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Article ; Online: Retracted publications in infectious diseases and clinical microbiology literature: an analysis using the retraction watch database.

Zilberman, Tal / Margalit, Ili / Yahav, Dafna / Tau, Noam

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases

2023

Abstract: Objectives: We aimed to examine the rate and characteristics of retracted articles in infectious diseases and clinical microbiology.: Methods: Using the Retraction Watch Database, we conducted a cross-sectional study for retracted publications ... ...

Abstract	Objectives: We aimed to examine the rate and characteristics of retracted articles in infectious diseases and clinical microbiology. Methods: Using the Retraction Watch Database, we conducted a cross-sectional study for retracted publications categorized as 'Infectious Disease' or 'Microbiology' until June 30 2022. We included publications for which citation information was available through the Web of Science database. Study characteristics, retraction trends and number of citations before and after the retraction year were analysed. Results: Overall, 1004 retracted publications were included, retracted between August 1968 and June 2022. The number of retractions climbed through the years, peaking in 2020-2021. A total of 614 retractions originated from USA, China, and India, of total 183 736 PubMed publications from these countries. Overall, 378 (38%) were retracted because of errors; 182 (18%) because of plagiarism; and 142 (14%) because of falsification/fabrication. Specific reasons included 'concerns/issues about data' (158, 16%); 'duplication of image' (127, 13%); and 'unreliable results' (116, 12%). Of the 347 retractions during 2020 to June 2022, 91 (26%) were COVID-19 related. Fifty of 895 (5.6%) first authors had two retracted papers, and 14 (1.6%) had ≥2 retractions. Of 824 publications cited at least once, 466 (57%) were cited more often after retraction. Discussion: Retractions of infectious diseases and clinical microbiology publications are increasing. Concerning reasons such as plagiarism, falsification/fabrication and errors are not uncommon. Nonetheless, these publications continue to be commonly cited after being retracted.
Language	English
Publishing date	2023-07-29
Publishing country	England
Document type	Journal Article
ZDB-ID	1328418-6
ISSN	1469-0691 ; 1470-9465 ; 1198-743X
ISSN (online)	1469-0691
ISSN	1470-9465 ; 1198-743X
DOI	10.1016/j.cmi.2023.07.022
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Zs.A 4541: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Concurrent Visual and Auditory Deficits in a Patient with Rickettsia conorii Infection.

Manor, Uri / Kfir, Jonathan / Livneh, Nir / Zilberman, Tal / Yelin, Dana / Meltzer, Eyal

The American journal of tropical medicine and hygiene

2023 Volume 109, Issue 3, Page(s) 501–502

MeSH term(s)	Humans ; Boutonneuse Fever/complications ; Boutonneuse Fever/diagnosis ; Boutonneuse Fever/drug therapy ; Rickettsia ; Patients
Language	English
Publishing date	2023-07-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2942-7
ISSN	1476-1645 ; 0002-9637
ISSN (online)	1476-1645
ISSN	0002-9637
DOI	10.4269/ajtmh.23-0173
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Article: Adverse Clinical Outcomes among Inflammatory Bowel Disease Patients Treated for Urinary Tract Infection.

Ukashi, Offir / Barash, Yiftach / Klang, Eyal / Zilberman, Tal / Ungar, Bella / Kopylov, Uri / Ben-Horin, Shomron / Veisman, Ido

Journal of clinical medicine

2022 Volume 11, Issue 5

Abstract: Background: Urinary tract infection (UTI) is the most common urologic complication among patients with inflammatory bowel disease (IBD). However, data regarding UTI outcomes in this population are scarce. We aimed to evaluate adverse outcomes of UTI ... ...

Abstract	Background: Urinary tract infection (UTI) is the most common urologic complication among patients with inflammatory bowel disease (IBD). However, data regarding UTI outcomes in this population are scarce. We aimed to evaluate adverse outcomes of UTI among patients with IBD. Methods: This was a retrospective cohort study of consecutive adult patients who visited the emergency room (ER) at Sheba Medical Center due to a UTI between 2012 and 2018. Data included demographic and clinical variables. UTI cases were extracted using ICD-10 coding. Results: Of 21,808 (ER) visits with a UTI, 122 were IBD patients (Crohn’s disease—52, ulcerative colitis—70). Contrary to non-IBD subjects, patients with IBD had higher rates of hospitalization, acute kidney injury (AKI) and 30 day-recurrent hospitalization (59.3% vs. 68.9%, p = 0.032; 4.6% vs. 13.9%, p < 0.001; 7.3% vs. 15.6%, p = 0.001, respectively). Among patients with IBD, advanced age (p = 0.005) and recent hospitalization (p = 0.037) were associated with increased risk for hospitalization, while hydronephrosis (p = 0.005), recent hospitalization (p = 0.011) and AKI (p = 0.017) were associated with increased 30-day recurrent hospitalization. Neither immunosuppressants nor biologics were associated with UTI outcomes among patients with IBD. Conclusions: Patients with IBD treated for a UTI had higher rates of hospitalization, AKI and 30-day recurrent hospitalization than non-IBD patients. No association was observed between immunosuppressants or biologics and UTI outcomes.
Language	English
Publishing date	2022-03-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662592-1
ISSN	2077-0383
ISSN	2077-0383
DOI	10.3390/jcm11051359
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Overlooked monkeypox cases among men having sex with men during the 2022 outbreak - a retrospective study.

Wieder-Feinsod, Anat / Zilberman, Tal / Erster, Oran / Kolasko, Gal Wagner / Biber, Asaf / Gophen, Ruth / Hoffman, Tomer / Litchevsky, Vladislav / Olmer, Liraz / Yahav, Dafna / Levy, Itzchak

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

2022 Volume 128, Page(s) 58–60

Abstract: Objectives: The aim of this study was to characterize overlooked cases of patients with monkeypox infection in the 2022 outbreak.: Methods: Clinical characteristics of 26 patients who were misdiagnosed with other diseases were described.: Results: ...

Abstract	Objectives: The aim of this study was to characterize overlooked cases of patients with monkeypox infection in the 2022 outbreak. Methods: Clinical characteristics of 26 patients who were misdiagnosed with other diseases were described. Results: Of the 26 patients who were misdiagnosed, six (23%) were given a diagnosis of bacterial tonsillitis, six (23%) were diagnosed with primary syphilis, five (19.2%) with oral or genital herpes, and four (15.3%) with bacterial proctitis or anal abscess. The average time interval between missed and right diagnosis was 4.4 days. There was no difference in the missed cases between the early and the later month of the outbreak. Conclusion: Monkeypox might still be commonly overlooked, especially in patients presenting with fever and sore throat or solitary ulcer as sole manifestations.
MeSH term(s)	Male ; Humans ; Retrospective Studies ; Mpox (monkeypox)/epidemiology ; Herpes Genitalis/epidemiology ; Proctitis/epidemiology ; Disease Outbreaks ; Homosexuality, Male
Language	English
Publishing date	2022-12-16
Publishing country	Canada
Document type	Journal Article
ZDB-ID	1331197-9
ISSN	1878-3511 ; 1201-9712
ISSN (online)	1878-3511
ISSN	1201-9712
DOI	10.1016/j.ijid.2022.12.014
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Zs.A 4516: Show issues

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Article: Membranous nephropathy associated with sarcoidosis: a primary or secondary glomerulopathy?

Zilberman, Tal / Zahavi, Tanya / Osadchy, Alexandra / Nacasch, Naomi / Korzets, Ze'ev

The Israel Medical Association journal : IMAJ

2014 Volume 16, Issue 6, Page(s) 390–392

MeSH term(s)	Adult ; Glomerulonephritis, Membranous/etiology ; Glomerulonephritis, Membranous/physiopathology ; Humans ; Kidney Diseases/physiopathology ; Microscopy, Electron/methods ; Sarcoidosis/complications ; Sarcoidosis/physiopathology ; Tomography, X-Ray Computed/methods
Language	English
Publishing date	2014-06
Publishing country	Israel
Document type	Case Reports ; Journal Article
ZDB-ID	2008291-5
ISSN	1565-1088 ; 0021-2180
ISSN	1565-1088 ; 0021-2180
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Zs.A 5470: Show issues

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Article: Progressive multifocal leukoencephalopathy in an HIV-negative patient following treatment with rituximab.

Khoury, Shafik / Shapira, Shirley / Zilberman, Tal / Mekori, Yoseph A / Hershko, Alon Y

The Israel Medical Association journal : IMAJ

2013 Volume 15, Issue 6, Page(s) 321–322

MeSH term(s)	Aged ; Antibodies, Monoclonal, Murine-Derived/administration & dosage ; Antibodies, Monoclonal, Murine-Derived/adverse effects ; Antineoplastic Agents/administration & dosage ; Antineoplastic Agents/adverse effects ; Cerebrospinal Fluid/virology ; Confusion/diagnosis ; Confusion/etiology ; Fatal Outcome ; Humans ; JC Virus/physiology ; Leukoencephalopathy, Progressive Multifocal/diagnosis ; Leukoencephalopathy, Progressive Multifocal/etiology ; Leukoencephalopathy, Progressive Multifocal/physiopathology ; Lymphoma, Large B-Cell, Diffuse/drug therapy ; Magnetic Resonance Imaging/methods ; Male ; Psychomotor Agitation/diagnosis ; Psychomotor Agitation/etiology ; Rituximab ; Tomography, X-Ray Computed/methods ; Virus Activation
Chemical Substances	Antibodies, Monoclonal, Murine-Derived ; Antineoplastic Agents ; Rituximab (4F4X42SYQ6)
Language	English
Publishing date	2013-06
Publishing country	Israel
Document type	Case Reports ; Journal Article
ZDB-ID	2008291-5
ISSN	1565-1088 ; 0021-2180
ISSN	1565-1088 ; 0021-2180
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Primary exposure to SARS-CoV-2 variants elicits convergent epitope specificities, immunoglobulin V gene usage and public B cell clones.

Lima, Noemia S / Musayev, Maryam / Johnston, Timothy S / Wagner, Danielle A / Henry, Amy R / Wang, Lingshu / Yang, Eun Sung / Zhang, Yi / Birungi, Kevina / Black, Walker P / O'Dell, Sijy / Schmidt, Stephen D / Moon, Damee / Lorang, Cynthia G / Zhao, Bingchun / Chen, Man / Boswell, Kristin L / Roberts-Torres, Jesmine / Davis, Rachel L /

Peyton, Lowrey / Narpala, Sandeep R / O'Connell, Sarah / Wang, Jennifer / Schrager, Alexander / Talana, Chloe Adrienna / Leung, Kwanyee / Shi, Wei / Khashab, Rawan / Biber, Asaf / Zilberman, Tal / Rhein, Joshua / Vetter, Sara / Ahmed, Afeefa / Novik, Laura / Widge, Alicia / Gordon, Ingelise / Guech, Mercy / Teng, I-Ting / Phung, Emily / Ruckwardt, Tracy J / Pegu, Amarendra / Misasi, John / Doria-Rose, Nicole A / Gaudinski, Martin / Koup, Richard A / Kwong, Peter D / McDermott, Adrian B / Amit, Sharon / Schacker, Timothy W / Levy, Itzchak / Mascola, John R / Sullivan, Nancy J / Schramm, Chaim A / Douek, Daniel C

bioRxiv : the preprint server for biology

2022

Abstract: An important consequence of infection with a SARS-CoV-2 variant is protective humoral immunity against other variants. The basis for such cross-protection at the molecular level is incompletely understood. Here we characterized the repertoire and epitope ...

Abstract	An important consequence of infection with a SARS-CoV-2 variant is protective humoral immunity against other variants. The basis for such cross-protection at the molecular level is incompletely understood. Here we characterized the repertoire and epitope specificity of antibodies elicited by Beta, Gamma and ancestral variant infection and assessed their cross-reactivity to these and the more recent Delta and Omicron variants. We developed a high-throughput approach to obtain immunoglobulin sequences and produce monoclonal antibodies for functional assessment from single B cells. Infection with any variant elicited similar cross-binding antibody responses exhibiting a remarkably conserved hierarchy of epitope immunodominance. Furthermore, convergent V gene usage and similar public B cell clones were elicited regardless of infecting variant. These convergent responses despite antigenic variation may represent a general immunological principle that accounts for the continued efficacy of vaccines based on a single ancestral variant.
Language	English
Publishing date	2022-06-30
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.03.28.486152
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Primary exposure to SARS-CoV-2 variants elicits convergent epitope specificities, immunoglobulin V gene usage and public B cell clones.

