU is accompanied by a probabilistic taxonomic classification, validated through comparison with expert evaluations. To examine the potential of the data for ecological analyses, we partitioned the variation in species distributions into spatial and seasonal components, showing a strong effect of the annual mean temperature on community composition.publishedVersio

The Prevalence of Trachomatous Trichiasis in People Aged 15 Years and Over in Six Evaluation Units of Gaoual, Labé, Dalaba and Beyla Districts, Guinea.

PURPOSE: Trachoma is a public health problem in 42 countries. Inflammation associated with repeated ocular infection with Chlamydia trachomatis can cause the eyelid to scar and turn inwards, resulting in the eyelashes rubbing against the eyeball, known as trachomatous trichiasis (TT). In Guinea, baseline surveys conducted in 2013 reported inflammatory trachoma prevalences below the World Health Organization (WHO) threshold for elimination, but TT prevalences above threshold. Given this epidemiological context and time since baseline survey, TT-only surveys were conducted in selected districts to determine current TT prevalence. The results of this study provide critical data for assessing Guinea's achievement of trachoma elimination targets. METHODS: Four health districts, consisting of six evaluation units (EU), were surveyed. In each EU, field teams visited 29 clusters with a minimum 30 households included in each. Participants aged≥15 years were examined by certified graders trained to identify TT and determine whether management had been offered. RESULTS: A total of 22,476 people were examined, with 48 TT cases across the six EUs identified. Five of six EUs had an age-and-gender adjusted TT-prevalence unknown to the health system less than 0.2%, whereas one EU, Beyla 2, had an adjusted TT prevalence of 0.24%. CONCLUSION: These TT-only surveys, along with findings from other trachoma interventions, suggest that Guinea is close to achieving elimination of trachoma as a public health problem. This study demonstrates the value of undertaking TT-only surveys in settings where baseline surveys indicated active trachoma prevalences below WHO elimination threshold, but TT prevalences above it

The ABCflux database : Arctic-boreal CO2 flux observations and ancillary information aggregated to monthly time steps across terrestrial ecosystems

Past efforts to synthesize and quantify the magnitude and change in carbon dioxide (CO2) fluxes in terrestrial ecosystems across the rapidly warming Arctic-boreal zone (ABZ) have provided valuable information but were limited in their geographical and temporal coverage. Furthermore, these efforts have been based on data aggregated over varying time periods, often with only minimal site ancillary data, thus limiting their potential to be used in large-scale carbon budget assessments. To bridge these gaps, we developed a standardized monthly database of Arctic-boreal CO2 fluxes (ABCflux) that aggregates in situ measurements of terrestrial net ecosystem CO2 exchange and its derived partitioned component fluxes: gross primary productivity and ecosystem respiration. The data span from 1989 to 2020 with over 70 supporting variables that describe key site conditions (e.g., vegetation and disturbance type), micrometeorological and environmental measurements (e.g., air and soil temperatures), and flux measurement techniques. Here, we describe these variables, the spatial and temporal distribution of observations, the main strengths and limitations of the database, and the potential research opportunities it enables. In total, ABCflux includes 244 sites and 6309 monthly observations; 136 sites and 2217 monthly observations represent tundra, and 108 sites and 4092 observations represent the boreal biome. The database includes fluxes estimated with chamber (19 % of the monthly observations), snow diffusion (3 %) and eddy covariance (78 %) techniques. The largest number of observations were collected during the climatological summer (June-August; 32 %), and fewer observations were available for autumn (September-October; 25 %), winter (December-February; 18 %), and spring (March-May; 25 %). ABCflux can be used in a wide array of empirical, remote sensing and modeling studies to improve understanding of the regional and temporal variability in CO2 fluxes and to better estimate the terrestrial ABZ CO2 budget. ABCflux is openly and freely available online (Virkkala et al., 2021b, https://doi.org/10.3334/ORNLDAAC/1934).Peer reviewe

Structural covariance of the ventral visual stream predicts posttraumatic intrusion and nightmare symptoms: a multivariate data fusion analysis

