12 research outputs found

    Overview of the interactive task in BioCreative V

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    Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These systems are not meant to replace biocurators, but instead to assist them in one or more literature curation steps. To do so, the user interface is an important aspect that needs to be considered for tool adoption. The BioCreative Interactive task (IAT) is a track designed for exploring user-system interactions, promoting development of useful TM tools, and providing a communication channel between the biocuration and the TM communities. In BioCreative V, the IAT track followed a format similar to previous interactive tracks, where the utility and usability of TM tools, as well as the generation of use cases, have been the focal points. The proposed curation tasks are user-centric and formally evaluated by biocurators. In BioCreative V IAT, seven TM systems and 43 biocurators participated. Two levels of user participation were offered to broaden curator involvement and obtain more feedback on usability aspects. The full level participation involved training on the system, curation of a set of documents with and without TM assistance, tracking of time-on-task, and completion of a user survey. The partial level participation was designed to focus on usability aspects of the interface and not the performance per se. In this case, biocurators navigated the system by performing pre-designed tasks and then were asked whether they were able to achieve the task and the level of difficulty in completing the task. In this manuscript, we describe the development of the interactive task, from planning to execution and discuss major findings for the systems tested

    Geo-spatial Tools for Assessing Soil Fertilty: A Review

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    Soil, as a precious non-renewable resource, plays a pivotal role in agricultural productivity, making the improvement of soil fertility a paramount objective. To ensure soil health and optimize resource utilization for food production while mitigating negative environmental impacts in the face of climate change, it is crucial to gather geographical information on soil and its fertility levels. This is where remote sensing (RS) and Geographic Information System (GIS) technologies, particularly high-resolution satellite data and geostatistical methods, have proven highly effective. Historically, most studies focused on evaluating a limited set of soil properties to gauge quality or fertility levels. However, it is now evident that adopting a holistic approach by integrating multiple soil indicators encompassing chemical, biological, and physical aspects is essential. Such a comprehensive assessment can offer valuable insights into specific land management techniques and environmental conditions, enabling better decision-making. In light of this necessity, the utilization of high-resolution remote sensing data in conjunction with ground observations has become pivotal in mapping and tracking soil fertility. RS and GIS technologies provide detailed, spatially explicit information, facilitating large-scale soil assessments and identifying trends and patterns over time. This integration empowers researchers and land managers to implement sustainable agricultural practices and conservation efforts, ultimately maximizing food production while preserving the environment. By harnessing the power of RS and GIS technologies, researchers can gain a deeper understanding of soil health, facilitating the development of effective land management strategies and resource utilization practices. In conclusion, the amalgamation of high-resolution remote sensing data and ground observations is crucial for comprehensive soil fertility assessment. This approach contributes significantly to sustainable land management, ensuring food security, and safeguarding our invaluable soil resource amidst the challenges posed by climate change

    <title>Photophysics and photochemistry of side-chain substituted liquid crystalline polyaryl cinnamates</title>

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    The synthesis and photochemistry of comb-like thermotropic liquid-crystalline (L.C.) polymers containing UV-sensitive cinnamate ester chromophores incorporated as part of the pendant groups is described. The methacrylate monomer was polymerized using AIBN as a free radical initiator. The acrylate monomer was resistant to polymerization under the same reaction conditions. The principle photochemical reactions on photolysis (313 nm) of solutions of the polymer as well as freshly cast films are photocycloaddition and photo-Fries rearrangement of the aryl cinnamate chromophore. Aggregation of chromophores was studied in films as a function of phase type at different temperatures. These results are compared with those obtained from main chain L.C. polyaryl cinnamates

    Enhancing Soil Degradation Assessment through the Integration of GIS and RS: A Comprehensive Review

