Issues importing from Embase

zotgsacc

Hi. I'm having issues when importing from Embase to Zotero using .ris files. In many citations, Zotero list the authors and authors contact information in place of the publication "issue", and the Embase Archive name after the "page number". For example:


Shimizu, K., Agata, K., Takasugi, S., Goto, S., Narita, Y., Asai, T., Magata, Y., & Oku, N. (2021). New strategy for MS treatment with autoantigen-modified liposomes and their therapeutic effect. Journal of Controlled Release, 335((Shimizu K., kshimizu@hama-med.ac.jp; Takasugi S.; Narita Y.; Magata Y.) Department of Molecular Imaging, Institute of Medical Photonics Research, Preeminent Medical Photonics Education&Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu City, Shizuoka, Japan), 389–397. Embase. https://doi.org/10.1016/j.jconrel.2021.05.027

I contact EMBASE and they told me this was a Zotero problem. Is there a way to fix this?

I don't remember having this issue several months ago.

Thank you and Happy Holidays and New Year!

dstillman

Can you open the .ris file in a text editor (e.g., Notepad or TextEdit), copy one of the relevant entries, and paste it here?

dstillman

Also, what we'd want to know here would be what fields in the Zotero item the values end up in. The citation will just use the data in the library, so it's not relevant for an import.

zotgsacc

Hi. I have the same issues when importing .ris format from Embase.
This is a relevant entry:
TY - JOUR
M3 - Article
Y1 - 2022
VL - 13
SN - 1664-3224
JF - Frontiers in Immunology
JO - Front. Immunol.
UR - https://www.embase.com/search/results?subaction=viewrecord&id=L2020938408&from=export
U2 - L2020938408
C5 - 36618427
DB - Embase
DB - Medline
U3 - 2023-01-10
U4 - 2023-01-24
L2 - http://dx.doi.org/10.3389/fimmu.2022.1072462
DO - 10.3389/fimmu.2022.1072462
A1 - Agarbati, S.
A1 - Benfaremo, D.
A1 - Viola, N.
A1 - Paolini, C.
A1 - Svegliati Baroni, S.
A1 - Funaro, A.
A1 - Moroncini, G.
A1 - Malavasi, F.
A1 - Gabrielli, A.
M1 - (Agarbati S.; Benfaremo D.; Paolini C.; Svegliati Baroni S.; Moroncini G., g.moroncini@univpm.it; Gabrielli A.) Department of Clinical and Molecular Sciences, Marche Polytechnic University, Ancona, Italy
M1 - (Benfaremo D.; Moroncini G., g.moroncini@univpm.it) Clinica Medica, Department of Internal Medicine, Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
M1 - (Viola N.) Immunologia Clinica, Department of Internal Medicine, Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
M1 - (Funaro A.; Malavasi F.) Department of Medical Sciences, University of Turin, Torino, Italy
M1 - (Malavasi F.) Fondazione Ricerca Molinette, Torino, Italy
AD - G. Moroncini, Department of Clinical and Molecular Sciences, Marche Polytechnic University, Ancona, Italy
T1 - Increased expression of the ectoenzyme CD38 in peripheral blood plasmablasts and plasma cells of patients with systemic sclerosis
LA - English
KW - flow cytometer
KW - ADP ribosyl cyclase/cyclic ADP ribose hydrolase 1
KW - allophycocyanin
KW - CD24 antigen
KW - CD3 antigen
KW - gamma interferon
KW - rituximab
KW - toll like receptor 9
KW - adult
KW - article
KW - B lymphocyte
KW - blood sampling
KW - CD4+ CD25+ T lymphocyte
KW - CD4+ T lymphocyte
KW - CD8+ T lymphocyte
KW - cell surface
KW - controlled study
KW - cytotoxic T lymphocyte
KW - diffuse scleroderma
KW - disease duration
KW - female
KW - flow cytometry
KW - fluorescence intensity
KW - gene expression
KW - human
KW - human experiment
KW - immune response
KW - immunophenotyping
KW - immunosuppressive treatment
KW - innate immunity
KW - male
KW - memory B lymphocyte
KW - middle aged
KW - natural killer cell
KW - natural killer T cell
KW - normal human
KW - peripheral blood mononuclear cell
KW - plasma cell
KW - plasmablast
KW - protein expression
KW - regulatory B lymphocyte
KW - regulatory T lymphocyte
KW - systemic sclerosis
KW - tumor associated leukocyte
KW - tumor microenvironment
KW - vaccination
KW - FacsCanto II
C3 - FacsCanto II(Becton Dickinson,United States)
C4 - Becton Dickinson(United States)
N2 - Objective: CD38 is a type II glycoprotein highly expressed on plasmablasts and on short- and long-lived plasma cells, but weakly expressed by lymphoid, myeloid, and non-hematopoietic cells. CD38 is a target for therapies aimed at depleting antibody-producing plasma cells. Systemic sclerosis (SSc) is an immune-mediated disease with a well-documented pathogenic role of B cells. We therefore analyzed CD38 expression in different subsets of peripheral blood mononuclear cells (PBMCs) from a cohort of SSc patients. Methods: Cell surface expression of CD38 was evaluated on PBMCs from SSc patients using eight-color flow cytometry analysis performed with a FacsCanto II (BD). Healthy individuals were used as controls (HC). Results: Forty-six SSc patients (mean age 56, range 23-79 years; 38 females and 8 males), and thirty-two age- and sex-matched HC were studied. Twenty-eight patients had the limited cutaneous form and eighteen the diffuse cutaneous form of SSc. The mean disease duration was 7 years. Fourteen patients were on immunosuppressive therapy (14 MMF, 5 RTX). The total percentages of T, B and NK cells were not different between SSc and HC. Compared to HC, SSc patients had higher levels of CD3+CD38+ T cells (p<0.05), higher percentage (p<0.001) of CD3+CD4+CD25+FOXP3+ regulatory T cells, lower percentage (p<0.05) of CD3+CD56+ NK T cells. Moreover, SSc patients had higher levels of CD24highCD19+CD38high regulatory B cells than HC (p<0.01), while the amount of CD24+CD19+CD38+CD27+ memory B cells was lower (p<0.001). Finally, the percentages of circulating CD38highCD27+ plasmablasts and CD138+CD38high plasma cells were both higher in the SSc group than in HC (p<0.001). We did not observe any correlations between these immunophenotypes and disease subsets or duration, and ongoing immunosuppressive treatment. Conclusions: The increased expression of CD38 in peripheral blood plasmablasts and plasma cells of SSc patients may suggest this ectoenzyme as a candidate therapeutic target, under the hypothesis that depletion of these cells may beneficially downregulate the chronic immune response in SSc patients. Validation of this data in multicenter cohorts shall be obtained prior to clinical trials with existing anti-CD38 drugs.
ER -

