bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Genomic Profiling of Metastatic Castration-Resistant Prostate Cancer Samples Resistant to Androgen Receptor Pathway Inhibitors
Authors: Menssouri Naoual , Poiraudeau Loïc , Helissey Carole , Bigot Ludovic , Sabio Jonathan , Ibrahim Tony , Pobel Cédric , Nicotra Claudio , Ngo-Camus Maud , Lacroix Ludovic , Rouleau Etienne , Tselikas Lambros , Chauchereau Anne , Blanc-Durand Félix , Bernard-Tessier Alice , Patrikidou Anna , Naoun Natacha , Flippot Ronan , Colomba Emeline , Fuerea Alina , Albiges Laurence , Lavaud Pernelle , van de Wiel Paul , den Biezen Eveline , Wesseling-Rozendaal Yvonne , Ponce Santiago , Michiels Stefan , Massard Christophe , Gautheret Daniel , Barlesi Fabrice , André Fabrice , Besse Benjamin , Scoazec Jean-Yves , Friboulet Luc , Fizazi Karim , Loriot Yohann
Published: July 2023

AbstractPurpose:
The androgen receptor axis inhibitors (ARPI; e.g., enzalutamide, abiraterone acetate) are administered in daily practice for men with metastatic castration-resistant prostate cancer (mCRPC). However, not all patients respond, and mechanisms of both primary and acquired resistance remain largely unknown.
Experimental Design:
In the prospective trial MATCH-R (NCT02517892), 59 patients with mCRPC underwent whole-exome sequencing (WES) and/or RNA sequencing (RNA-seq) of samples collected before starting ARPI. Also, 18 patients with mCRPC underwent biopsy at time of resistance. The objectives were to identify genomic alterations associated with resistance to ARPIs as well as to describe clonal evolution. Associations of genomic and transcriptomic alterations with primary resistance were determined using Wilcoxon and Fisher exact tests.
Results:
WES analysis indicated that no single-gene genomic alterations were strongly associated with primary resistance. RNA-seq analysis showed that androgen receptor (AR) gene alterations and expression levels were similar between responders and nonresponders. RNA-based pathway analysis found that patients with primary resistance had a higher Hedgehog pathway score, a lower AR pathway score and a lower NOTCH pathway score than patients with a response. Subclonal evolution and acquisition of new alterations in AR-related genes or neuroendocrine differentiation are associated with acquired resistance. ARPIs do not induce significant changes in the tumor transcriptome of most patients; however, programs associated with cell proliferation are enriched in resistant samples.
Conclusions:
Low AR activity, activation of stemness programs, and Hedgehog pathway were associated with primary ARPIs’ resistance, whereas most acquired resistance was associated with subclonal evolution, AR-related events, and neuroendocrine differentiation.
Supplemental Table 2 from Allele-specific Gene Regulation, Phenotypes, and Therapeutic Vulnerabilities in Estrogen Receptor Alpha–mutant Endometrial Cancer
Authors: Blanchard Zannel , Rush Craig M. , Arnesen Spencer , Vahrenkamp Jeffery M. , Rodriguez Adriana C. , Jarboe Elke A. , Brown Callie , Chang Matthew E.K. , Flory Mark R. , Mohammed Hisham , Modzelewska Katarzyna , Lum David H. , Gertz Jason
Published: July 2023

Overlap between prolonged E2 treatment and differentially expressed genes in vitro
Supplemental Figure 2 from Mitochondrial Uncoupling Inhibits Reductive Carboxylation in Cancer Cells
Authors: Jiang Haowen , He Clifford Jiajun , Li Albert M. , He Bo , Li Yang , Zhou Meng-Ning , Ye Jiangbin
Published: July 2023

S2. Mitochondrial uncoupler NEN accelerates forward TCA cycle and inhibits reductive carboxylation.
Supplemental Figure 1 from Mitochondrial Uncoupling Inhibits Reductive Carboxylation in Cancer Cells
Authors: Jiang Haowen , He Clifford Jiajun , Li Albert M. , He Bo , Li Yang , Zhou Meng-Ning , Ye Jiangbin
Published: July 2023

S1. Mitochondrial uncoupler NEN increases cellular NAD+/NADH ratio and inhibits reductive carboxylation.
Supplemental Figure 5 from Allele-specific Gene Regulation, Phenotypes, and Therapeutic Vulnerabilities in Estrogen Receptor Alpha–mutant Endometrial Cancer
Authors: Blanchard Zannel , Rush Craig M. , Arnesen Spencer , Vahrenkamp Jeffery M. , Rodriguez Adriana C. , Jarboe Elke A. , Brown Callie , Chang Matthew E.K. , Flory Mark R. , Mohammed Hisham , Modzelewska Katarzyna , Lum David H. , Gertz Jason
Published: July 2023

ER-Y537S and ER-D538G mutants drive proliferative gene expression signatures in vivo
Supplemental Figure 3 from Allele-specific Gene Regulation, Phenotypes, and Therapeutic Vulnerabilities in Estrogen Receptor Alpha–mutant Endometrial Cancer
Authors: Blanchard Zannel , Rush Craig M. , Arnesen Spencer , Vahrenkamp Jeffery M. , Rodriguez Adriana C. , Jarboe Elke A. , Brown Callie , Chang Matthew E.K. , Flory Mark R. , Mohammed Hisham , Modzelewska Katarzyna , Lum David H. , Gertz Jason
Published: July 2023

ER binding is altered by the Y537S and D538G mutations
Supplementary Table 7 from LncRNA-Encoded Micropeptide ACLY-BP Drives Lipid Deposition and Cell Proliferation in Clear Cell Renal Cell Carcinoma via Maintenance of ACLY Acetylation
Authors: Zhang Shenghua , Zhang Zheng , Liu Xiaolong , Deng Yibin , Zheng Jian , Deng Jieqiong , Wang Yirong , Guo Binbin , Li Fanrong , Chen Xiaoyue , Pan Yacheng , Wang Jieyu , Lu Jiachun , Wu Siqi , Guo Qiang , Zhou Yifeng
Published: July 2023

Homer Known Motif Enrichment Results (GATA_peaks_on_LINC00887_Promoter_motif)
Supplementary Table 5 from LncRNA-Encoded Micropeptide ACLY-BP Drives Lipid Deposition and Cell Proliferation in Clear Cell Renal Cell Carcinoma via Maintenance of ACLY Acetylation
Authors: Zhang Shenghua , Zhang Zheng , Liu Xiaolong , Deng Yibin , Zheng Jian , Deng Jieqiong , Wang Yirong , Guo Binbin , Li Fanrong , Chen Xiaoyue , Pan Yacheng , Wang Jieyu , Lu Jiachun , Wu Siqi , Guo Qiang , Zhou Yifeng
Published: July 2023

Sequences of LINC00887 and ACLY-BP cDNA
Supplementary Table 3 from LncRNA-Encoded Micropeptide ACLY-BP Drives Lipid Deposition and Cell Proliferation in Clear Cell Renal Cell Carcinoma via Maintenance of ACLY Acetylation
Authors: Zhang Shenghua , Zhang Zheng , Liu Xiaolong , Deng Yibin , Zheng Jian , Deng Jieqiong , Wang Yirong , Guo Binbin , Li Fanrong , Chen Xiaoyue , Pan Yacheng , Wang Jieyu , Lu Jiachun , Wu Siqi , Guo Qiang , Zhou Yifeng
Published: July 2023

Antibodies used in this study
Supplementary Materials and Methods from LncRNA-Encoded Micropeptide ACLY-BP Drives Lipid Deposition and Cell Proliferation in Clear Cell Renal Cell Carcinoma via Maintenance of ACLY Acetylation
Authors: Zhang Shenghua , Zhang Zheng , Liu Xiaolong , Deng Yibin , Zheng Jian , Deng Jieqiong , Wang Yirong , Guo Binbin , Li Fanrong , Chen Xiaoyue , Pan Yacheng , Wang Jieyu , Lu Jiachun , Wu Siqi , Guo Qiang , Zhou Yifeng
Published: July 2023

Supplementary Materials and Methods
Supplementary Figure 3 from LncRNA-Encoded Micropeptide ACLY-BP Drives Lipid Deposition and Cell Proliferation in Clear Cell Renal Cell Carcinoma via Maintenance of ACLY Acetylation
Authors: Zhang Shenghua , Zhang Zheng , Liu Xiaolong , Deng Yibin , Zheng Jian , Deng Jieqiong , Wang Yirong , Guo Binbin , Li Fanrong , Chen Xiaoyue , Pan Yacheng , Wang Jieyu , Lu Jiachun , Wu Siqi , Guo Qiang , Zhou Yifeng
Published: July 2023

Related information to figure 2, figure 3, and figure 5
Supplementary Figure 2 from LncRNA-Encoded Micropeptide ACLY-BP Drives Lipid Deposition and Cell Proliferation in Clear Cell Renal Cell Carcinoma via Maintenance of ACLY Acetylation
Authors: Zhang Shenghua , Zhang Zheng , Liu Xiaolong , Deng Yibin , Zheng Jian , Deng Jieqiong , Wang Yirong , Guo Binbin , Li Fanrong , Chen Xiaoyue , Pan Yacheng , Wang Jieyu , Lu Jiachun , Wu Siqi , Guo Qiang , Zhou Yifeng
Published: July 2023

Related to Figure 2
Supplementary Table S1 from Progressive Spreading of DNA Methylation in the GSTP1 Promoter CpG Island across Transitions from Precursors to Invasive Prostate Cancer
Authors: Gupta Harshath , Inoue Hitoshi , Nakai Yasutomo , Nakayama Masashi , Jones Tracy , Hicks Jessica L. , Kumar Balasubramanian , Gurel Meltem , Nelson William G. , De Marzo Angelo M. , Yegnasubramanian Srinivasan
Published: July 2023

Supplementary Table S1 shows patient and tumor characteristics from the patients who underwent radical prostatectomies for this study.
Supplementary Figure S1 from Progressive Spreading of DNA Methylation in the GSTP1 Promoter CpG Island across Transitions from Precursors to Invasive Prostate Cancer
Authors: Gupta Harshath , Inoue Hitoshi , Nakai Yasutomo , Nakayama Masashi , Jones Tracy , Hicks Jessica L. , Kumar Balasubramanian , Gurel Meltem , Nelson William G. , De Marzo Angelo M. , Yegnasubramanian Srinivasan
Published: July 2023

Supplementary Figure S1 shows the phased methylation by allele of the GSTP1 promoter region classified by density of methylation.
Supplementary Video S1 Legend from RLY-4008, the First Highly Selective FGFR2 Inhibitor with Activity across FGFR2 Alterations and Resistance Mutations
Authors: Subbiah Vivek , Sahai Vaibhav , Maglic Dejan , Bruderek Kamil , Touré B. Barry , Zhao Songping , Valverde Roberto , O'Hearn Patrick J. , Moustakas Demetri T. , Schönherr Heike , Gerami-Moayed Nastaran , Taylor Alexander M. , Hudson Brandi M. , Houde Damian J. , Pal Debjani , Foster Lindsey , Gunaydin Hakan , Ayaz Pelin , Sharon Dina A. , Goyal Lipika , Schram Alison M. , Kamath Suneel , Sherwin Cori Ann , Schmidt-Kittler Oleg , Jen Kai Yu , Ricard Fabien , Wolf Beni B. , Shaw David E. , Bergstrom Donald A. , Watters James , Casaletto Jessica B.
Published: July 2023

Supplementary video legend describing schematic video of P-loop dynamics
Supplementary Table S4 from RLY-4008, the First Highly Selective FGFR2 Inhibitor with Activity across FGFR2 Alterations and Resistance Mutations
Authors: Subbiah Vivek , Sahai Vaibhav , Maglic Dejan , Bruderek Kamil , Touré B. Barry , Zhao Songping , Valverde Roberto , O'Hearn Patrick J. , Moustakas Demetri T. , Schönherr Heike , Gerami-Moayed Nastaran , Taylor Alexander M. , Hudson Brandi M. , Houde Damian J. , Pal Debjani , Foster Lindsey , Gunaydin Hakan , Ayaz Pelin , Sharon Dina A. , Goyal Lipika , Schram Alison M. , Kamath Suneel , Sherwin Cori Ann , Schmidt-Kittler Oleg , Jen Kai Yu , Ricard Fabien , Wolf Beni B. , Shaw David E. , Bergstrom Donald A. , Watters James , Casaletto Jessica B.
Published: July 2023

In vivo exposures of pan-FGFRi in mouse studies
Supplementary References from RLY-4008, the First Highly Selective FGFR2 Inhibitor with Activity across FGFR2 Alterations and Resistance Mutations
Authors: Subbiah Vivek , Sahai Vaibhav , Maglic Dejan , Bruderek Kamil , Touré B. Barry , Zhao Songping , Valverde Roberto , O'Hearn Patrick J. , Moustakas Demetri T. , Schönherr Heike , Gerami-Moayed Nastaran , Taylor Alexander M. , Hudson Brandi M. , Houde Damian J. , Pal Debjani , Foster Lindsey , Gunaydin Hakan , Ayaz Pelin , Sharon Dina A. , Goyal Lipika , Schram Alison M. , Kamath Suneel , Sherwin Cori Ann , Schmidt-Kittler Oleg , Jen Kai Yu , Ricard Fabien , Wolf Beni B. , Shaw David E. , Bergstrom Donald A. , Watters James , Casaletto Jessica B.
Published: July 2023

three references cited in supplementary data
Supplementary Figure S2 from RLY-4008, the First Highly Selective FGFR2 Inhibitor with Activity across FGFR2 Alterations and Resistance Mutations
Authors: Subbiah Vivek , Sahai Vaibhav , Maglic Dejan , Bruderek Kamil , Touré B. Barry , Zhao Songping , Valverde Roberto , O'Hearn Patrick J. , Moustakas Demetri T. , Schönherr Heike , Gerami-Moayed Nastaran , Taylor Alexander M. , Hudson Brandi M. , Houde Damian J. , Pal Debjani , Foster Lindsey , Gunaydin Hakan , Ayaz Pelin , Sharon Dina A. , Goyal Lipika , Schram Alison M. , Kamath Suneel , Sherwin Cori Ann , Schmidt-Kittler Oleg , Jen Kai Yu , Ricard Fabien , Wolf Beni B. , Shaw David E. , