Biology subjects

Nishizawa, M.

Publications and source records attributed to Nishizawa, M..

6 recordsLinked to original sources

bioRxiv2024

Preprints vs. Journal Articles: Citation Impact in COVID-19 Research

Focusing on article and citation count, this study examined 110 academic journals whose papers on COVID-19 were indexed in PubMed from 2020 to 2023. To analyze these journals characteristics, this study introduced the concepts of paper ratio, citation ratio, and citation impact. Journals with similar trends in paper and citation count were positioned near the diagonal on a two-dimensional graph (y=x) with paper ratio on the x-axis and citation ratio on the y-axis, indicating a slope close to 1. Conversely, the greater the disparity between paper ratio and citation ratio, the wider the angle between the journals position and the diagonal. Of the 110 journals in 2020, 83 were above the diagonal with a citation impact greater than 1, while 27 were below the diagonal with a citation impact of 1 or lower. Notably, nine journals--BMC Health Services Research, Genome Medicine, Nature, Annals of Epidemiology, BMC Bioinformatics, Nature Microbiology, PLoS Computational Biology, Medicine (Baltimore), and Journal of Clinical Investigation--showed high citation impact, with preprint-distributed papers being cited nearly five times more than directly submitted papers. This study demonstrates that articles initially distributed as preprints in these journals tend to receive substantially more citations than directly submitted ones.

scientific communication and education↗

bioRxiv2024

A Novel Approach to Reducing Spinal Implant-Associated Infections

Implant-associated infection is a severe complication of instrumented spinal surgery. Preventive measures against biofilm formation, such as chemical modifications of devices with antibiotics or bactericidal substances, have been explored to decrease infection rates and enhance therapeutic outcomes. However, this approach remains challenging, and the safety issues associated with antibiotic resistance and cellular toxicity need to be addressed. Hence, there is an unmet clinical need for implants that resist biofilm formation. Ultrafine-grained material (UFG), which has a nanoscale grain structure, is a novel form of metal with exceptional mechanical and biocompatibility properties that may also have antimicrobial activity. This study investigates the extent to which UFG stainless steel implants resist biofilm formation by Staphylococcus aureus in vitro and in vivo. The results show that the UFG stainless steel wire significantly reduced biofilm formation at early time points after bacterial infection compared to a standard wire. In mouse models of implant-associated infection below the skin or the fascia, the UFG wire had significantly less biofilm formation at early time points. The UFG wire appeared to delay initial bacterial adhesion and biofilm maturation. These findings suggest that UFG implants may resist initial biofilm formation and maturation, leading to promising antibacterial materials for patients.

microbiology↗

bioRxiv2024

The Impact of Preprints on the Citations of Journal Articles Related to COVID-19

To investigate the impact of preprints on the citation counts of COVID-19-related papers, this study compares the number of citations received by drafts initially distributed as preprints and later published in journals with those received by papers directly submitted to journals. The difference in the median number of citations between COVID-19 preprint-distributed papers and COVID-19 directly submitted papers published in 184 journals was tested using the Mann-Whitney U test. The results showed that 129 journals had a statistically significant higher median citation count for COVID-19 preprint-distributed papers compared to directly submitted papers, with a p-value of less than 0.05. In contrast, no journals had a statistically significant higher median citation count for COVID-19 directly submitted papers. This indicates that 70.11% of the journals that published preprint-distributed papers experienced a significant increase in citations. We also identified that among the 184 journals, 13 journals garnered a substantial number of citations. Among the 74,037 COVID-19 papers, preprint-distributed papers (9,028) accounted for only 12.19%. However, among the 2,015,997 citations received by COVID-19 papers, preprint-distributed papers garnered 542,715 citations, representing a substantial 26.92%. These results suggest that distributing preprints prior to formal publication may help COVID-19 research reach a wider audience, potentially leading to increased readership and citations.

scientific communication and education↗

bioRxiv2024

The Impact of Preprints on COVID-19 Research Dissemination: A Quantitative Analysis of Journal Publications

