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Playbook workflow builder: Interactive construction of bioinformatics workflows
Full text linkThe Playbook Workflow Builder (PWB) is a web-based platform to dynamically construct and execute bioinformatics workflows by utilizing a growing network of input datasets, semantically annotated API endpoints, and data visualization tools contributed by an ecosystem of collaborators. Via a user-friendly user interface, workflows can be constructed from contributed building-blocks without technical expertise. The output of each step of the workflow is added into reports containing textual descriptions, figures, tables, and references. To construct workflows, users can click on cards that represent each step in a workflow, or construct workflows via a chat interface that is assisted by a large language model (LLM). Completed workflows are compatible with Common Workflow Language (CWL) and can be published as research publications, slideshows, and posters. To demonstrate how the PWB generates meaningful hypotheses that draw knowledge from across multiple resources, we present several use cases. For example, one of these use cases prioritizes drug targets for individual cancer patients using data from the NIH Common Fund programs GTEx, LINCS, Metabolomics, GlyGen, and ExRNA. The workflows created with PWB can be repurposed to tackle similar use cases using different inputs. The PWB platform is available from: https://playbook-workflow-builder.cloud/
Co‐Occurring Atmospheric Features and Their Contributions to Precipitation Extremes
Full text linkAbstract Object‐based identification algorithms for atmospheric features are commonly utilized to attribute global precipitation. This study employs a systematic approach to examine feature co‐occurrences and their relationships to mean and extreme precipitation. Four features are identified using existing data sets for atmospheric rivers (ARs), mesoscale convective systems (MCSs), low‐pressure systems (LPSs), and fronts (FTs). Often, a single atmospheric phenomenon satisfies the criteria set by multiple feature identification algorithms, yielding an association between precipitation and multiple features. Over the extra‐tropics, the number of features attributed to a single event typically increases with precipitation intensity. Over two‐thirds of the precipitation is from co‐occurring features, with a considerable fraction related to AR‐FT co‐occurrences. Over the tropics, about one‐quarter of precipitation is associated with co‐occurring features, with LPS‐MCS co‐occurrences contributing substantially in monsoon regions. MCSs are the leading single‐feature contributors over tropical land and oceans. In the extra‐tropics, FTs, ARs, and their co‐occurrences account for over half of the total precipitation over oceans. AR‐FT‐MCS and FT‐MCS co‐occurrences contribute to extremes (precipitation exceeding the 95th percentile) over both oceans (over 30%) and land (over 20%). Any combination of features involving MCSs shows a larger contribution to high percentiles of precipitation intensity. A case analysis indicates that AR‐FT‐MCS co‐occurrences exhibit convective instability and deep vertical motion, suggesting that the feature trackers and reanalysis are capturing physics relevant to both convective and frontal systems. The results here emphasize the need for simultaneous identifications of multiple features when attributing precipitation to atmospheric phenomena.
Plain Language Summary This research study examines how different types of weather systems contribute to global precipitation. Instead of studying individual weather systems separately, the study investigates how frequently these systems occur together and how that impacts precipitation. Identification algorithms have been used to pinpoint these co‐occurring systems. The findings indicate that co‐occurring systems are more prevalent over mid‐latitudes than the tropics, and highlight specific weather combinations that significantly contribute to heavy precipitation. For extreme precipitation, combinations such as atmospheric river‐front (FT)‐mesoscale convective system (MCS) and FT‐MCS are vital over oceanic and land regions, respectively. The findings emphasize the importance of simultaneously identifying multiple features to enhance understanding and prediction of rainfall patterns. Additionally, combinations involving MCSs contribute significantly to high percentiles of rainfall intensity. Extra‐tropical MCSs are associated with greater convective instability, as observed in the tropical MCSs.
