bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data from Genomic and Evolutionary Characterization of Concurrent Intraductal Carcinoma and Adenocarcinoma of the Prostate
Authors: Zhao Jinge , Xu Nanwei , Zhu Sha , Nie Ling , Zhang Mengni , Zheng Linmao , Cai Diming , Sun Xiaomeng , Chen Junru , Dai Jindong , Ni Yuchao , Wang Zhipeng , Zhang Xingming , Liang Jiayu , Chen Yuntian , Hu Xu , Pan Xiuyi , Yin Xiaoxue , Liu Haoyang , Zhao Fengnian , Zhang Bei , Chen Hao , Miao Jiashun , Qin Cong , Zhao Xiaochen , Yao Jin , Liu Zhenhua , Liao Banghua , Wei Qiang , Li Xiang , Liu Jiyan , Gao Allen C. , Huang Haojie , Shen Pengfei , Chen Ni , Zeng Hao , Sun Guangxi
Published: January 2024

Supplementary figure 1-15
Supplementary Figure S4 from Targeting Transcriptional Regulation with a CDK9 Inhibitor Suppresses Growth of Endocrine- and Palbociclib-Resistant ER+ Breast Cancers
Authors: Soosainathan Arany , Iravani Marjan , El-Botty Rania , Alexander John , Sourd Laura , Morisset Ludivine , Painsec Pierre , Orha Rebecca , Nikitorowicz-Buniak Joanna , Pancholi Sunil , Haider Syed , Dowsett Mitch , Marangoni Elisabetta , Martin Lesley-Ann , Isacke Clare M.
Published: January 2024

Supplementary Figure S4
Supplementary Figure S2 from Targeting Transcriptional Regulation with a CDK9 Inhibitor Suppresses Growth of Endocrine- and Palbociclib-Resistant ER+ Breast Cancers
Authors: Soosainathan Arany , Iravani Marjan , El-Botty Rania , Alexander John , Sourd Laura , Morisset Ludivine , Painsec Pierre , Orha Rebecca , Nikitorowicz-Buniak Joanna , Pancholi Sunil , Haider Syed , Dowsett Mitch , Marangoni Elisabetta , Martin Lesley-Ann , Isacke Clare M.
Published: January 2024

Supplementary Figure S2
Data from Genomic and Evolutionary Characterization of Concurrent Intraductal Carcinoma and Adenocarcinoma of the Prostate
Authors: Zhao Jinge , Xu Nanwei , Zhu Sha , Nie Ling , Zhang Mengni , Zheng Linmao , Cai Diming , Sun Xiaomeng , Chen Junru , Dai Jindong , Ni Yuchao , Wang Zhipeng , Zhang Xingming , Liang Jiayu , Chen Yuntian , Hu Xu , Pan Xiuyi , Yin Xiaoxue , Liu Haoyang , Zhao Fengnian , Zhang Bei , Chen Hao , Miao Jiashun , Qin Cong , Zhao Xiaochen , Yao Jin , Liu Zhenhua , Liao Banghua , Wei Qiang , Li Xiang , Liu Jiyan , Gao Allen C. , Huang Haojie , Shen Pengfei , Chen Ni , Zeng Hao , Sun Guangxi
Published: January 2024

Abstract
Intraductal carcinoma of the prostate (IDC-P) is a lethal prostate cancer subtype that generally coexists with invasive high-grade prostate acinar adenocarcinoma (PAC) but exhibits distinct biological features compared with concomitant adenocarcinoma. In this study, we performed whole-exome, RNA, and DNA-methylation sequencing of IDC-P, concurrent invasive high-grade PAC lesions, and adjacent normal prostate tissues isolated from 22 radical prostatectomy specimens. Three evolutionary patterns of concurrent IDC-P and PAC were identified: early divergent, late divergent, and clonally distant. In contrast to those with a late divergent evolutionary pattern, tumors with clonally distant and early divergent evolutionary patterns showed higher genomic, epigenomic, transcriptional, and pathologic heterogeneity between IDC-P and PAC. Compared with coexisting PAC, IDC-P displayed increased expression of adverse prognosis–associated genes. Survival analysis based on an independent cohort of 505 patients with metastatic prostate cancer revealed that IDC-P carriers with lower risk International Society of Urological Pathology (ISUP) grade 1–4 adenocarcinoma displayed a castration-resistant free survival as poor as those with the highest risk ISUP grade 5 tumors that lacked concurrent IDC-P. Furthermore, IDC-P exhibited robust cell-cycle progression and androgen receptor activities, characterized by an enrichment of cellular proliferation–associated master regulators and genes involved in intratumoral androgen biosynthesis. Overall, this study provides a molecular groundwork for the aggressive behavior of IDC-P and could help identify potential strategies to improve treatment of IDC-P.
Significance:
The genomic, transcriptomic, and epigenomic characterization of concurrent intraductal carcinoma and adenocarcinoma of the prostate deepens the biological understanding of this lethal disease and provides a genetic basis for developing targeted therapies.
Supplementary Data from Phase I Dose-Escalation Trial of MIW815 (ADU-S100), an Intratumoral STING Agonist, in Patients with Advanced/Metastatic Solid Tumors or Lymphomas
Authors: Meric-Bernstam Funda , Sweis Randy F. , Hodi F. Stephen , Messersmith Wells A. , Andtbacka Robert H.I. , Ingham Matthew , Lewis Nancy , Chen Xinhui , Pelletier Marc , Chen Xueying , Wu Jincheng , Dubensky Thomas W. , McWhirter Sarah M. , Müller Thomas , Nair Nitya , Luke Jason J.
Published: January 2024

Supplementary tables and figure legends
Figure S2 from Phase I Dose-Escalation Trial of MIW815 (ADU-S100), an Intratumoral STING Agonist, in Patients with Advanced/Metastatic Solid Tumors or Lymphomas
Authors: Meric-Bernstam Funda , Sweis Randy F. , Hodi F. Stephen , Messersmith Wells A. , Andtbacka Robert H.I. , Ingham Matthew , Lewis Nancy , Chen Xinhui , Pelletier Marc , Chen Xueying , Wu Jincheng , Dubensky Thomas W. , McWhirter Sarah M. , Müller Thomas , Nair Nitya , Luke Jason J.
Published: January 2024

