bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utility of atherosclerosis-associated serum antibodies against colony-stimulating factor 2 in predicting the onset of acute ischemic stroke and prognosis of colorectal cancer
Authors: Li Shu-Yang , Yoshida Yoichi , Kubota Masaaki , Zhang Bo-Shi , Matsutani Tomoo , Ito Masaaki , Yajima Satoshi , Yoshida Kimihiko , Mine Seiichiro , Machida Toshio , Hayashi Aiko , Takemoto Minoru , Yokote Koutaro , Ohno Mikiko , Nishi Eiichiro , Kitamura Kenichiro , Kamitsukasa Ikuo , Takizawa Hirotaka , Sata Mizuki , Yamagishi Kazumasa , Iso Hiroyasu , Sawada Norie , Tsugane Shoichiro , Iwase Katsuro , Shimada Hideaki , Iwadate Yasuo , Hiwasa Takaki 
Published: February 2023

IntroductionAutoantibodies against inflammatory cytokines may be used for the prevention of atherosclerosis. Preclinical studies consider colony-stimulating factor 2 (CSF2) as an essential cytokine with a causal relationship to atherosclerosis and cancer. We examined the serum anti-CSF2 antibody levels in patients with atherosclerosis or solid cancer.MethodsWe measured the serum anti-CSF2 antibody levels via amplified luminescent proximity homogeneous assay-linked immunosorbent assay based on the recognition of recombinant glutathione S-transferase-fused CSF2 protein or a CSF2-derived peptide as the antigen.ResultsThe serum anti-CSF2 antibody (s-CSF2-Ab) levels were significantly higher in patients with acute ischemic stroke (AIS), acute myocardial infarction (AMI), diabetes mellitus (DM), and chronic kidney disease (CKD) compared with healthy donors (HDs). In addition, the s-CSF2-Ab levels were associated with intima-media thickness and hypertension. The analyzes of samples obtained from a Japan Public Health Center-based prospective study suggested the utility of s-CSF2-Ab as a risk factor for AIS. Furthermore, the s-CSF2-Ab levels were higher in patients with esophageal, colorectal, gastric, and lung cancer than in HDs but not in those with mammary cancer. In addition, the s-CSF2-Ab levels were associated with unfavorable postoperative prognosis in colorectal cancer (CRC). In CRC, the s-CSF2-Ab levels were more closely associated with poor prognosis in patients with p53-Ab-negative CRC despite the lack of significant association of the anti-p53 antibody (p53-Ab) levels with the overall survival.ConclusionS-CSF2-Ab was useful for the diagnosis of atherosclerosis-related AIS, AMI, DM, and CKD and could discriminate poor prognosis, especially in p53-Ab-negative CRC.
The impact of biomass burning emissions on aerosol concentrations and depositions in the northern South China Sea region
Authors: Li Jiawei , Zhang Zhisheng , Tao Jun , Pan Yuepeng , Luo Li , Han Zhiwei 
Published: February 2023

The impact of biomass burning (BB) emissions on concentrations and depositions of major aerosol components in the northern South China Sea (NSCS) region (105∼115°E and 15∼21°N) from December 2020 to April 2021 has been investigated using the WRF-chem model (weather research and forecasting model coupled with chemistry) in combination with aerosol composition measurement at a mountain site in the Hainan Island of China. Model comparisons with observations in Hainan demonstrated the effectiveness of WRF-chem in simulating aerosol components (PM2.5, black carbon (BC), organic matter (OM), sulfate, nitrate, and ammonium) in the NSCS region. The influences of BB emissions were significant on near-surface PM2.5, BC, and OM but nearly negligible on secondary inorganic components (i.e., sulfate, nitrate, and ammonium). The NSCS regional and period mean PM2.5, BC, and OM concentrations were 17.2 μg/m3, 0.65 μg/m3, and 6.7 μg/m3, in which 20%, 13%, and 35%, respectively, were from BB emissions. The mean PM2.5, BC, and OM deposition fluxes were 73.8 mg/m2/month, 2.9 mg/m2/month, and 29.3 mg/m2/month, respectively, and 22%, 15%, and 38% of these depositions were from BB emissions. Dry deposition dominated the removal of aerosols. For both aerosol concentrations and depositions, the influences of BB emissions exhibited evidently larger contributions in spring (March and April) than those in winter (December to February). Most of the BB emissions were from mainland Southeast Asia (MSEA), in terms of period mean, 79%, 72%, and 81% of the BB PM2.5, BB BC, and BB OM concentrations and 82%, 77%, and 83% of their depositions in the NSCS region were attributed to the MSEA region. The results of this study suggested that BB emissions have strong implications for air quality and biogeochemical cycle of the NSCS region.
Evaluation of genetic alterations in hereditary cancer susceptibility genes in the Ashkenazi Jewish women community of Mexico
Authors: Díaz-Velásquez Clara Estela , Gitler Rina , Antoniano Adriana , Kershenovich Sefchovich Ronny , De La Cruz-Montoya Aldo Hugo , Martínez-Gregorio Héctor , Rojas-Jiménez Ernesto Arturo , Cortez Cardoso Penha Ricardo , Terrazas Luis Ignacio , Wegman-Ostrosky Talia , Levi-Lahad Ephrat , Zabaleta Jovanny , Perdomo Sandra , Vaca-Paniagua Felipe 
Published: February 2023