Peyton, Lowrey / Narpala, Sandeep R / O'Connell, Sarah / Serebryannyy, Leonid / Wang, Jennifer / Schrager, Alexander / Talana, Chloe Adrienna / Shimberg, Geoffrey / Leung, Kwanyee / Shi, Wei / Khashab, Rawan / Biber, Asaf / Zilberman, Tal / Rhein, Joshua / Vetter, Sara / Ahmed, Afeefa / Novik, Laura / Widge, Alicia / Gordon, Ingelise / Guech, Mercy / Teng, I-Ting / Phung, Emily / Ruckwardt, Tracy J / Pegu, Amarendra / Misasi, John / Doria-Rose, Nicole A / Gaudinski, Martin / Koup, Richard A / Kwong, Peter D / McDermott, Adrian B / Amit, Sharon / Schacker, Timothy W / Levy, Itzchak / Mascola, John R / Sullivan, Nancy J / Schramm, Chaim A / Douek, Daniel C

Nature communications

2022 Volume 13, Issue 1, Page(s) 7733

Abstract: An important consequence of infection with a SARS-CoV-2 variant is protective humoral immunity against other variants. However, the basis for such cross-protection at the molecular level is incompletely understood. Here, we characterized the repertoire ... ...

Abstract	An important consequence of infection with a SARS-CoV-2 variant is protective humoral immunity against other variants. However, the basis for such cross-protection at the molecular level is incompletely understood. Here, we characterized the repertoire and epitope specificity of antibodies elicited by infection with the Beta, Gamma and WA1 ancestral variants and assessed their cross-reactivity to these and the more recent Delta and Omicron variants. We developed a method to obtain immunoglobulin sequences with concurrent rapid production and functional assessment of monoclonal antibodies from hundreds of single B cells sorted by flow cytometry. Infection with any variant elicited similar cross-binding antibody responses exhibiting a conserved hierarchy of epitope immunodominance. Furthermore, convergent V gene usage and similar public B cell clones were elicited regardless of infecting variant. These convergent responses despite antigenic variation may account for the continued efficacy of vaccines based on a single ancestral variant.
MeSH term(s)	Humans ; Immunoglobulin Variable Region ; Epitopes/genetics ; SARS-CoV-2/genetics ; COVID-19 ; Clone Cells ; Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Immunoglobulin Variable Region ; Epitopes ; Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-12-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-35456-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Convergent epitope specificities, V gene usage and public clones elicited by primary exposure to SARS-CoV-2 variants

Lima, Noemia S / Mukhamedova, Maryam / Johnston, Timothy S / Wagner, Danielle A / Henry, Amy R / Wang, Lingshu / Yang, Eun Sung / Zhang, Yi / Birungi, Kevina / Black, Walker P / O'Dell, Sijy / Schmidt, Stephen D / Moon, Damee / Lorang, Cynthia G / Zhao, Bingchun / Chen, Man / Boswell, Kristin / Roberts-Torres, Jesmine / Davis, Rachel L /

Peyton, Lowrey / Narpala, Sandeep R / O'Connell, Sarah / Wang, Jennifer / Schrager, Alexander / Talana, Chloe Adrienna / Leung, Kwanyee / Shi, Wei / Khashab, Rawan / Biber, Asaf / Zilberman, Tal / Rhein, Joshua / Vetter, Sara / Ahmed, Afeefa / Novik, Laura / Widge, Alicia / Gordon, Ingelise / Guech, Mercy / Teng, I-Ting / Phung, Emily / Ruckwardt, Tracy / Pegu, Amarendra / Misasi, John / Doria-Rose, Nicole A / Gaudinski, Martin / Koup, Richard A / Kwong, Peter D / McDermott, Adrian B / Amit, Sharon / Schacker, Timothy W / Levy, Itzchak / Mascola, John R / Sullivan, Nancy J / Schramm, Chaim A / Douek, Daniel C

bioRxiv

Abstract: While humoral immune responses to infection or vaccination with ancestral SARS-CoV-2 have been well-characterized, responses elicited by infection with variants are less understood. Here we characterized the repertoire, epitope specificity, and cross- ... ...

Abstract	While humoral immune responses to infection or vaccination with ancestral SARS-CoV-2 have been well-characterized, responses elicited by infection with variants are less understood. Here we characterized the repertoire, epitope specificity, and cross-reactivity of antibodies elicited by Beta and Gamma variant infection compared to ancestral virus. We developed a high-throughput approach to obtain single-cell immunoglobulin sequences and isolate monoclonal antibodies for functional assessment. Spike-, RBD- and NTD-specific antibodies elicited by Beta- or Gamma-infection exhibited a remarkably similar hierarchy of epitope immunodominance for RBD and convergent V gene usage when compared to ancestral virus infection. Additionally, similar public B cell clones were elicited regardless of infecting variant. These convergent responses may account for the broad cross-reactivity and continued efficacy of vaccines based on a single ancestral variant.
Keywords	covid19
Language	English
Publishing date	2022-03-29
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2022.03.28.486152
Database	COVID19

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