Visual components of trauma memories are often vividly re-experienced by survivors with deleterious consequences for normal function. Neuroimaging research on trauma has primarily focused on threat-processing circuitry as core to trauma-related dysfunction. Conversely, limited attention has been given to visual circuitry which may be particularly relevant to posttraumatic stress disorder (PTSD). Prior work suggests that the ventral visual stream is directly related to the cognitive and affective disturbances observed in PTSD and may be predictive of later symptom expression. The present study used multimodal magnetic resonance imaging data (n = 278) collected two weeks after trauma exposure from the AURORA study, a longitudinal, multisite investigation of adverse posttraumatic neuropsychiatric sequelae. Indices of gray and white matter were combined using data fusion to identify a structural covariance network (SCN) of the ventral visual stream 2 weeks after trauma. Participant\u27s loadings on the SCN were positively associated with both intrusion symptoms and intensity of nightmares. Further, SCN loadings moderated connectivity between a previously observed amygdala-hippocampal functional covariance network and the inferior temporal gyrus. Follow-up MRI data at 6 months showed an inverse relationship between SCN loadings and negative alterations in cognition in mood. Further, individuals who showed decreased strength of the SCN between 2 weeks and 6 months had generally higher PTSD symptom severity over time. The present findings highlight a role for structural integrity of the ventral visual stream in the development of PTSD. The ventral visual stream may be particularly important for the consolidation or retrieval of trauma memories and may contribute to efficient reactivation of visual components of the trauma memory, thereby exacerbating PTSD symptoms. Potentially chronic engagement of the network may lead to reduced structural integrity which becomes a risk factor for lasting PTSD symptoms

Decadal increases in carbon uptake offset by respiratory losses across northern permafrost ecosystems

Tundra and boreal ecosystems encompass the northern circumpolar permafrost region and are experiencing rapid environmental change with important implications for the global carbon (C) budget. We analysed multi-decadal time series containing 302 annual estimates of carbon dioxide (CO2) flux across 70 permafrost and non-permafrost ecosystems, and 672 estimates of summer CO2 flux across 181 ecosystems. We find an increase in the annual CO2 sink across non-permafrost ecosystems but not permafrost ecosystems, despite similar increases in summer uptake. Thus, recent non-growing-season CO2 losses have substantially impacted the CO2 balance of permafrost ecosystems. Furthermore, analysis of interannual variability reveals warmer summers amplify the C cycle (increase productivity and respiration) at putatively nitrogen-limited sites and at sites less reliant on summer precipitation for water use. Our findings suggest that water and nutrient availability will be important predictors of the C-cycle response of these ecosystems to future warming

The AURORA Study: A Longitudinal, Multimodal Library of Brain Biology and Function after Traumatic Stress Exposure

Adverse posttraumatic neuropsychiatric sequelae (APNS) are common among civilian trauma survivors and military veterans. These APNS, as traditionally classified, include posttraumatic stress, postconcussion syndrome, depression, and regional or widespread pain. Traditional classifications have come to hamper scientific progress because they artificially fragment APNS into siloed, syndromic diagnoses unmoored to discrete components of brain functioning and studied in isolation. These limitations in classification and ontology slow the discovery of pathophysiologic mechanisms, biobehavioral markers, risk prediction tools, and preventive/treatment interventions. Progress in overcoming these limitations has been challenging because such progress would require studies that both evaluate a broad spectrum of posttraumatic sequelae (to overcome fragmentation) and also perform in-depth biobehavioral evaluation (to index sequelae to domains of brain function). This article summarizes the methods of the Advancing Understanding of RecOvery afteR traumA (AURORA) Study. AURORA conducts a large-scale (n = 5000 target sample) in-depth assessment of APNS development using a state-of-the-art battery of self-report, neurocognitive, physiologic, digital phenotyping, psychophysical, neuroimaging, and genomic assessments, beginning in the early aftermath of trauma and continuing for 1 year. The goals of AURORA are to achieve improved phenotypes, prediction tools, and understanding of molecular mechanisms to inform the future development and testing of preventive and treatment interventions

Virological failure and development of new resistance mutations according to CD4 count at combination antiretroviral therapy initiation

Objectives: No randomized controlled trials have yet reported an individual patient benefit of initiating combination antiretroviral therapy (cART) at CD4 counts > 350 cells/μL. It is hypothesized that earlier initiation of cART in asymptomatic and otherwise healthy individuals may lead to poorer adherence and subsequently higher rates of resistance development. Methods: In a large cohort of HIV-positive individuals, we investigated the emergence of new resistance mutations upon virological treatment failure according to the CD4 count at the initiation of cART. Results: Of 7918 included individuals, 6514 (82.3%), 996 (12.6%) and 408 (5.2%) started cART with a CD4 count ≤ 350, 351-499 and ≥ 500 cells/μL, respectively. Virological rebound occurred while on cART in 488 (7.5%), 46 (4.6%) and 30 (7.4%) with a baseline CD4 count ≤ 350, 351-499 and ≥ 500 cells/μL, respectively. Only four (13.0%) individuals with a baseline CD4 count > 350 cells/μL in receipt of a resistance test at viral load rebound were found to have developed new resistance mutations. This compared to 107 (41.2%) of those with virological failure who had initiated cART with a CD4 count < 350 cells/μL. Conclusions: We found no evidence of increased rates of resistance development when cART was initiated at CD4 counts above 350 cells/μL. HIV Medicin