Key Points Global precipitation variability linked to atmospheric features is systematically analyzed for their co‐occurring instances Contributors to total/extreme precipitation in the tropics and extra‐tropics are highlighted, with the latter dominated by co‐occurring features Features involving mesoscale convective systems have a larger contribution to high percentiles of precipitation intensit
Between hope and harm: the fragmentary effects of resettlement for Congolese refugees in Uganda
Full text linkMolecular basis for human respiratory syncytial virus transcriptional regulator NS1 interactions with MED25
Full text linkThe Mediator complex facilitates interactions between transcription factors and RNA polymerase II, a process that is required for host gene transcription, including in response to viral infections. Among the many subunits in the Mediator complex, the MED25 subunit has been shown to be a target for viral activators during infection. Here we provide the molecular basis for the interaction between human respiratory syncytial virus (hRSV) nonstructural 1 protein (NS1) and the activator interaction domain (ACID) of MED25. The X-ray crystal structure of the complex revealed that NS1 straddles and binds two faces of MED25 ACID. This interaction is distinct from previously known viral activators. Importantly, our data support the conformational flexibility of viral transcriptional regulators. Furthermore, ChIP-seq and RNA-seq analysis identified the ATF3 transcription factor and a role for NS1/Mediator/ATF3 interaction in host gene regulation in hRSV infections. Our findings provide a molecular basis for hRSV NS1-based regulation of host gene transcription and reveal how viruses exploit the conformational heterogeneity at fuzzy transcription activator interfaces
An embodied multi-articulatory multimodal language framework: A commentary on Karadöller, Sümer and Özyürek
No full textWhile many researchers working in spoken languages have used modality to distinguish language and gesture, this is not possible for sign language researchers. We argue that co-sign gestures must be considered alongside co-speech gestures in theories of language acquisition. Focusing on how the same function is served in embodied communication in speech and embodied communication in sign promotes a truly multimodal view of language acquisition. An embodied multi-articulatory multimodal framework is needed to make broader claims about language acquisition
Beneath the surface: Unsolved questions in soil virus ecology
Full text linkSoil virus ecology is an exciting but still nascent field of research in soil microbiology. While there has been a recent surge in soil virus research studies, many fundamental questions remain unanswered, and a range of technical and bioinformatic challenges need to be overcome. In this perspective article, we present a series of key questions that highlight fruitful research areas for ongoing and future efforts. These include describing the challenges involved in understanding soil viral abundance and activity, spatiotemporal dynamics, life strategy prevalence, virus-mediated biogeochemical impacts, viral protein function, host prediction, and soil RNA virus discovery. In the near term, combining approaches (e.g., cultivation-based, meta-omics, biogeochemical, experimental, and bioinformatic) will be key to assessing the ecological and biogeochemical impacts of soil viruses from the microscopic to the field and global scales. Still, we stress that results must be tempered by current methodological limitations and highlight knowledge gaps that are most pressing to fill via new methods or measurements, such as the prevalence of different viral replication strategies across soils, the fate of microbial necromass carbon after viral lysis, the frequency of virus-host encounters that do not lead to successful infections yet could be bioinformatically mistaken as infections, and the diversity and ecological impacts of RNA viruses in soil
Arsenic modifies the microbial community assembly of soil–root habitats in Pteris vittata
Full text linkPteris vittata, renowned for its ability to hyperaccumulate arsenic, presents a promising solution to the escalating issue of global soil arsenic contamination. This fern cultivates a unique underground microbial community to enhance its environmental adaptability. However, our understanding of the assembly process and the long-term ecological impacts of this community remains limited, hindering the development of effective soil remediation strategies. This study addresses this gap by investigating soil-root habitats from three geographically diverse fields comprising a gradient of arsenic contamination, complemented by a time-scale greenhouse experiment. Field investigations reveal that arsenic stress influences community assembly dynamics in the rhizosphere by enhancing processes of homogeneous selection. Greenhouse experiments further reveal that arsenic exposure alters the assembly trajectory of rhizosphere communities by promoting key microbial modules. Specifically, arsenic exposure increases the enrichment of a core taxon (i.e. Rhizobiaceae) in the rhizosphere, both in field and greenhouse settings, boosting their abundance from undetectable levels to 0.02% in the soil after phytoremediation. Notably, arsenic exposure also promotes a pathogenic group (i.e. Spirochaetaceae) in the rhizosphere, increasing their abundance from undetectable levels to 0.1% in the greenhouse. This raise concerns that warrant further investigation in future phytoremediation studies. Overall, this study elucidates the assembly dynamics of the soil microbiome following the introduction of a remediation plant and emphasizes the often-overlooked impacts on soil microbial community following phytoremediation. By probing the ecological impacts of remediation plants, this work advances a more nuanced understanding of the complex ecological implications inherent in phytoremediation processes
“You [God] Gotta Go Through It With Me”: Black Women Navigating Spirituality During the Breast Cancer Journey
Full text linkBACKGROUND: Black women generally report high levels of spirituality. Less is known about Black women's spiritual coping with a cancer diagnosis. Persisting health disparities between Black breast cancer survivors and other racial groups necessitate examining whether spirituality can be a contextual and personal resource for Black women with breast cancer.
AIMS: This qualitative study's goals were to: (1) characterize positive and negative dimensions of spirituality in a sample of Black women diagnosed with breast cancer; and (2) examine whether and how women used spirituality during their cancer experience.
METHODS: Three Gatherings (i.e., culturally curated focus groups) were conducted as part of Project SOAR (Speaking Our African American Realities), a community-academic partnership. In these all-Black women Gatherings, participants (N = 37) discussed their breast cancer experience, including how spirituality played a role.
RESULTS: Through reflexive thematic analysis, six themes were identified: (1) faith is central to my identity even through challenging times; (2) meaningful, ineffective, or non-existent support from my spiritual community; (3) grappling with spiritual discontent during breast cancer; (4) God is omnipotent; (5) spiritual anchors helped me persevere through the breast cancer journey; (6) breast cancer reflections enhanced my spiritual gratitude and growth.
CONCLUSIONS: Participants' experiences highlight the complexities of spirituality when confronting breast cancer. Many Black women reflected on the centrality of spirituality to their lives and cited spirituality as a resource and effective coping process during their cancer experience. Findings have important implications for understanding how spirituality can be incorporated to support Black women with breast cancer
A Systematic Review: State of the Science on Diagnostics of Hidden Hearing Loss
Full text linkBackground/Objectives: A sizeable population of patients with normal pure-tone audiograms endorse a consistent difficulty of following conversations in noisy environments. Termed hidden hearing loss (HHL), this condition evades traditional diagnostic methods for hearing loss and thus is significantly under-diagnosed and untreated. This review sought to identify emerging methods of diagnosing HHL via measurement of its histopathologic correlate: cochlear synaptopathy, the loss of synapses in the auditory nerve pathway. Methods: A thorough literature search of multiple databases was conducted to identify studies with objective, electrophysiological measures of synaptopathy. The PRISMA protocol was employed to establish criteria for the selection of relevant literature. Results: A total of 21 studies were selected with diagnostic methods, including the auditory brainstem response (ABR), electrocochleography (EcochG), middle ear muscle reflex (MEMR), and frequency-following response (FFR). Measures that may indicate the presence of synaptopathy include a reduced wave I amplitude of ABR, reduced SP amplitude of EcochG, and abnormal MEMR, among other measurements. Behavioral measures were often performed alongside electrophysiological measures, the most common of which was the speech-in-noise assessment. Conclusions: ABR was the most common diagnostic method for assessing HHL. Though ABR, EcochG, and MEMR may be sensitive to measuring synaptopathy, more literature comparing these methods is necessary. A two-pronged approach combining behavioral and electrophysiological measures may prove useful as a criterion for diagnosing and estimating the extent of pathology in affected patients