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  • 1
    Online Resource
    Online Resource
    Large expert-curated database for benchmarking document similarity detection in biomedical literature search
    Oxford University Press (OUP) ; 2019
    In:  Database Vol. 2019 ( 2019-01-01)
    Details
    In: Database, Oxford University Press (OUP), Vol. 2019 ( 2019-01-01)
    Abstract: Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.
    Type of Medium: Online Resource
    ISSN: 1758-0463
    URL: Article
    DOI: 10.1093/database/baz085
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2496706-3
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  • 2
    Online Resource
    Online Resource
    Experience of Treating COVID-19 With Remdesivir and Convalescent Plasma in a Resource-Limited Setting: A Prospective, Observational Study
    Oxford University Press (OUP) ; 2021
    In:  Open Forum Infectious Diseases Vol. 8, No. 8 ( 2021-08-01)
    Details
    In: Open Forum Infectious Diseases, Oxford University Press (OUP), Vol. 8, No. 8 ( 2021-08-01)
    Abstract: Convalescent plasma therapy (CPT) and remdesivir (REM) have been approved for investigational use to treat coronavirus disease 2019 (COVID-19) in Nepal. Methods In this prospective, multicentered study, we evaluated the safety and outcomes of treatment with CPT and/or REM in 1315 hospitalized COVID-19 patients over 18 years in 31 hospitals across Nepal. REM was administered to patients with moderate, severe, or life-threatening infection. CPT was administered to patients with severe to life-threatening infections who were at high risk for progression or clinical worsening despite REM. Clinical findings and outcomes were recorded until discharge or death. Results Patients were classified as having moderate (24.2%), severe (64%), or life-threatening (11.7%) COVID-19 infection. The majority of CPT and CPT + REM recipients had severe to life-threatening infections (CPT 98.3%; CPT + REM 92.1%) and were admitted to the intensive care unit (ICU; CPT 91.8%; CPT + REM 94.6%) compared with those who received REM alone (73.3% and 57.5%, respectively). Of 1083 patients with reported outcomes, 78.4% were discharged and 21.6% died. The discharge rate was 84% for REM (n = 910), 39% for CPT (n = 59), and 54.4% for CPT + REM (n = 114) recipients. In a logistic model comparing death vs discharge and adjusted for age, gender, steroid use, and severity, the predicted margin for discharge was higher for recipients of remdesivir alone (0.82; 95% CI, 0.79–0.84) compared with CPT (0.58; 95% CI, 0.47–0.70) and CPT + REM (0.67; 95% CI, 0.60–0.74) recipients. Adverse events of remdesivir and CPT were reported in  & lt;5% of patients. Conclusions This study demonstrates a safe rollout of CPT and REM in a resource-limited setting. Remdesivir recipients had less severe infection and better outcomes. ClinicalTrials.gov identifier. NCT04570982.
    Type of Medium: Online Resource
    ISSN: 2328-8957
    URL: Article
    DOI: 10.1093/ofid/ofab391
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2757767-3
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  • 3
    Online Resource
    Online Resource
    Chronic constrictive pericarditis complicated with huge right atrial thrombus in a child with abdominal tuberculosis: a rare life-threatening condition
    Oxford University Press (OUP) ; 2019
    In:  Journal of Surgical Case Reports Vol. 2019, No. 11 ( 2019-11-01)
    Details
    In: Journal of Surgical Case Reports, Oxford University Press (OUP), Vol. 2019, No. 11 ( 2019-11-01)
    Abstract: Chronic constrictive pericarditis (CCP) is the most common pericardial pathology. CCP complicating with intracardiac thrombus is a rare entity, the detection of thrombus preoperatively is life-saving in avoiding the risk of pulmonary thromboembolism during anterior pericardiectomy. Transesophageal echocardiography has been shown to have better sensitivity in detecting atrial thrombus than transthoracic echocardiography. Surgical removal of right atrial thrombus under cardiopulmonary bypass should be considered.
    Type of Medium: Online Resource
    ISSN: 2042-8812
    URL: Article
    DOI: 10.1093/jscr/rjz295
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2580919-2
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  • 4
    Online Resource
    Online Resource
    Histochemical Techniques in Plant Science: More Than Meets the Eye
    Oxford University Press (OUP) ; 2021
    In:  Plant and Cell Physiology Vol. 62, No. 10 ( 2021-12-03), p. 1509-1527
    Details
    In: Plant and Cell Physiology, Oxford University Press (OUP), Vol. 62, No. 10 ( 2021-12-03), p. 1509-1527
    Abstract: Histochemistry is an essential analytical tool interfacing extensively with plant science. The literature is indeed constellated with examples showing its use to decipher specific physiological and developmental processes, as well as to study plant cell structures. Plant cell structures are translucent unless they are stained. Histochemistry allows the identification and localization, at the cellular level, of biomolecules and organelles in different types of cells and tissues, based on the use of specific staining reactions and imaging. Histochemical techniques are also widely used for the in vivo localization of promoters in specific tissues, as well as to identify specific cell wall components such as lignin and polysaccharides. Histochemistry also enables the study of plant reactions to environmental constraints, e.g. the production of reactive oxygen species (ROS) can be traced by applying histochemical staining techniques. The possibility of detecting ROS and localizing them at the cellular level is vital in establishing the mechanisms involved in the sensitivity and tolerance to different stress conditions in plants. This review comprehensively highlights the additional value of histochemistry as a complementary technique to high-throughput approaches for the study of the plant response to environmental constraints. Moreover, here we have provided an extensive survey of the available plant histochemical staining methods used for the localization of metals, minerals, secondary metabolites, cell wall components, and the detection of ROS production in plant cells. The use of recent technological advances like CRISPR/Cas9-based genome-editing for histological application is also addressed. This review also surveys the available literature data on histochemical techniques used to study the response of plants to abiotic stresses and to identify the effects at the tissue and cell levels.