Pre- and on-treatment images of injected lesions from patients with a confirmed or unconfirmed response
Table S1 from Metabolic Hallmarks for Purine Nucleotide Biosynthesis in Small Cell Lung Carcinoma
Authors: Tabata Sho , Umemura Shigeki , Narita Miyu , Udagawa Hibiki , Ishikawa Takamasa , Tsuboi Masahiro , Goto Koichi , Ishii Genichiro , Tsuchihara Katsuya , Ochiai Atsushi , Kobayashi Susumu S. , Soga Tomoyoshi , Makinoshima Hideki
Published: January 2024

Assessment of IHC for SCLC tumors
Figure S8 from Metabolic Hallmarks for Purine Nucleotide Biosynthesis in Small Cell Lung Carcinoma
Authors: Tabata Sho , Umemura Shigeki , Narita Miyu , Udagawa Hibiki , Ishikawa Takamasa , Tsuboi Masahiro , Goto Koichi , Ishii Genichiro , Tsuchihara Katsuya , Ochiai Atsushi , Kobayashi Susumu S. , Soga Tomoyoshi , Makinoshima Hideki
Published: January 2024

Metabolic profile in SCLC patient's plasma
Figure S5 from Metabolic Hallmarks for Purine Nucleotide Biosynthesis in Small Cell Lung Carcinoma
Authors: Tabata Sho , Umemura Shigeki , Narita Miyu , Udagawa Hibiki , Ishikawa Takamasa , Tsuboi Masahiro , Goto Koichi , Ishii Genichiro , Tsuchihara Katsuya , Ochiai Atsushi , Kobayashi Susumu S. , Soga Tomoyoshi , Makinoshima Hideki
Published: January 2024

Hematoxylin/eosin and anti-HPRT1 immunohistochemistry staining to visualize HPRT1 expression
Figure S2 from Metabolic Hallmarks for Purine Nucleotide Biosynthesis in Small Cell Lung Carcinoma
Authors: Tabata Sho , Umemura Shigeki , Narita Miyu , Udagawa Hibiki , Ishikawa Takamasa , Tsuboi Masahiro , Goto Koichi , Ishii Genichiro , Tsuchihara Katsuya , Ochiai Atsushi , Kobayashi Susumu S. , Soga Tomoyoshi , Makinoshima Hideki
Published: January 2024

Levels of HPRT1 mRNA in human SCLC tumors
Figure S1 from Metabolic Hallmarks for Purine Nucleotide Biosynthesis in Small Cell Lung Carcinoma
Authors: Tabata Sho , Umemura Shigeki , Narita Miyu , Udagawa Hibiki , Ishikawa Takamasa , Tsuboi Masahiro , Goto Koichi , Ishii Genichiro , Tsuchihara Katsuya , Ochiai Atsushi , Kobayashi Susumu S. , Soga Tomoyoshi , Makinoshima Hideki
Published: January 2024

Levels of HPRT1 mRNA in SCLC cells
Supplementary Table 1 from SP4 Facilitates Esophageal Squamous Cell Carcinoma Progression by Activating PHF14 Transcription and Wnt/Β-Catenin Signaling
Authors: Wei Li , Deng Chaowei , Zhang Bo , Wang Guanghui , Meng Yan , Qin Hao
Published: January 2024

Association of SP4 mRNA expression with clinicopathological characteristics of EC (n = 73).
Supplementary Figure 5 from SP4 Facilitates Esophageal Squamous Cell Carcinoma Progression by Activating PHF14 Transcription and Wnt/Β-Catenin Signaling
Authors: Wei Li , Deng Chaowei , Zhang Bo , Wang Guanghui , Meng Yan , Qin Hao
Published: January 2024

Proposed model for the roles of SP4 on ESCC proliferation.
Supplementary Table 1 from Whole-Exome Sequencing Identifies Mutation Profile and Mutation Signature-Based Clustering Associated with Prognosis in Appendiceal Pseudomyxoma Peritonei
Authors: Lin Yu-Lin , Zhu Jun-Qi , Ma Rui-Qing , Meng Wei , Wang Zi-Yue , Li Xin-Bao , Ma Ru , Wu He-Liang , Xu Hong-Bin , Gao Ying , Li Yan
Published: January 2024

The clinicopathological characteristics of 49 PMP
Supplementary Table 8 from Distinct microRNA Signature and Suppression of ZFP36L1 Define ASCL1-Positive Lung Adenocarcinoma
Authors: Enokido Takayoshi , Horie Masafumi , Yoshino Seiko , Suzuki Hiroshi I. , Matsuki Rei , Brunnström Hans , Micke Patrick , Nagase Takahide , Saito Akira , Miyashita Naoya
Published: January 2024

ZFP36L1 staining and clinical characteristics of the Uppsala cohort.
Supplementary Table 6 from Distinct microRNA Signature and Suppression of ZFP36L1 Define ASCL1-Positive Lung Adenocarcinoma
Authors: Enokido Takayoshi , Horie Masafumi , Yoshino Seiko , Suzuki Hiroshi I. , Matsuki Rei , Brunnström Hans , Micke Patrick , Nagase Takahide , Saito Akira , Miyashita Naoya
Published: January 2024

Genes upregulated by miR-124-3p inhibitors in VMRC-LCD cells.
Supplementary Table 1 from Distinct microRNA Signature and Suppression of ZFP36L1 Define ASCL1-Positive Lung Adenocarcinoma
Authors: Enokido Takayoshi , Horie Masafumi , Yoshino Seiko , Suzuki Hiroshi I. , Matsuki Rei , Brunnström Hans , Micke Patrick , Nagase Takahide , Saito Akira , Miyashita Naoya
Published: January 2024

Public datasets used in this study.
Supplementary Figure 3 from Whole-Exome Sequencing Identifies Mutation Profile and Mutation Signature-Based Clustering Associated with Prognosis in Appendiceal Pseudomyxoma Peritonei
Authors: Lin Yu-Lin , Zhu Jun-Qi , Ma Rui-Qing , Meng Wei , Wang Zi-Yue , Li Xin-Bao , Ma Ru , Wu He-Liang , Xu Hong-Bin , Gao Ying , Li Yan
Published: January 2024

