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  • Oxford University Press (OUP)  (20)
  • 1
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    Protecting stable biological nomenclatural systems enables universal communication: A collective international appeal
    Oxford University Press (OUP) ; 2024
    In:  BioScience ( 2024-06-19)
    Details
    In: BioScience, Oxford University Press (OUP), ( 2024-06-19)
    Abstract: The fundamental value of universal nomenclatural systems in biology is that they enable unambiguous scientific communication. However, the stability of these systems is threatened by recent discussions asking for a fairer nomenclature, raising the possibility of bulk revision processes for “inappropriate” names. It is evident that such proposals come from very deep feelings, but we show how they can irreparably damage the foundation of biological communication and, in turn, the sciences that depend on it. There are four essential consequences of objective codes of nomenclature: universality, stability, neutrality, and transculturality. These codes provide fair and impartial guides to the principles governing biological nomenclature and allow unambiguous universal communication in biology. Accordingly, no subjective proposals should be allowed to undermine them.
    Type of Medium: Online Resource
    ISSN: 0006-3568 , 1525-3244
    URL: Article
    DOI: 10.1093/biosci/biae043
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 2066019-4
    SSG: 12
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  • 2
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    Prognostic Nomogram Based on Histological Characteristics of Fibrotic Tumor Stroma in Patients Who Underwent Curative Resection for Intrahepatic Cholangiocarcinoma
    Oxford University Press (OUP) ; 2018
    In:  The Oncologist Vol. 23, No. 12 ( 2018-12-01), p. 1482-1493
    Details
    In: The Oncologist, Oxford University Press (OUP), Vol. 23, No. 12 ( 2018-12-01), p. 1482-1493
    Abstract: Fibrotic tumor stroma (FTS) has been implicated in cancer promotion in several neoplasms. The histological features of FTS are convenient and easily accessible in clinical routine in intrahepatic cholangiocarcinoma (ICC) specimens. The goal of this study was to explore prognostic impacts of the quantity and maturity of FTS on surgical ICC patients. Moreover, we aimed to propose an efficient prognostic nomogram for postoperative ICC patients. Materials and Methods The clinical profiles of 154 consecutive postoperative ICC patients were retrospectively analyzed. Tumor-stroma ratio and morphological maturity of FTS were evaluated on hematoxylin and eosin-stained tumor sections. CD3, CD8, and α-smooth muscle actin (α-SMA) staining were performed on corresponding tissue microarrays. The nomogram was established on variables selected by multivariate analyses and was validated in 10-fold cross-validation. Results Rich tumor stroma and strong α-SMA expression were associated with poor overall survival (OS). However, in multivariate analyses, these two biomarkers failed to stratify both OS and recurrence-free survival (RFS). Immature FTS was correlated with tumor multiplicity, advanced clinical stage, and sparser CD3 and CD8 positive tumor-infiltrating lymphocytes (TILs) and was identified as an independent prognostic indicator for both OS and RFS. The nomogram comprising FTS maturity, tumor number, microvascular invasion, and lymph node metastasis possessed higher predictive power relative to conventional staging systems. Conclusion Immature FTS was an independent risk factor for survival and was associated with sparser CD3 and CD8 positive TILs in ICC. The prognostic nomogram integrating the maturity of FTS offers a more accurate risk stratification for postoperative ICC patients. Implications for Practice Accumulating evidence has suggested that fibrotic components in tumor microenvironment (TME) play a complicated and vital role in TME reprogramming and cancer progression. However, in clinical practice, the evaluation of fibrotic tumor stroma (FTS) is still neglected to some extent. This study's findings indicated that, in intrahepatic cholangiocarcinoma (ICC), the histological maturity of FTS is a robust prognostic indicator for patients who underwent curative resection. Moreover, prognostic nomogram constructed on the maturity of FTS possessed higher predictive power relative to the conventional tumor-node-metastasis staging systems. Taken together, the evaluation of FTS should be emphasized in clinical routine for more accurate prognostic prediction in postoperative ICC patients.