Background: Individuals of Ashkenazi Jewish ancestry have been identified as having higher prevalence of specific pathogenic variants associated with susceptibility to specific rare and chronic diseases. In Mexico, the prevalence and composition of rare cancer predisposing germline variants in Ashkenazi Jewish individuals has not been evaluated.Aim and methods: We aimed to evaluate the prevalence of pathogenic variants by massive parallel sequencing in a panel of 143 cancer-predisposing genes in 341 women from the Ashkenazi Jewish community of Mexico, who were contacted and invited to participate in the study through the ALMA Foundation for Cancer Reconstruction. Pre- and posttest genetic counseling was given and a questionnaire on personal, gyneco-obstetric, demographic and lifestyle variables was conducted. From peripheral blood DNA, the complete coding region, and splicing sites of a panel of 143 cancer susceptibility genes, including 21 clinically relevant genes, were sequenced. The Mexican founder mutation BRCA1 ex9-12del [NC_000017.10(NM_007294):c. (825+1–826-1)_(4,589+1–4,590-1)del] was also evaluated.Results: Among study participants (mean age ±standard deviation: 47 ± 14) 15% reported a personal history of cancer (50/341). Fourteen percent of participants (48/341) were carriers of pathogenic and likely pathogenic variants distributed among seven high-risk genes (APC, CHEK2, MSH2, BMPR1A, MEN1, MLH1, and MSH6), whereas 18.2% (62/341) had variants of uncertain clinical significance in genes associated with breast and ovarian cancer susceptibility (list of genes with VUS). Pathogenic and likely pathogenic variants in 16 susceptibility genes with ambiguous or non-well-established risk association for cancer were detected in 17.6% (60/341) of participants. Sixty four percent of participants reported current alcohol consumption compared with the 39 percent prevalence of alcohol consumption in Mexican women. None of the participants carried the recurrent Ashkenazi and Mexican founder mutations in BRCA1 or BRCA2, but 2% (7/341) had pathogenic Ashkenazi Jewish founder variants in BLM.Conclusion: Our findings show a diverse pathogenic variant composition among the recruited individuals of Ashkenazi Jewish ancestry in Mexico consistent with being a high-risk population for genetic diseases, which warrants further investigation to adequately assess the burden of hereditary breast cancer in this group and implement appropriate preventative programs.
Preclinical evaluation of CD70-specific CAR T cells targeting acute myeloid leukemia
Authors: Wu Gongqiang , Guo Shanshan , Luo Qian , Wang Xiaoxia , Deng Wenhai , Ouyang Guifang , Pu Jeffrey J. , Lei Wen , Qian Wenbin 
Published: February 2023