Flow-chart of patient selection. Only appendiceal PMP with complete clinicopathological information and successful whole-exome sequencing were included.
Supplementary Figure 7 from Distinct microRNA Signature and Suppression of ZFP36L1 Define ASCL1-Positive Lung Adenocarcinoma
Authors: Enokido Takayoshi , Horie Masafumi , Yoshino Seiko , Suzuki Hiroshi I. , Matsuki Rei , Brunnström Hans , Micke Patrick , Nagase Takahide , Saito Akira , Miyashita Naoya
Published: January 2024

Cell proliferation assay in A549 and H441 cells following ZFP36L1 transfection
Supplementary Table 3 from RNF185 Control of COL3A1 Expression Limits Prostate Cancer Migration and Metastatic Potential
Authors: Van Espen Benjamin , Oo Htoo Zarni , Collins Colin , Fazli Ladan , Molinolo Alfredo , Yip Kevin , Murad Rabi , Gleave Martin , Ronai Ze'ev A.
Published: January 2024

List of genes driving the enrichment score for HALLMARL_EMT in MPC3.shRNF185#3 compared to MPC3.pLKO in GSEA analysis.
Supplementary Figure 3 from RNF185 Control of COL3A1 Expression Limits Prostate Cancer Migration and Metastatic Potential
Authors: Van Espen Benjamin , Oo Htoo Zarni , Collins Colin , Fazli Ladan , Molinolo Alfredo , Yip Kevin , Murad Rabi , Gleave Martin , Ronai Ze'ev A.
Published: January 2024

S3. RT-qPCR validation of genes that are differentially expressed in both RNF185 KD MPC3 and PC3 cells.
Supplementary Table 2 from Impact of Rare and Multiple Concurrent Gene Fusions on Diagnostic DNA Methylation Classifier in Brain Tumors
Authors: Galbraith Kristyn , Serrano Jonathan , Shen Guomiao , Tran Ivy , Slocum Cheyanne C. , Ketchum Courtney , Abdullaev Zied , Turakulov Rust , Bale Tejus , Ladanyi Marc , Sukhadia Purvil , Zaidinski Michael , Mullaney Kerry , DiNapoli Sara , Liechty Benjamin L. , Barbaro Marissa , Allen Jeffrey C. , Gardner Sharon L. , Wisoff Jeffrey , Harter David , Hidalgo Eveline Teresa , Golfinos John G. , Orringer Daniel A. , Aldape Kenneth , Benhamida Jamal , Wrzeszczynski Kazimierz O. , Jour George , Snuderl Matija
Published: January 2024

List of all gene fusions and associated DNA methylation classes and scores
Supplementary Table 1 from Impact of Rare and Multiple Concurrent Gene Fusions on Diagnostic DNA Methylation Classifier in Brain Tumors
Authors: Galbraith Kristyn , Serrano Jonathan , Shen Guomiao , Tran Ivy , Slocum Cheyanne C. , Ketchum Courtney , Abdullaev Zied , Turakulov Rust , Bale Tejus , Ladanyi Marc , Sukhadia Purvil , Zaidinski Michael , Mullaney Kerry , DiNapoli Sara , Liechty Benjamin L. , Barbaro Marissa , Allen Jeffrey C. , Gardner Sharon L. , Wisoff Jeffrey , Harter David , Hidalgo Eveline Teresa , Golfinos John G. , Orringer Daniel A. , Aldape Kenneth , Benhamida Jamal , Wrzeszczynski Kazimierz O. , Jour George , Snuderl Matija
Published: January 2024

List of genes in the fusion panels
Data from Metabolic Hallmarks for Purine Nucleotide Biosynthesis in Small Cell Lung Carcinoma
Authors: Tabata Sho , Umemura Shigeki , Narita Miyu , Udagawa Hibiki , Ishikawa Takamasa , Tsuboi Masahiro , Goto Koichi , Ishii Genichiro , Tsuchihara Katsuya , Ochiai Atsushi , Kobayashi Susumu S. , Soga Tomoyoshi , Makinoshima Hideki
Published: January 2024

Abstract
Small cell lung cancer (SCLC) has a poor prognosis, emphasizing the necessity for developing new therapies. The de novo synthesis pathway of purine nucleotides, which is involved in the malignant growth of SCLC, has emerged as a novel therapeutic target. Purine nucleotides are supplied by two pathways: de novo and salvage. However, the role of the salvage pathway in SCLC and the differences in utilization and crosstalk between the two pathways remain largely unclear. Here, we found that deletion of the HPRT1 gene, which codes for the rate-limiting enzyme of the purine salvage pathway, significantly suppressed tumor growth in vivo in several SCLC cells. We also demonstrated that HPRT1 expression confers resistance to lemetrexol (LMX), an inhibitor of the purine de novo pathway. Interestingly, HPRT1-knockout had less effect on SCLC SBC-5 cells, which are more sensitive to LMX than other SCLC cell lines, suggesting that a preference for either the purine de novo or salvage pathway occurs in SCLC. Furthermore, metabolome analysis of HPRT1-knockout cells revealed increased intermediates in the pentose phosphate pathway and elevated metabolic flux in the purine de novo pathway, indicating compensated metabolism between the de novo and salvage pathways in purine nucleotide biosynthesis. These results suggest that HPRT1 has therapeutic implications in SCLC and provide fundamental insights into the regulation of purine nucleotide biosynthesis.
Implications:
SCLC tumors preferentially utilize either the de novo or salvage pathway in purine nucleotide biosynthesis, and HPRT1 has therapeutic implications in SCLC.
Figure S4 from Inhibition of PRL2 Upregulates PTEN and Attenuates Tumor Growth in Tp53-deficient Sarcoma and Lymphoma Mouse Models
Authors: Nguele Meke Frederick , Bai Yunpeng , Ruiz-Avila Diego , Carlock Colin , Ayub Jinan , Miao Jinmin , Hu Yanyang , Li Qinglin , Zhang Zhong-Yin
Published: January 2024