    Type of Medium: Online Resource
    ISSN: 1083-7159 , 1549-490X
    URL: Article
    DOI: 10.1634/theoncologist.2017-0439
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2018
    detail.hit.zdb_id: 2023829-0
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  • 3
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    Prognostic Nomograms Stratify Survival of Patients with Hepatocellular Carcinoma Without Portal Vein Tumor Thrombosis After Curative Resection
    Oxford University Press (OUP) ; 2017
    In:  The Oncologist Vol. 22, No. 5 ( 2017-05-01), p. 561-569
    Details
    In: The Oncologist, Oxford University Press (OUP), Vol. 22, No. 5 ( 2017-05-01), p. 561-569
    Abstract: The prognosis of patients with hepatocellular carcinoma (HCC) without portal vein tumor thrombosis (PVTT) after curative resection is at variance. We identified the risk factors of poor postoperative prognosis and consequently developed prognostic nomograms generating individual risk of death and recurrence for this subgroup of patients with HCC. Methods The risk factors were identified and nomograms were developed based on a retrospective study of 734 patients in the primary cohort who underwent curative resection for HCC from 2010 to 2012. The predictive accuracy and discriminative ability of the nomograms were determined by concordance index (C-index) and calibration curve and compared with traditional staging systems of HCC. The results were validated in an independent cohort of 349 patients operated at the same institution in 2007. Results All of the independent factors for survival in multivariate analysis in the primary cohort were selected into the nomograms. The calibration curve for probability of survival showed good agreement between prediction by nomograms and actual observation. The C-indices of the nomograms for predicting overall survival and recurrence-free survival were 0.755 (95% confidence interval [CI], 0.752–0.758) and 0.665 (95% CI, 0.662–0.668), respectively, which were statistically higher than the C-indices of other HCC prognostic models. The results were further confirmed in the validation cohort. Conclusion The proposed nomograms resulted in more accurate prognostic prediction for patients with HCC without PVTT after curative resection.
    Type of Medium: Online Resource
    ISSN: 1083-7159 , 1549-490X
    URL: Article
    DOI: 10.1634/theoncologist.2016-0231
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2017
    detail.hit.zdb_id: 2023829-0
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  • 4
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    Manipulating Hubbard-type Coulomb blockade effect of metallic wires embedded in an insulator
    Oxford University Press (OUP) ; 2023
    In:  National Science Review Vol. 10, No. 3 ( 2023-02-28)
    Details
    In: National Science Review, Oxford University Press (OUP), Vol. 10, No. 3 ( 2023-02-28)
    Abstract: Correlated states have emerged in low-dimensional systems owing to enhanced Coulomb interactions. Elucidating these states requires atomic-scale characterization and delicate control capabilities. Herein, spectroscopic imaging-scanning tunneling microscopy was employed to investigate the correlated states residing in 1D electrons of the monolayer and bilayer MoSe2 mirror twin boundary (MTB). The Coulomb energies, determined by the wire length, drive the MTB into two types of ground states with distinct respective out-of-phase and in-phase charge orders. The two ground states can be reversibly converted through a metastable zero-energy state with in situ voltage pulses, which tune the electron filling of the MTB via a polaronic process, substantiated by first-principles calculations. Our Hubbard model calculation with an exact diagonalization method reveals the ground states as correlated insulators from an on-site U-originated Coulomb interaction, dubbed the Hubbard-type Coulomb blockade effect. Our study lays a foundation for understanding and tailoring correlated physics in complex systems.
    Type of Medium: Online Resource
    ISSN: 2095-5138 , 2053-714X
    URL: Article
    DOI: 10.1093/nsr/nwac210
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2745465-4
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  • 5
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    Super-Eddington accretion of the first Galactic ultra-luminous X-ray pulsar Swift J0243.6+6124
    Oxford University Press (OUP) ; 2022
    In:  Monthly Notices of the Royal Astronomical Society Vol. 512, No. 4 ( 2022-04-14), p. 5686-5692
    Details
    In: Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol. 512, No. 4 ( 2022-04-14), p. 5686-5692
    Abstract: We present a detailed timing study of the pulse profile of Swift J0243.6+6124 with Hard X-ray Modulation Telescope (HXMT) and Fermi/GBM (Gamma-ray Burst Monitor) data during its 2017 giant outburst. The double-peak profile at luminosity above 5 × 1038 erg s−1 is found to be 0.25 phase offset from that below 1.5 × 1038erg s−1, which strongly supports for a transition from a pencil beam to a fan beam, and thus for the formation of shock dominated accretion column. During the rising stage of the high double-peak regime, the faint peak got saturated in 10–100 keV band above a luminosity of Lt ∼ 1.3 × 1039erg s−1, which is coincident with sudden spectral changes of both the main and faint peaks. They imply a sudden change of emission pattern around Lt. The spin-up rate ($\dot{\nu }$) is linearly correlated with luminosity (L) below Lt, consistent with the prediction of a radiation pressure dominated disc. The $\dot{\nu }-L$ relation flattens above Lt, indicating a less efficient transfer of angular momentum and a change of accretion disc geometry above Lt. It is likely due to irradiation of the disc by the central accretion column and indicates significant radiation feedback well before the inner disc radius reaching the spherization radius.
    Type of Medium: Online Resource
    ISSN: 0035-8711 , 1365-2966
    URL: Article
    DOI: 10.1093/mnras/stac836
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2016084-7
    SSG: 16,12
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  • 6
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    Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires
    Oxford University Press (OUP) ; 2023
    In:  Nucleic Acids Research Vol. 51, No. W1 ( 2023-07-05), p. W17-W24
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 51, No. W1 ( 2023-07-05), p. W17-W24
    Abstract: The utilization of high-throughput sequencing (HTS) for B-cell receptor (BCR) immune repertoire analysis has become widespread in the fields of adaptive immunity and antibody drug development. However, the sheer volume of sequences generated by these experiments presents a challenge in data processing. Specifically, multiple sequence alignment (MSA), a critical aspect of BCR analysis, remains inadequate for handling massive BCR sequencing data and lacks the ability to provide immunoglobulin-specific information. To address this gap, we introduce Abalign, a standalone program specifically designed for ultrafast MSA of BCR/antibody sequences. Benchmark tests demonstrate that Abalign achieves comparable or even better accuracy than state-of-the-art MSA tools, and shows remarkable advantages in terms of speed and memory consumption, reducing the time required for high-throughput analysis from weeks to hours. In addition to its alignment capabilities, Abalign offers a broad range of BCR analysis features, including extracting BCRs, constructing lineage trees, assigning VJ genes, analyzing clonotypes, profiling mutations, and comparing BCR immune repertoires. With its user-friendly graphic interface, Abalign can be easily run on personal computers instead of computing clusters. Overall, Abalign is an easy-to-use and effective tool that enables researchers to analyze massive BCR/antibody sequences, leading to new discoveries in the field of immunoinformatics. The software is freely available at http://cao.labshare.cn/abalign/.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkad400
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1472175-2
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  • 7
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    FAM46B is a prokaryotic-like cytoplasmic poly(A) polymerase essential in human embryonic stem cells
    Oxford University Press (OUP) ; 2020
    In:  Nucleic Acids Research Vol. 48, No. 5 ( 2020-03-18), p. 2733-2748
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 48, No. 5 ( 2020-03-18), p. 2733-2748
    Abstract: Family with sequence similarity (FAM46) proteins are newly identified metazoan-specific poly(A) polymerases (PAPs). Although predicted as Gld-2-like eukaryotic non-canonical PAPs, the detailed architecture of FAM46 proteins is still unclear. Exact biological functions for most of FAM46 proteins also remain largely unknown. Here, we report the first crystal structure of a FAM46 protein, FAM46B. FAM46B is composed of a prominently larger N-terminal catalytic domain as compared to known eukaryotic PAPs, and a C-terminal helical domain. FAM46B resembles prokaryotic PAP/CCA-adding enzymes in overall folding as well as certain inter-domain connections, which distinguishes FAM46B from other eukaryotic non-canonical PAPs. Biochemical analysis reveals that FAM46B is an active PAP, and prefers adenosine-rich substrate RNAs. FAM46B is uniquely and highly expressed in human pre-implantation embryos and pluripotent stem cells, but sharply down-regulated following differentiation. FAM46B is localized to both cell nucleus and cytosol, and is indispensable for the viability of human embryonic stem cells. Knock-out of FAM46B is lethal. Knock-down of FAM46B induces apoptosis and restricts protein synthesis. The identification of the bacterial-like FAM46B, as a pluripotent stem cell-specific PAP involved in the maintenance of translational efficiency, provides important clues for further functional studies of this PAP in the early embryonic development of high eukaryotes.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkaa049
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 8
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    The roles of ADAMDEC1 in trophoblast differentiation during normal pregnancy and preeclampsia
    Oxford University Press (OUP) ; 2022
    In:  Molecular Human Reproduction Vol. 28, No. 5 ( 2022-04-29)
    Details
    In: Molecular Human Reproduction, Oxford University Press (OUP), Vol. 28, No. 5 ( 2022-04-29)
    Abstract: Human cytotrophoblast (CTB) differentiation into syncytiotrophoblast (STB) is essential for placental formation and function. Understanding the molecular mechanisms involved in trophoblast differentiation is necessary as it would help in the development of novel therapeutic agents to treat placentation-mediated pregnancy complications. In this study, we found a common upregulated gene, ADAM-like Decysin-1 (ADAMDEC1), from five published microarray and RNA-sequencing datasets. Interference to ADAMDEC1 impaired forskolin-induced BeWo cells differentiation, while ADAMDEC1 overexpression promoted BeWo cells and 3D JEG-3 spheroids differentiation. Interestingly, ADAMDEC1 may inhibit Thrombospondin 1 rather than E-cadherin to trigger the activation of the cAMP signal pathway during CTB differentiation into STB. More importantly, a decreasing in ADAMDEC1 might be involved in the development of preeclampsia. Therefore, ADAMDEC1 is expected to become a new target for prediction of and intervention in placenta-derived pregnancy diseases.