BackgroundsChimeric antigen receptor (CAR)-T cell therapy has achieved unprecedented success in treating hematopoietic malignancies. However, this cell therapy is hampered in treating acute myeloid leukemia (AML) due to lack of ideal cell surface targets that only express on AML blasts and leukemia stem cells (LSCs) but not on normal hematopoietic stem cells (HSCs).MethodsWe detected the CD70 expression on the surfaces of AML cell lines, primary AML cells, HSC, and peripheral blood cells and generated a second-generation CD70-specific CAR-T cells using a construct containing a humanized 41D12-based scFv and a 41BB-CD3ζ intracellular signaling domain. Cytotoxicity, cytokine release, and proliferation in antigen stimulation, CD107a assay, and CFSE assays were used to demonstrate the potent anti-leukemia activity in vitro. A Molm-13 xenograft mouse model was established to evaluate the anti-leukemic activity of CD70 CAR-T in vivo. CFU assay was explored to assess the safety of CD70 CAR-T on HSC.ResultsCD70 heterogeneously expressed on AML primary cells, including leukemia blasts, leukemic progenitor, and stem cells, but not expressed on normal HSCs and majority of blood cells. Anti-CD70 CAR-T cells exhibited potent cytotoxicity, cytokines production, and proliferation when incubated with CD70+ AML cell lines. It also displayed robust anti-leukemia activity and prolonged survival in Molm-13 xenograft mouse model. However, such CAR-T cell therapy did not completely eliminate leukemia in vivo.DiscussionOur study reveals that anti-CD70 CAR-T cells are a new potential treatment for AML. However, such CAR-T cell therapy did not completely eliminate leukemia in vivo, suggesting that future studies aiming to generate innovative combinatorial CAR constructs or to increase CD70 expression density on leukemia cell surface to prolong the life-span of CAR-T cells in the circulation will be needed in order to optimize CAR-T cell responses for AML.
Design of a multi-epitope vaccine against six Nocardia species based on reverse vaccinology combined with immunoinformatics
Authors: Zhu Fei , Tan Caixia , Li Chunhui , Ma Shiyang , Wen Haicheng , Yang Hang , Rao Mingjun , Zhang Peipei , Peng Wenzhong , Cui Yanhui , Chen Jie , Pan Pinhua 
Published: February 2023

BackgroundNocardia genus, a complex group of species classified to be aerobic actinomycete, can lead to severe concurrent infection as well as disseminated infection, typically in immunocompromised patients. With the expansion of the susceptible population, the incidence of Nocardia has been gradually growing, accompanied by increased resistance of the pathogen to existing therapeutics. However, there is no effective vaccine against this pathogen yet. In this study, a multi-epitope vaccine was designed against the Nocardia infection using reverse vaccinology combined with immunoinformatics approaches.MethodsFirst, the proteomes of 6 Nocardia subspecies Nocardia subspecies (Nocardia farcinica, Nocardia cyriacigeorgica, Nocardia abscessus, Nocardia otitidiscaviarum, Nocardia brasiliensis and Nocardia nova) were download NCBI (National Center for Biotechnology Information) database on May 1st, 2022 for the target proteins selection. The essential, virulent-associated or resistant-associated, surface-exposed, antigenic, non-toxic, and non-homologous with the human proteome proteins were selected for epitope identification. The shortlisted T-cell and B-cell epitopes were fused with appropriate adjuvants and linkers to construct vaccines. The physicochemical properties of the designed vaccine were predicted using multiple online servers. The Molecular docking and molecular dynamics (MD) simulation were performed to understand the binding pattern and binding stability between the vaccine candidate and Toll-like receptors (TLRs). The immunogenicity of the designed vaccines was evaluated via immune simulation.Results3 proteins that are essential, virulent-associated or resistant-associated, surface-exposed, antigenic, non-toxic, and non-homologous with the human proteome were selected from 218 complete proteome sequences of the 6 Nocardia subspecies epitope identification. After screening, only 4 cytotoxic T lymphocyte (CTL) epitopes, 6 helper T lymphocyte (HTL) epitopes, and 8 B cell epitopes that were antigenic, non-allergenic, and non-toxic were included in the final vaccine construct. The results of molecular docking and MD simulation showed that the vaccine candidate has a strong affinity for TLR2 and TLR4 of the host and the vaccine-TLR complexes were dynamically stable in the natural environment. The results of the immune simulation indicated that the designed vaccine had the potential to induce strong protective immune responses in the host. The codon optimization and cloned analysis showed that the vaccine was available for mass production.ConclusionThe designed vaccine has the potential to stimulate long-lasting immunity in the host, but further studies are required to validate its safety and efficacy.
Density regulation of aquaculture production and its effects on commercial profit and quality as food in the cosmopolitan edible seaweed Undaria pinnatifida
Authors: Sato Yoichi , Fujiwara Takayuki , Endo Hikaru 
Published: February 2023

Aquaculture of marine macroalgae (i.e. seaweeds) such as the kelp Undaria pinnatifida is expected to contribute to future food and biomass production. Although macroalgal survival, biomass, and morphology are strongly affected by the density of individual plants in natural environments, little is known about the cultivation density (individuals per 1 m of cultivation rope) of macroalgae required to optimize aquaculture production, commercial profit (sales – labor expenses for processing), and quality as food. The present study examined the effect of increasing the cultivation density of U. pinnatifida from 10 to 200 individuals m-1 on survival rate, biomass production, profit, and morphological features related to quality as food. Survival rate was almost 100% in all treatments, indicating self-thinning did not occur. Biomass production increased with increasing density, suggesting that the maximum density possible is in excess of 200 individuals m-1. However, although profit rose with increasing density from 10 to 120 individuals m-1, it did not rise further if density was further increased. Moreover, some morphological features related to quality increased or decreased with increasing density. On balance, these results suggest that 80-120 individuals m-1 is an appropriate density range to optimize production of this species in terms of both profit and quality as food. However, only 10-30 individuals m-1 was the density best suited to enhance production of the sporophyll form, which is known to be a nutritious food both for humans and sea urchins.
Bacterial microbiome variation across symbiotic states and clonal lines in a cnidarian model
Authors: Curtis Ezra , Moseley Joanne , Racicot Riccardo , Wright Rachel M. 
Published: February 2023

IntroductionExaiptasia diaphana is a popular model organism for exploring the symbiotic relationship observed between cnidarians and their microsymbionts. While physiological roles of algal photosymbionts (Symbiodinaceae) are well studied, the contributions of bacterial communities are less defined in this system.MethodsWe investigated microbial variation between distinct parts of the body and symbiotic state across four genets held in identical environmental conditions using 16s rRNA gene amplicon sequencing.ResultsWe found differentially abundant taxa between body part and symbiotic state that highlight the roles these bacteria may play in holobiont heterotrophy and nutrient cycling. Beta-diversity analysis revealed distinct communities between symbiotic states consistent with previous studies; however, we did not observe the presence of previously reported core microbiota. We also found community differences across clonal lines, despite years of identical rearing conditions. ConclusionThese findings suggest the Exaiptasia bacterial microbiome is greatly influenced by host genetics and unpredictable environmental influences.
Urogenital tract and rectal microbiota composition and its influence on reproductive outcomes in infertile patients
Authors: Dong Yong-Hong , Fu Zhong , Zhang Ning-Nan , Shao Jing-Yi , Shen Jie , Yang En , Sun Shi-Yi , Zhao Zhi-Min , Xiao An , Liu Chen-Jian , Li Xiao-Ran 
Published: February 2023

IntroductionMicrobiota in the human body are closely related to human diseases. Female urogenital tract and rectal microbes have been considered as important factors affecting female pregnancy, but the mechanism is unknown.MethodsCervical, vaginal, urethral, and rectal swabs were collected from 22 infertile patients and 10 controls, and follicular fluid was extracted from 22 infertile patients. The microbial composition of different sampling sites of infertile patients was examined. By comparing the microbial composition difference between infertile patients and controls and combining bioinformatics methods to analyze the potential impact of the female urogenital tract (cervical, vaginal and urethral) and rectal microbial diversity on female infertility and pregnancy outcomes.ResultsLactobacillus predominated in the female urogenital tract, but its abundance decreased in infertile patients, whereas the abundance of Gardnerella and Atopobium increased. The microbial changes in the urethra had the same trend as that in the vagina. Compared with healthy controls, the cervical and rectal microbial diversity of infertile patients were significantly increased and decreased, respectively. There might be interactions between microbes in different parts of female. Geobacillus thermogeniticans was enriched in the urogenital tract and rectum of infertile patients, and has a good predictive effect on infertility. Compared with infertile patients, L. johnsonii was enriched in the vagina, urethra, and intestine of the control group. L. acidophilus in follicular fluid might be associated with Non-pregnancy.ConclusionThis study found that the microbial composition of infertile patients was changed compared with that of healthy people. The translocation of Lactobacillus between the rectum and urogenital tract might play a protective barrier role. The changes of Lactobacillus and Geobacillus might be related to female infertility or pregnancy outcome. The study provided a theoretical basis for the future treatment of female infertility from the perspective of microorganisms by detecting the microbial changes associated with female infertility.
Deletion of histone demethylase Lsd1 (Kdm1a) during retinal development leads to defects in retinal function and structure
Authors: Ferdous Salma , Shelton Debresha A. , Getz Tatiana E. , Chrenek Micah A. , L’Hernault Nancy , Sellers Jana T. , Summers Vivian R. , Iuvone P. Michael , Boss Jeremy M. , Boatright Jeffrey H. , Nickerson John M. 
Published: February 2023

PurposeThe purpose of this study was to investigate the role of Lysine specific demethylase 1 (Lsd1) in murine retinal development. LSD1 is a histone demethylase that can demethylate mono- and di-methyl groups on H3K4 and H3K9. Using Chx10-Cre and Rho-iCre75 driver lines, we generated novel transgenic mouse lines to delete Lsd1 in most retinal progenitor cells or specifically in rod photoreceptors. We hypothesize that Lsd1 deletion will cause global morphological and functional defects due to its importance in neuronal development.MethodsWe tested the retinal function of young adult mice by electroretinogram (ERG) and assessed retinal morphology by in vivo imaging by fundus photography and SD-OCT. Afterward, eyes were enucleated, fixed, and sectioned for subsequent hematoxylin and eosin (H&amp;E) or immunofluorescence staining. Other eyes were plastic fixed and sectioned for electron microscopy.ResultsIn adult Chx10-Cre Lsd1fl/fl mice, we observed a marked reduction in a-, b-, and c-wave amplitudes in scotopic conditions compared to age-matched control mice. Photopic and flicker ERG waveforms were even more sharply reduced. Modest reductions in total retinal thickness and outer nuclear layer (ONL) thickness were observed in SD-OCT and H&amp;E images. Lastly, electron microscopy revealed significantly shorter inner and outer segments and immunofluorescence showed modest reductions in specific cell type populations. We did not observe any obvious functional or morphological defects in the adult Rho-iCre75 Lsd1fl/fl animals.ConclusionLsd1 is necessary for neuronal development in the retina. Adult Chx10-Cre Lsd1fl/fl mice show impaired retinal function and morphology. These effects were fully manifested in young adults (P30), suggesting that Lsd1 affects early retinal development in mice.
Operationalisation of a standardised scoring system to assess adherence to the World Cancer Research Fund/American Institute for Cancer Research cancer prevention recommendations in the UK biobank
Authors: Malcomson Fiona C. , Parra-Soto Solange , Lu Liya , Ho Frederick K. , Perez-Cornago Aurora , Shams-White Marissa M. , van Zutphen Moniek , Kampman Ellen , Winkels Renate M. , Mitrou Panagiota , Wiseman Martin , Romaguera Dora , Celis-Morales Carlos , Sharp Linda , Mathers John C. 
Published: February 2023

IntroductionIn 2018, The World Cancer Research Fund (WCRF)/American Institute for Cancer Research (AICR) published ten evidence-based Cancer Prevention Recommendations designed to reduce the risk of cancer via improved lifestyle behaviours. In 2019, Shams-White and colleagues created the “2018 WCRF/AICR Score” which aimed to standardise how adherence to these recommendations is assessed. The standardised scoring system includes seven of the recommendations concerning weight, physical activity and diet, with an optional eighth recommendation on breastfeeding. To promote transparency and reproducibility, the present paper describes the methodology for operationalisation of the standardised scoring system in the UK Biobank.MethodsUK Biobank recruited &gt;500,000 individuals aged 37–73 years, between 2006 and 2010. In 2021, we held a workshop with experts which aimed to reach consensus on how to operationalise the scoring system using data available within UK Biobank. We used data on anthropometric measurements, physical activity and diet to calculate adherence scores. 24 h dietary assessment data were used to measure adherence to the following recommendations: “Eat a diet rich in wholegrains, vegetables, fruit, and beans”, “Limit consumption of “fast foods” and other processed foods high in fat, starches or sugars” and “Limit consumption of sugar-sweetened drinks”; food frequency questionnaire data were used to assess adherence to “Limit consumption of red and processed meat” and “Limit alcohol consumption”. Participants were allocated points for meeting, partially meeting or not meeting each recommendation, using cut-offs defined in the standardised scoring system.ResultsAt our workshop, discussions included the use of national guidelines to assess adherence to the recommendation on alcohol consumption, as well as challenges faced including defining the adapted ultra-processed food variables. A total score was calculated for 158,415 participants (mean 3.9 points, range 0–7 points). We also describe the methodology to derive a partial 5-point adherence score using data from the food frequency questionnaire in 314,616 participants.ConclusionWe describe the methodology used to estimate adherence to the 2018 WCRF/AICR Cancer Prevention Recommendations for participants in the UK Biobank, including some of the challenges faced operationalising the standardised scoring system.