Prl2 deletion upregulates PTEN to inhibit Akt signaling and hinder tumor cell proliferation in Tp53 heterozygous mice
FIGURE 5 from Inhibition of PRL2 Upregulates PTEN and Attenuates Tumor Growth in Tp53-deficient Sarcoma and Lymphoma Mouse Models
Authors: Nguele Meke Frederick , Bai Yunpeng , Ruiz-Avila Diego , Carlock Colin , Ayub Jinan , Miao Jinmin , Hu Yanyang , Li Qinglin , Zhang Zhong-Yin
Published: January 2024

Prl2 deletion upregulates PTEN to inhibit Akt signaling and hinder tumor cell proliferation in inducible Tp53−/− mice. A, Representative Western blot analysis from inducible Tp53−/− and inducible Tp53−/−; Prl2−/−–derived thymic lymphomas to determine expression of PTEN, PUMA, BAX, p21, cyclin D1, p27, as well as the expression and activation of Akt and Akt targets. The actin loading control shown is the same as that in Fig. 4A. B, Dot plot for quantification of PTEN and Akt activation. C, Dot plot for quantification of Western blot analysis for the activation of Akt targets mTOR and GSK3β. D, Dot plot for quantification of the expression of Tp53 targets PUMA, BAX, p21, and cyclin D1. E, Dot plot for quantification of FoxOs activation and p27 expression. Data shown as mean ± SEM for samples obtained 12 weeks after tamoxifen treatment, Tp53−/− n = 10–20, Tp53−/−; Prl2−/− n = 10–14; *, P < 0.05; ***, P < 0.001; ****, P < 0.0001.
FIGURE 3 from Inhibition of PRL2 Upregulates PTEN and Attenuates Tumor Growth in Tp53-deficient Sarcoma and Lymphoma Mouse Models
Authors: Nguele Meke Frederick , Bai Yunpeng , Ruiz-Avila Diego , Carlock Colin , Ayub Jinan , Miao Jinmin , Hu Yanyang , Li Qinglin , Zhang Zhong-Yin
Published: January 2024

Prl2 deletion enhances survival and hinders tumor growth rate in tamoxifen-inducible Tp53−/− mouse but does not affect tumor initiation. A, PCR genotyping to identify different genotypes in the study. B, Kaplan–Meier survival plot for thymic lymphoma-free survival in tamoxifen-inducible Tp53−/− n = 43 and inducible Tp53−/−; Prl2−/− n = 33. C, Bar graph representing percent tumor incidence in inducible Tp53−/− background with or without inducible Prl2 deletion. Dot plots representing: The mass of thymus/thymic lymphoma over time in inducible Tp53−/− n = 9–20 per timepoint and inducible Tp53−/−; Prl2−/− n = 8–14 per timepoint (D). E, Thymocyte population ratios 9 weeks after inducing Tp53 deletion with or without Prl2 deletion. F, Thymocyte population ratios 12 weeks after inducing Tp53 deletion with or without Prl2 deletion. DP: Double positive (CD4+ CD8+). DN: Double negative (CD4− CD8−). log-rank test performed for Kaplan–Meier survival curves and Student t test performed for all other analysis. Data are shown as mean ± SEM. *, P < 0.05; **, P < 0.01; ***, P < 0.001.
Data from Inhibition of PRL2 Upregulates PTEN and Attenuates Tumor Growth in Tp53-deficient Sarcoma and Lymphoma Mouse Models
Authors: Nguele Meke Frederick , Bai Yunpeng , Ruiz-Avila Diego , Carlock Colin , Ayub Jinan , Miao Jinmin , Hu Yanyang , Li Qinglin , Zhang Zhong-Yin
Published: January 2024

Abstract
The phosphatases of regenerating liver (PRL) are oncogenic when overexpressed. We previously found that PRL2 deletion increases PTEN, decreases Akt activity, and suppresses tumor development in a partial Pten-deficient mouse model. The current study aims to further establish the mechanism of PTEN regulation by PRL2 and expand the therapeutic potential for PTEN augmentation mediated by PRL2 inhibition in cancers initiated without PTEN alteration. The TP53 gene is the most mutated tumor suppressor in human cancers, and heterozygous or complete deletion of Tp53 in mice leads to the development of sarcomas and thymic lymphomas, respectively. There remains a lack of adequate therapies for the treatment of cancers driven by Tp53 deficiency or mutations. We show that Prl2 deletion leads to PTEN elevation and attenuation of Akt signaling in sarcomas and lymphomas developed in Tp53 deficiency mouse models. This results in increased survival and reduced tumor incidence because of impaired tumor cell proliferation. In addition, inhibition of PRL2 with a small-molecule inhibitor phenocopies the effect of genetic deletion of Prl2 and reduces Tp53 deficiency–induced tumor growth. Taken together, the results further establish PRL2 as a negative regulator of PTEN and highlight the potential of PRL2 inhibition for PTEN augmentation therapy in cancers with wild-type PTEN expression.
Significance:
Prl2 deletion attenuates Tp53 deficiency–induced tumor growth by increasing PTEN and reducing Akt activity. Targeting Tp53-null lymphoma with PRL inhibitors lead to reduced tumor burden, providing a therapeutic approach via PTEN augmentation.
Ensino da argumentação: uma análise propositiva do gênero comentário online
Authors: Severo Júnior José Paulo Tavares , Santos Maria de Fátima Silva dos
Published: January 2024

Este artigo objetiva examinar a ocorrência de relações discursivo-argumentativas em textos do gênero comentário online que são postados em redes sociais, paralelamente à reflexão sobre a abordagem da argumentação no ensino de Língua Portuguesa. Caracteriza-se como estudo exploratório, de natureza qualitativa e delineado por pesquisa bibliográfica. O corpus de análise é composto por um post de notícia publicado no perfil do jornal Estadão, no Instagram, e pelos comentários reativos à postagem. Os resultados da análise indicaram a ocorrência de diferentes relações argumentativas nos comentários em que os enunciados são encadeados por articuladores textuais, o que sugere a importância do trabalho com os elementos linguístico-discursivos no ensino da argumentação, sobretudo em textos contemporâneos veiculados virtualmente.
Nos bastidores da ciência: argumentação, história e filosofia no ensino de Física
Authors: França Érika Cristina Meneses de , Leal Aline Dortas
Published: January 2024