Preprints have played an unprecedented role in disseminating COVID-19-related science results to the public. The study aims to elucidate the role of preprints during the COVID-19 public health emergency (2020-2023) through a quantitative analysis of journal papers. Among the 247,854 COVID-19-related papers published in PubMed, 12,152 were initially released as preprints and were eventually published in 1,380 journals. This number is more than five times the 246 journals to which submissions can be made directly from bioRxiv through the B2J program. Journals with higher impact factors and Normalized Eigenfactor scores tend to publish a larger number of preprint-derived articles. The proportion of preprints among PubMed papers was 0.049, but this varies significantly by journal. In the top 30 journals, most exceed this proportion, indicating that these journals are preferred by authors for submitting their work. These findings highlight the growing acceptance and impact of preprints in the scientific community, particularly in high-impact journals.

scientific communication and education↗

bioRxiv2021

Subacute SARS-CoV-2 replication can be controlled in the absence of CD8+ T cells in cynomolgus macaques

SARS-CoV-2 infection presents clinical manifestations ranging from asymptomatic to fatal respiratory failure. Despite the induction of functional SARS-CoV-2-specific CD8+ T-cell responses in convalescent individuals, the role of virus-specific CD8+ T-cell responses in the control of SARS-CoV-2 replication remains unknown. In the present study, we show that subacute SARS-CoV-2 replication can be controlled in the absence of CD8+ T cells in cynomolgus macaques. Eight macaques were intranasally inoculated with 105 or 106 TCID50 of SARS-CoV-2, and three of the eight macaques were treated with a monoclonal anti-CD8 antibody on days 5 and 7 post-infection. In these three macaques, CD8+ T cells were undetectable on day 7 and thereafter, while virus-specific CD8+ T-cell responses were induced in the remaining five untreated animals. Viral RNA was detected in nasopharyngeal swabs for 10-17 days post-infection in all macaques, and the kinetics of viral RNA levels in pharyngeal swabs and plasma neutralizing antibody titers were comparable between the anti-CD8 antibody treated and untreated animals. SARS-CoV-2 RNA was detected in the pharyngeal mucosa and/or retropharyngeal lymph node obtained at necropsy on day 21 in two of the untreated group but undetectable in all macaques treated with anti-CD8 antibody. CD8+ T-cell responses may contribute to viral control in SARS-CoV-2 infection, but our results indicate possible containment of subacute viral replication in the absence of CD8+ T cells, implying that CD8+ T-cell dysfunction may not solely lead to viral control failure. Author SummarySARS-CoV-2 infection presents a wide spectrum of clinical manifestations ranging from asymptomatic to fatal respiratory failure. The determinants for failure in viral control and/or fatal disease progression have not been elucidated fully. Both acquired immune effectors, antibodies and CD8+ T cells, are considered to contribute to viral control. However, it remains unknown whether a deficiency in either of these two arms is directly linked to failure in the control of SARS-CoV-2 replication. In the present study, to know the requirement of CD8+ T cells for viral control after the establishment of infection, we examined the effect of CD8+ cell depletion by monoclonal anti-CD8 antibody administration in the subacute phase on SARS-CoV-2 replication in cynomolgus macaques. Unexpectedly, our analysis revealed no significant impact of CD8+ cell depletion on viral replication, indicating that subacute SARS-CoV-2 replication can be controlled in the absence of CD8+ T cells. CD8+ T-cell responses may contribute to viral control in SARS-CoV-2 infection, but this study suggests that CD8+ T-cell dysfunction may not solely lead to viral control failure or fatal disease progression.

microbiology↗

bioRxiv2019

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments

Hadal trench bottom (>6,000 m below sea level) sediments harbor higher microbial cell abundance compared to adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been explored yet. Here, we carried out small subunit ribosomal RNA gene tag sequencing for 92 sediment subsamples of seven abyssal and seven hadal sediment cores collected from three trench regions in the northwest Pacific Ocean: the Japan, Izu-Ogasawara, and Mariana Trenches. Tag-sequencing analyses showed specific distribution patterns of several phyla associated with oxygen and nitrate. The community structure was distinct between abyssal and hadal sediments, following geographic locations and factors represented by sediment depth. Co-occurrence network revealed six potential prokaryotic consortiums that covaried across regions. Our results further support that the endogenous OM cycle is driven by hadal currents and/or rapid burial shapes microbial community structures at trench bottom sites, in addition to vertical deposition from the surface ocean. Our trans-trench analysis highlights intra- and inter-trench distributions of microbial assemblages and geochemistry in surface seafloor sediments, providing novel insights into ultra-deep-sea microbial ecology, one of the last frontiers on our planet.

microbiology↗