I get in Zotero the following:
Agarbati, S., Benfaremo, D., Viola, N., Paolini, C., Svegliati Baroni, S., Funaro, A., Moroncini, G., Malavasi, F., and Gabrielli, A. (2022). Increased expression of the ectoenzyme CD38 in peripheral blood plasmablasts and plasma cells of patients with systemic sclerosis. Frontiers in Immunology, 13((Agarbati S.; Benfaremo D.; Paolini C.; Svegliati Baroni S.; Moroncini G., g.moroncini@univpm.it; Gabrielli A.) Department of Clinical and Molecular Sciences, Marche Polytechnic University, Ancona, Italy). Embase. https://doi.org/10.3389/fimmu.2022.1072462

instead of (from Pubmed):
Agarbati, S., Benfaremo, D., Viola, N., Paolini, C., Svegliati Baroni, S., Funaro, A., Moroncini, G., Malavasi, F., and Gabrielli, A. (2022). Increased expression of the ectoenzyme CD38 in peripheral blood plasmablasts and plasma cells of patients with systemic sclerosis. Frontiers in Immunology, 13, 1072462. https://doi.org/10.3389/fimmu.2022.1072462

This issue happens for about 20-30% of Embase exports but not for all of them. For example, this one looks OK (except for the database added to the citation):

Cattaruzza, F., Nazeer, A., To, M., Hammond, M., Koski, C., Liu, L. Y., Pete Yeung, V., Rennerfeldt, D. A., Henkensiefken, A., Fox, M., Lam, S., Morrissey, K. M., Lange, Z., Podust, V. N., Derynck, M. K., Irving, B. A., and Schellenberger, V. (2023). Precision-activated T-cell engagers targeting HER2 or EGFR and CD3 mitigate on-target, off-tumor toxicity for immunotherapy in solid tumors. Nature Cancer, 4(4), 485–501. Embase. https://doi.org/10.1038/s43018-023-00536-9

Thank you very much for your help and great job with Zotero. We appreciate it very much.
Best,
GS.

zotgsacc

Oh! I just noticed that I was the one that opened this discussion two years ago; I probably overlooked your reply then. My apologies.
Yes, the issue continues and I have to fix it manually every time. I use the APA style for my references.
Thanks.