Pesquisas na área de ensino de ciências vêm evidenciando a importância de abordagens histórico-filosóficas e da argumentação para uma formação reflexiva. O presente artigo tem como objetivo compreender a importância da história e filosofia da ciência aliadas ao ensino de argumentação na Física, tendo como foco as leis de Newton. Para atingir esse objetivo, foi realizada uma revisão de literatura sobre o tema, seguida do desenvolvimento e da aplicação de atividades junto a alunos do Ensino Médio de uma escola da rede pública estadual de Aracaju/SE. Os resultados apontam o desenvolvimento de uma compreensão mais contextualizada acerca da ciência, na incorporação de procedimentos próprios do fazer científico, como a construção de explicações e o emprego de justificativas, a maior sofisticação dos argumentos à medida que os temas debatidos envolviam aspectos sociais e éticos e a mobilização de conhecimentos adquiridos dentro e fora das aulas de Física.
Establishment of a neotype for Antipathes flabellum Pallas, 1766 (Anthozoa: Hexacorallia: Antipatharia)
Authors: TERRANA LUCAS , HOROWITZ JEREMY , OPRESKO DENNIS M.
Published: January 2024

A neotype is designated for the antipatharian coral Antipathes flabellum Pallas, 1766. The neotype was collected off Madagascar (the original type locality is given as the “Oceanus Indicus”). Morphologically, the neotype corresponds closely in corallum shape and skeletal spination to specimens that have traditionally been identified as Antipathes flabellum. Another specimen of A. flabellum from Madagascar, morphologically almost identical to the neotype and described here, has been sequenced using ultra conserved elements and exon nuclear loci, which showed that it falls within the family currently recognized as Antipathidae.
Two new species of Amaurobius C. L. Koch, 1837 (Araneae, Amaurobiidae) from Sichuan Province, China
Authors: LU YING , LIN YEJIE , LI SHUQIANG
Published: January 2024

In this paper, two new species of the genus Amaurobius C. L. Koch, 1837 of the family Amaurobiidae Thorell, 1869 are reported from Sichuan Province, China: A. danba Lin & Li, sp. nov. (♂♀) and A. yaan Lin & Li, sp. nov. (♂♀). Photos and morphological descriptions of the new species are presented; the type specimens of the new species are deposited in the Institute of Zoology, Chinese Academy of Sciences (IZCAS), Beijing.
Rapid locomotion via reinforcement learning
Authors: Margolis Gabriel B. , Yang Ge , Paigwar Kartik , Chen Tao , Agrawal Pulkit
Published: January 2024

Agile maneuvers such as sprinting and high-speed turning in the wild are challenging for legged robots. We present an end-to-end learned controller that achieves record agility for the MIT Mini Cheetah, sustaining speeds up to 3.9 m/s. This system runs and turns fast on natural terrains like grass, ice, and gravel and responds robustly to disturbances. Our controller is a neural network trained in simulation via reinforcement learning and transferred to the real world. The two key components are (i) an adaptive curriculum on velocity commands and (ii) an online system identification strategy for sim-to-real transfer. Videos of the robot’s behaviors are available at https://agility.csail.mit.edu/ .
Exploring Transparency–Sustainability Linkage: Analysis of CSR Disclosures
Authors: Calderon Ricardo T. , Gurtu Amulya , Holly Michael A.
Published: January 2024

Corporate social responsibility (CSR) reporting is a strategy for communicating sustainability data to stakeholders. Sharing data with stakeholders is the key to the effectiveness and validity of CSR. However, the often-voluntary nature of CSR disclosure reporting results in perceived bias. Consequently, the relationship between CSR disclosure transparency and the sustainable character of a company remains unclear. The article suggests a methodology for evaluating corporate transparency through t-value analysis. The t-value analysis of CSR reports from Corporate Knights’ 2021 Global 100 Most Sustainable Corporations quantifies the total number of negative disclosures in a CSR report. This research shows a lack of correlation (p value = .805) between observable levels of transparency and third-party sustainability rankings amongst the sustainability elite of the corporate world.
Roast: a tool for reference-free optimization of supertranscriptome assemblies
Authors: Shabbir Madiha , Mithani Aziz
Published: January 2024

Background

Transcriptomic studies involving organisms for which reference genomes are not available typically start by generating de novo transcriptome or supertranscriptome assembly from the raw RNA-seq reads. Assembling a supertranscriptome is, however, a challenging task due to significantly varying abundance of mRNA transcripts, alternative splicing, and sequencing errors. As a result, popular de novo supertranscriptome assembly tools generate assemblies containing contigs that are partially-assembled, fragmented, false chimeras or have local mis-assemblies leading to decreased assembly accuracy. Commonly available tools for assembly improvement rely primarily on running BLAST using closely related species making their accuracy and reliability conditioned on the availability of the data for closely related organisms.

Results

We present ROAST, a tool for optimization of supertranscriptome assemblies that uses paired-end RNA-seq data from Illumina sequencing platform to iteratively identify and fix assembly errors solely using the error signatures generated by RNA-seq alignment tools including soft-clips, unexpected expression coverage, and reads with mates unmapped or mapped on a different contig to identify and fix various supertranscriptome assembly errors without performing BLAST searches against other organisms. Evaluation results using simulated as well as real datasets show that ROAST significantly improves assembly quality by identifying and fixing various assembly errors.

Conclusion

ROAST provides a reference-free approach to optimizing supertranscriptome assemblies highlighting its utility in refining de novo supertranscriptome assemblies of non-model organisms.
High-quality genome resource of Lasiodiplodia pseudotheobromae associated with die-back on Eucalyptus trees
Authors: Lu LinQin , Li GuoQing , Liu FeiFei
Published: January 2024

Objectives

Lasiodiplodia pseudotheobromae is an important fungal pathogen associated with die-back, canker and shoot blight in many plant hosts with a wide geographic distribution. The aim of our study was to provide high-quality genome assemblies and sequence annotation resources of L. pseudotheobromae, to facilitate future studies on the systematics, population genetics and genomics of the fungal pathogen L. pseudotheobromae.