    Type of Medium: Online Resource
    ISSN: 0032-0781 , 1471-9053
    URL: Article
    DOI: 10.1093/pcp/pcab022
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2020758-X
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Ethylene Renders Silver Nanoparticles Stress Tolerance in Rice Seedlings by Regulating Endogenous Nitric Oxide Accumulation
    Oxford University Press (OUP) ; 2023
    In:  Plant and Cell Physiology Vol. 63, No. 12 ( 2023-01-30), p. 1954-1967
    Details
    In: Plant and Cell Physiology, Oxford University Press (OUP), Vol. 63, No. 12 ( 2023-01-30), p. 1954-1967
    Abstract: Developments in the field of nanotechnology over the past few years have increased the prevalence of silver nanoparticles (AgNPs) in the environment, resulting in increased exposure of plants to AgNPs. Recently, various studies have reported the effect of AgNPs on plant growth at different concentrations. However, identifying the mechanisms and signaling molecules involved in plant responses against AgNPs stress is crucial to find an effective way to deal with the phytotoxic impacts of AgNPs on plant growth and development. Therefore, this study was envisaged to investigate the participation of ethylene in mediating the activation of AgNPs stress tolerance in rice (Oryza sativa L.) through a switch that regulates endogenous nitric oxide (NO) accumulation. Treatment of AgNPs alone hampered the growth of rice seedlings due to severe oxidative stress as a result of decline in sulfur assimilation, glutathione (GSH) biosynthesis and alteration in the redox status of GSH. These results are also accompanied by the higher endogenous NO level. However, addition of ethephon (a donor of ethylene) reversed the AgNP-induced effects. Though the application of silicon nanoparticles (SiNPs) alone promoted the growth of rice seedlings but, interestingly their application in combination with AgNPs enhanced the AgNP-induced toxicity in the seedlings through the same routes as exhibited in the case of AgNPs alone treatment. Interestingly, addition of ethephon reversed the negative effects of SiNPs under AgNPs stress. These results suggest that ethylene might act as a switch to regulate the level of endogenous NO, which in turn could be associated with AgNPs stress tolerance in rice. Furthermore, the results also indicated that addition of l-NG-nitro arginine methyl ester (l-NAME) (an inhibitor of endogenous NO synthesis) also reversed the toxic effects of SiNPs together with AgNPs, further suggesting that the low level of endogenous NO was associated with AgNPs stress tolerance. Overall, the results indicate that the low level of endogenous NO triggers AgNPs stress tolerance, while high level leads to AgNPs toxicity by regulating sulfur assimilation, GSH biosynthesis, redox status of GSH and oxidative stress markers. The results revealed that ethylene might act as a switch for regulating AgNPs stress in rice seedlings by controlling endogenous NO accumulation.
    Type of Medium: Online Resource
    ISSN: 0032-0781 , 1471-9053
    URL: Article
    DOI: 10.1093/pcp/pcac159
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2020758-X
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Dissecting the nutrient partitioning mechanism in rice grain using spatially resolved gene expression profiling
    Oxford University Press (OUP) ; 2021
    In:  Journal of Experimental Botany Vol. 72, No. 6 ( 2021-03-17), p. 2212-2230
    Details
    In: Journal of Experimental Botany, Oxford University Press (OUP), Vol. 72, No. 6 ( 2021-03-17), p. 2212-2230
    Abstract: Rice, a staple food worldwide, contains varying amounts of nutrients in different grain tissues. The underlying molecular mechanism of such distinct nutrient partitioning remains poorly investigated. Here, an optimized rapid laser capture microdissection (LCM) approach was used to individually collect pericarp, aleurone, embryo and endosperm from grains 10 days after fertilization. Subsequent RNA-Seq analysis in these tissues identified 7760 differentially expressed genes. Analysis of promoter sequences of tissue-specific genes identified many known and novel cis-elements important for grain filling and seed development. Using the identified differentially expressed genes, comprehensive spatial gene expression pathways were built for accumulation of starch, proteins, lipids, and iron. The extensive transcriptomic analysis provided novel insights about nutrient partitioning mechanisms; for example, it revealed a gradient in seed storage protein accumulation across the four tissue types analysed. The analysis also revealed that the partitioning of various minerals, such as iron, is most likely regulated through transcriptional control of their transporters. We present the extensive analysis from this study as an interactive online tool that provides a much-needed resource for future functional genomics studies aimed to improve grain quality and seed development.
    Type of Medium: Online Resource
    ISSN: 0022-0957 , 1460-2431
    URL: Article
    DOI: 10.1093/jxb/eraa536
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1466717-4
    SSG: 12
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