    Type of Medium: Online Resource
    ISSN: 1360-9947 , 1460-2407
    URL: Article
    DOI: 10.1093/molehr/gaac014
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1497467-8
    SSG: 12
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  • 9
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    Leachates from municipal solid waste disposal sites harbor similar, novel nitrogen-cycling bacterial communities
    Oxford University Press (OUP) ; 2007
    In:  FEMS Microbiology Letters Vol. 267, No. 2 ( 2007-02), p. 236-242
    Details
    In: FEMS Microbiology Letters, Oxford University Press (OUP), Vol. 267, No. 2 ( 2007-02), p. 236-242
    Type of Medium: Online Resource
    ISSN: 0378-1097 , 1574-6968
    URL: Issue
    URL: Article
    DOI: 10.1111/fml.2007.267.issue-2
    DOI: 10.1111/j.1574-6968.2006.00560.x
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2007
    detail.hit.zdb_id: 1501716-3
    SSG: 12
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  • 10
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    Development and internal validation of a Wasp Sting Severity Score to assess severity and indicate blood purification in persons with Asian wasp stings
    Oxford University Press (OUP) ; 2022
    In:  Clinical Kidney Journal Vol. 15, No. 2 ( 2022-02-04), p. 320-327
    Details
    In: Clinical Kidney Journal, Oxford University Press (OUP), Vol. 15, No. 2 ( 2022-02-04), p. 320-327
    Abstract: In recent years, the incidence of wasp sting has increased annually in China. Organ damage and high mortality due to mass wasp envenomation remain major challenges. Timely and appropriate medical intervention can improve survival. However, there are currently no normalized tools for early assessment of severity. Methods The clinical data of wasp sting patients hospitalized from 2011 to 2019 were used as a training set. Logistic regression was used to explore major risk factors for the development of a severe case of wasp sting (SC). The Wasp Sting Severity Score (WSS) was determined considering these risk factors to identify SCs and was tested in a validation dataset that was prospectively collected in 2020. Results The data of 1131 wasp sting patients from 2011 to 2019 were included in the training set. Logistic regression analysis showed that tea-colored urine, number of stings, and lactate dehydrogenase and total bilirubin levels were risk factors for developing an SC. The WSS was developed considering these four risk factors, and the total possible WSS was 20 points. The WSS was tested using the validation dataset, comprising the data of 153 patients, in 2020, and we found that a WSS ≥3 points was an important indication for blood purification, with a sensitivity of 71.9%, specificity of 92.6% and an area under the curve of 0.918 (95% confidence interval 0.873–0.962). Among patients with more than 30 stings, mortality in those who underwent plasma exchange (PE) within 24 h after admission was significantly lower than that in those who did not receive PE treatment (14.3% versus 46.9%, P = 0.003). However, continuous venovenous hemofiltration (CVVH) (P = 0.317) and hemoperfusion (HP) (P = 0.869) did not significantly reduce mortality. Conclusions Patients with WSS scores ≥3 should be considered for blood purification as early as possible in addition to routine treatment. In addition, PE is better than CVVH and HP at reducing mortality in patients suffering from severe wasp stings.
    Type of Medium: Online Resource
    ISSN: 2048-8505 , 2048-8513
    URL: Article
    DOI: 10.1093/ckj/sfab201
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2656786-6
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