Data description

High-quality genomes of five L. pseudotheobromae isolates were sequenced based on Oxford Nanopore technology (ONT) and Illumina HiSeq sequencing platform. The total size of each assembly ranged from 43 Mb to 43.86 Mb and over 11,000 protein-coding genes were predicted from each genome. The proteins of predicted genes were annotated using multiple public databases, among the annotated protein-coding genes, more than 4,300 genes were predicted as potential virulence genes by the Pathogen Host Interactions (PHI) database. Moreover, the genome comparative analysis among L. pseudotheobromae and other closely related species revealed that 7,408 gene clusters were shared among them and 152 gene clusters unique to L. pseudotheobromae. This genome and associated datasets provided here will serve as a useful resource for further analyses of this fungal pathogen species.
A preliminary exploration on the mechanism of the carbapenem-resistance transformation of Serratia marcescens in vivo
Authors: Xu Qian , Zheng Beiwen , Li Kaixuan , Shen Ping , Xiao Yonghong
Published: January 2024

Background

The infection of carbapenem-resistant organisms was a huge threat to human health due to their global spread. Dealing with a carbapenem-resistant Serratia marcescens (CRSM) infection poses a significant challenge in clinical settings. This study aims to provide insights into strategies for controlling CRSM infection by exploring the transformation mechanism of carbapenem-resistance.

Methods

We used whole genome sequencing (WGS) to investigate the mechanism of carbapenem resistance in 14 S. marcescens isolates in vivo. The expression level of related genes and the minimum inhibitory concentration of meropenem (MICMEM) were also evaluated to confirm the mechanism of carbapenem resistance.

Results

Seven groups of S. marcescens, each consisting of two strains, were collected from a hospital and displayed a shift in MICMEM from low to high levels. Homology analysis revealed that the isolates in five groups were significantly different from the remaining two. WGS and experimental evidence indicated that four groups of strains developed carbapenem resistance by acquiring the blaKPC (obtaining group), while two groups (persisting group) increased the expression level of the blaKPC. In contrast, isolates in the last group (missing group) did not carry the blaKPC. All strains possessed multiple β-lactamase genes, including blaCTX−M−14, blaSRT−1, and blaSRT−2. However, only in the missing group, the carbapenem-resistant strain lost an outer membrane protein-encoding gene, leading to increased blaCTX−M−14 expression compared to the carbapenem-susceptible strain.

Conclusion

The study findings suggest that S. marcescens strains developed diverse carbapenem resistance in vivo through the evolution of drug resistance, rather than through clone replacement. We hypothesize that carbapenem resistance in S. marcescens was due to certain clonal types with a distinct mechanism.
Genomic insights into Penicillium chrysogenum adaptation to subseafloor sedimentary environments
Authors: Liu Xuan , Wang Xinran , Zhou Fan , Xue Yarong , Liu Changhong
Published: January 2024

Background

Penicillium chrysogenum is a filamentous fungal species with diverse habitats, yet little is known about its genetics in adapting to extreme subseafloor sedimental environments.

Results

Here, we report the discovery of P. chrysogenum strain 28R-6-F01, isolated from deep coal-bearing sediments 2306 m beneath the seafloor. This strain possesses exceptional characteristics, including the ability to thrive in extreme conditions such as high temperature (45 °C), high pressure (35 Mpa), and anaerobic environments, and exhibits broad-spectrum antimicrobial activity, producing the antibiotic penicillin at a concentration of 358 μg/mL. Genome sequencing and assembly revealed a genome size of 33.19 Mb with a GC content of 48.84%, containing 6959 coding genes. Comparative analysis with eight terrestrial strains identified 88 unique genes primarily associated with penicillin and aflatoxins biosynthesis, carbohydrate degradation, viral resistance, and three secondary metabolism gene clusters. Furthermore, significant expansions in gene families related to DNA repair were observed, likely linked to the strain’s adaptation to its environmental niche.

Conclusions

Our findings provide insights into the genomic and biological characteristics of P. chrysogenum adaptation to extreme anaerobic subseafloor sedimentary environments, such as high temperature and pressure.
Effect of ultrasound-guided stellate ganglion block on inflammatory cytokines and postoperative recovery after partial hepatectomy: a randomised clinical trial
Authors: Lao Wei-long , Sang Shuang , Huang Li-cai , Yi Sheng-hua , Guo Mo-chi , Dong Hui-min , Zhou Guo-zhong , Chen Zhong-hua
Published: January 2024

Background

Stellate ganglion block (SGB) has been shown to reduce perioperative complications in various surgeries. Because laparoscopic techniques and instruments have advanced during the past two decades, laparoscopic liver resection is being increasingly adopted worldwide. Lesser blood loss, fewer postoperative complications, and shorter postoperative hospital stays are the advantages of laparoscopic liver resection, as compared to conventional open surgery. There is an urgent need for an effective intervention to reduce perioperative complications and accelerate postoperative recovery. This study investigated the effect of ultrasound-guided SGB on enhanced recovery after laparoscopic partial hepatectomy.

Methods

We compared patients who received SGB with 0.5% ropivacaine (group S) with those who received SGB with 0.9% saline (group N). A total of 58 patients with partial hepatectomy were enrolled (30 S) and (28 N). Before induction of anesthesia, SGB was performed with 0.5% ropivacaine in group S and 0.9% saline in group N. Main outcome: Comparison of serum inflammatory cytokines concentration at each time point.

Results

Main outcome: When comparing IL-6 and IL-10 concentrations among groups, group S showed less variation over time compared to group N. For comparison between groups, the serum IL-6 concentration in group S was lower than that in group N at 6 and 24 h after operation (P < 0.01), and there was a significant linear relationship between serum IL-6 concentration at 24 h after operation and hospitalization situation.

Conclusions

Ultrasound-guided SGB can stabilize perioperative inflammatory cytokines plays a positive role in the enhanced recovery of patients after laparoscopic partial hepatectomy. The serum IL-6 level within 24 h after surgery may be used as a predictor of hospitalization.

Trial registration

The study was registered at the ClinicalTrials.gov (Registration date: 13/09/2021; Trial ID: NCT05042583).
A case of endocardial dissection caused by Micra implantation
Authors: Zhang Jianghua , Shang Shuai , Dong Zhenyu , Zhou Xianhui , Li Yaodong , Lu Yanmei , Xing Qiang , Tuerhong Zukela , Guo Yankai , Xiaokereti Jiasuoer , Tang Baopeng
Published: January 2024

Background

Leadless pacemakers are a recent technological advancement. It has many advantages, but there are still a few serious complications.

Case presentation

This article reports the case of a patient with an endocardial tear and dissection caused by contact with the tip of the Micra cup during surgery and summarises the relevant data.

Conclusions

This case report details the occurrence and management of the incident and provides some guidance for future clinical management.
Characteristics and correlation of body fat distribution and brachial-ankle pulse wave velocity in adults aged 20–59 years: a cross-sectional study
Authors: Wang Shengya , Shi Haiyan , Luo Laiyuan , He Hui
Published: January 2024

Background

Fat distribution is closely related to vascular stiffness. This study aimed to investigate age and sex differences in fat distribution and brachial-ankle pulse wave velocity (baPWV), and the association between fat parameters and baPWV.

Methods

A total of 10,811 participants aged 20–59 years were recruited. Measures included waist and hip circumference, waist-to-hip ratio (WHR), body mass index (BMI), percentage body fat (PBF), subcutaneous fat area (SFA), visceral fat area (VFA), and baPWV.

Results

The results confirm that fat accumulates with age and that men tend to carry more abdominal fat than women in the same age group. The findings also indicate that baPWV increases with age and is significantly higher in men than in women in the same age group. In addition, WHR, VFA, and baPWV were more strongly correlated than baPWV and BMI, SFA, and PBF. Finally, the effects of age, PBF, WHR, and VFA on baPWV were greater for the higher quantiles.

Conclusions

There are age and sex differences in fat distribution and baPWV. Abdominal obesity is more closely linked to arterial stiffness than overall obesity, and people with higher baPWV are more affected by obesity parameters.
Long term all-cause mortality after myocardial infarction with non-obstructed vs obstructed coronary artery disease: a meta-analysis of adjusted data
Authors: Lu Xueli , Zhu Shengnan , Lu Yanjiao , Li Yanming
Published: January 2024

Background

The difference in the long-term outcomes of myocardial infarction in patients with non-obstructed coronary arteries (MINOCA) and patients with myocardial infarction with obstructed coronary artery disease (MI-CAD) is not clear. The current study aimed to pool adjusted data to compare long-term outcomes of MINOCA vs MI-CAD.

Methods

Electronic literature search of PubMed, Embase, CENTRAL, and Google Scholar databases was done for publications up to 18th June 2023. Only studies reporting multivariable-adjusted data with > 1 year of follow-up were included.

Results

Sixteen studies met the inclusion criteria. Our meta-analysis revealed no statistically significant difference in the risk of all-cause mortality between MINOCA and MI-CAD patients (HR: 0.90 95% CI 0.68, 1.19 I2 = 94% p = 0.48). Analysis of the limited data showed a reduced combined risk of all-cause mortality and MI (HR: 0.54 95% CI 0.39, 0.76 I2 = 72% p = 0.003) and major adverse cardiac events (MACE) (HR: 0.66 95% CI 0.51, 0.84 I2 = 51% p = 0.0009) in patients with MINOCA vs MI-CAD, and no difference in the risk of cardiovascular mortality (HR: 0.81 95% CI 0.54, 1.22 I2 = 0% p = 0.31) and readmission between the two groups (HR: 0.85 95% CI 0.61, 1.19 I2 = 90% p = 0.35).

Conclusion

A pooled analysis of adjusted outcomes from the available studies indicated that MINOCA and MI-CAD patients have similar long-term all-cause mortality risk. Our conclusions on the risk of cardiovascular mortality, MACE and readmission rates need to be taken with caution due to a lack of adequate studies. Further research is needed to strengthen the evidence on this important subject.
A novel pathogenic variant in the carnitine transporter gene, SLC22A5, in association with metabolic carnitine deficiency and cardiomyopathy features
Authors: Jolfayi Amir Ghaffari , Naderi Niloofar , Ghasemi Serwa , Salmanipour Alireza , Adimi Sara , Maleki Majid , Kalayinia Samira
Published: January 2024

Background

Primary carnitine deficiency (PCD) denotes low carnitine levels with an autosomal recessive pattern of inheritance. Cardiomyopathy is the most common cardiac symptom in patients with PCD, and early diagnosis can prevent complications. Next-generation sequencing can identify genetic variants attributable to PCD efficiently.

Objective

We aimed to detect the genetic cause of the early manifestations of hypertrophic cardiomyopathy and metabolic abnormalities in an Iranian family.

Methods

We herein describe an 8-year-old boy with symptoms of weakness and lethargy diagnosed with PCD through clinical evaluations, lab tests, echocardiography, and cardiac magnetic resonance imaging. The candidate variant was confirmed through whole-exome sequencing, polymerase chain reaction, and direct Sanger sequencing. The binding efficacy of normal and mutant protein-ligand complexes were evaluated via structural modeling and docking studies.

Results

Clinical evaluations, echocardiography, and cardiac magnetic resonance imaging findings revealed hypertrophic cardiomyopathy as a clinical presentation of PCD. Whole-exome sequencing identified a new homozygous variant, SLC22A5 (NM_003060.4), c.821G > A: p.Trp274Ter, associated with carnitine transport. Docking analysis highlighted the impact of the variant on carnitine transport, further indicating its potential role in PCD development.

Conclusions

The c.821G > A: p.Trp274Ter variant in SLC22A5 potentially acted as a pathogenic factor by reducing the binding affinity of organic carnitine transporter type 2 proteins for carnitine. So, the c.821G > A variant may be associated with carnitine deficiency, metabolic abnormalities, and cardiomyopathic characteristics.
Primary care occupational, physical, and respiratory therapy role adaptation in the first year of the COVID-19 pandemic
Authors: Brown Cara L. , Chartrand Louise , Vollebregt Brontë , Kaur Dayajyot , Crawford Tory , Thille Patricia
Published: January 2024

Background

Occupational, physical and respiratory therapists are relatively new to primary care settings, and thus their roles are still emerging. The COVID-19 pandemic was a time of abrupt changes in professional roles. Professional role adaptations are integral to the ability of health care teams to respond to day-to-day care delivery challenges, such as the current physician and nurse shortage, as well as disaster situations. This study explored the role adaptation of occupational, physical, and respiratory therapists in Canadian primary care settings throughout the first year of the COVID-19 pandemic, as well as barriers and facilitators to adaptation.