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    GIS and RS are powerful tools that play a crucial role in natural resource management, especially when it comes to assessing soil degradation. Soil degradation is a long-standing global problem, and to understand the role of GIS and RS in addressing it, data from secondary sources were collected and analyzed. Several researchers have utilized GIS and RS, integrated with the Universal Soil Loss Equation (USLE), to assess soil degradation. Their findings reveal that soil erosion, triggered primarily by water, is a critical form of land degradation. This erosion significantly reduces the potential capacity of the soil, posing threats to economic growth, environmental resources, and social assets. Furthermore, the severity of soil erosion varies across different regions of the country. Despite the valuable insights gained through studies using GIS and RS for soil degradation assessment, their contributions are not yet widely recognized by government organizations, NGOs, policymakers, decision-makers, environmentalists, and researchers. This lack of recognition hinders the attention and action that could be directed towards mitigating soil degradation. To address this issue, this paper aims to comprehensively review the contributions of GIS and RS in assessing soil degradation. By doing so, it seeks to raise awareness among key stakeholders and foster greater attention and support for tackling this critical environmental challenge

    Mononuclear phagocyte intercellular crosstalk facilitates transmission of cell-targeted nanoformulated antiretroviral drugs to human brain endothelial cells

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    Despite the successes of antiretroviral therapy (ART), HIV-associated neurocognitive disorders remain prevalent in infected people. This is due, in part, to incomplete ART penetration across the blood–brain barrier (BBB) and lymph nodes and to the establishment of viral sanctuaries within the central nervous system. In efforts to improve ART delivery, our laboratories developed a macrophage-carriage system for nanoformulated crystalline ART (nanoART) (atazanavir, ritonavir, indinavir, and efavirenz). We demonstrate that nanoART transfer from mononuclear phagocytes (MP) to human brain microvascular endothelial cells (HBMEC) can be realized through cell-to-cell contacts, which can facilitate drug passage across the BBB. Coculturing of donor MP containing nanoART with recipient HBMEC facilitates intercellular particle transfer. NanoART uptake was observed in up to 52% of HBMEC with limited cytotoxicity. Folate coating of nanoART increased MP to HBMEC particle transfer by up to 77%. To translate the cell assays into relevant animal models of disease, ritonavir and atazanavir nanoformulations were injected into HIV-1-infected NOD/scid-γcnull mice reconstituted with human peripheral blood lymphocytes. Atazanavir and ritonavir levels in brains of mice treated with folate-coated nanoART were three- to four-fold higher than in mice treated with noncoated particles. This was associated with decreased viral load in the spleen and brain, and diminished brain CD11b-associated glial activation. We postulate that monocyte-macrophage transfer of nanoART to brain endothelial cells could facilitate drug entry into the brain

    The lineage stability and suppressive program of regulatory T cells require protein O-GlcNAcylation

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    The transcription factor Foxp3 and Stat5 modulate lineage stability and function of regulatory T (Treg) cells to promote immune homeostasis. Here the authors show that O-GlcNAcylation of Foxp3 and Stat5, mediated by O-GlcNAc transferase (OGT), is essential for Treg-mediate immune balance, with Treg-specific deficiency of OGT leading to severe autoimmunity

    An NK-like CAR T&nbsp;cell transition in CAR T&nbsp;cell dysfunction.

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    Chimeric antigen receptor (CAR) T&nbsp;cell therapy has achieved remarkable success in hematological malignancies but remains ineffective in solid tumors, due in part to CAR T&nbsp;cell exhaustion in the solid tumor microenvironment. To study dysfunction of mesothelin-redirected CAR T&nbsp;cells in pancreatic cancer, we establish a robust model of continuous antigen exposure that recapitulates hallmark features of T&nbsp;cell exhaustion and discover, both in&nbsp;vitro and in CAR T&nbsp;cell patients, that CAR dysregulation is associated with a CD8+ T-to-NK-like T&nbsp;cell transition. Furthermore, we identify a gene signature defining CAR and TCR dysregulation and transcription factors, including SOX4 and ID3 as key regulators of CAR T&nbsp;cell exhaustion. Our findings shed light on the plasticity of human CAR T&nbsp;cells and demonstrate that genetic downmodulation of ID3 and SOX4 expression can improve the efficacy of CAR T&nbsp;cell therapy in solid tumors by preventing or delaying CAR T&nbsp;cell dysfunction
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