Methods

This longitudinal interpretative descriptive study purposively sampled primary care occupational, physical, and respiratory therapists from two Canadian provinces (Manitoba and Ontario). We asked participants to prepare at least 10 semi-structured audio-diary entries during a 12-week period (April – Oct 2020), followed by two semi-structured interviews (Dec 2020, Apr 2021). Questions focused on changes happening in their practice over time. Analysis was iterative, including developing a individual summaries and coding data using both inductive and pre-determined codes. We then entered an immersion/crystallization process to develop key themes related to role adaptation.

Results

We represent our findings with the metaphor of the game of Role Adaptation Snakes and Ladders (aka Chutes and Ladders). The pandemic was certainly not a game, but this metaphor represents the tension of being a pawn to circumstance while also being expected to take control of one’s professional and personal life during a disaster. The object of the game is to move through three phases of role adaptation, from Disorienting, through Coping and Waiting, to Adapting. In the Adapting phase, the therapists creatively found ways to provide vital services for the pandemic response. The therapists were influenced both negatively and positively (snakes and ladders) by their personal circumstances, and professional meso and macro contexts. Each therapist moved across the board in a unique trajectory and timeline based on these contexts.

Conclusions

Rehabilitation professionals, with adequate meso and macro system supports, can maximize their role on primary care teams by adapting their services to work to their full scope of practice.
Experiences with smoking habits and the need for cessation among habitual smokers in Japan: a qualitative study based on semi-structured interviews
Authors: Shiratani Kae , Shimasawa Junko , Mizutani Mayumi
Published: January 2024

Background

Although more than half of the habitual smokers recognize that they want to quit smoking cigarettes, approximately half have failed to quit and experienced distress relapse; therefore, there is an urgent need to focus on these populations. When chronic behavior occurs, it is necessary to view the behavior in the context of the entire life of the person involved, considering the history of the person. In this study, we aimed to describe experiences with smoking from the onset to the present and the need for smoking cessation among habitual smokers in Japan and to explore efforts to address them.

Methods

Semi-structured interviews that lasted for 55–90 min were conducted with the cooperation of 16 habitual smokers who smoked cigarettes daily. The content of the interviews included demographic characteristics, experiences with smoking from the onset to the present, whether they have attempted to quit and related experiences, and their thoughts on smoking. Interviews were transcribed verbatim and analyzed qualitatively. The Medical Research Ethics Review Committee of Jikei University approved this study (approval number: 33–384(11008)).

Results

The participants were aged 26–59 years (mean ± SD: 40.8 ± 8.9 years) and included 10 men and 6 women. The participants started smoking between age 13 and 24 years. The highest number of cigarettes smoked in the participants’ lives ranged from 10 to 80 daily, and 12 participants had attempted to quit smoking so far without success. Regarding experiences with smoking from the onset to the present, four themes of “expand one’s world,” “unconscious attachment,” “attempts and failures,” and “losing oneself” were extracted. Regarding the need for smoking cessation, four themes of “empowerment from experts,” “peer interaction,” “social commitment,” and “recovery of confidence” were extracted.

Conclusion

To support smoking cessation from the perspective of habitual smokers, in addition to improvements through the existing approaches, it is important to recover their confidence using ongoing activities in peer groups according to the target background and support from experts incorporating visual assessments of lung function, along with multiple short-term goals. It is also necessary to raise awareness in communities through activities.
A retrospective cohort study on oesophageal food bolus obstruction in the North Denmark region in 2021—two thirds were never diagnosed with a cause
Authors: Terkelsen Jacob Holmen , Hollænder Martin , Bredal Kasper , Nielsen Sara Munk , Thomsen Kristoffer Vittrup Koed , Baggerman Amanda , Ofverlind Emilia , Koc Alptug Mertcan , Pakes Hannah , Mahdi Marco Bassam , Larsen Sanne Ørnfeldt , Gonzalez Vanessa Parra , Riis Johannes , Frandsen Line Tegtmeier , Melgaard Dorte , Krarup Anne Lund
Published: January 2024

Background

Food bolus obstruction (FBO) leading to hospital treatment is often associated with eosinophilic oesophagitis (EoE), stenosis, or oesophageal cancer (1). Danish national guidelines recommend that patients with FBO undergo a diagnostic upper endoscopy within two weeks of presentation to exclude possible malignancy, and histological evaluation of eight biopsies (2, 3).

Aims

The aims of this study were to (1) report the incidence and describe the causes and treatment of FBO in the North Denmark Region (NDR), (2) determine the proportion of patients who underwent upper endoscopy and biopsy according to regional and national guidelines, and (3) identify International Classification of Diseases 10th Revision (ICD-10) diagnosis and procedure codes applied to the hospital visits due to FBO in the NDR.

Methods

Among all acute hospital visits in the NDR in 2021, all visits with ICD-10 codes possibly reflecting FBO, as well as a random sample of 14,400 visits with unspecific ICD-10 codes (R and Z codes), were screened manually for possible FBO. Diagnosis, follow-up, and treatment of all patients with FBO were recorded.

Results

The median patient age was 66.0 (Q1-Q3: 49.8–81.0) years, and half of the patients had experienced FBO before. Two thirds of patients (66.0%) were never diagnosed with a cause of FBO, followed by 17.3% with EoE. 30% of patients did not undergo upper endoscopy within two weeks of the hospital visit, and 50.7% were never biopsied in the oesophagus. Of 1886 hospital visits with registry ICD-10 codes that possibly reflected FBO, 8.4% were due to FBO, while FBO was present in 0.028% of the random sample of unspecific ICD-10 codes.

Conclusions

Most hospitalized FBO patients in the NDR in 2021 were never diagnosed with a cause. In these patients there is a high risk of overlooked EoE or upper gastrointestinal cancers. The area needs immediate focus and changed routines to improve treatment and prevent new FBO.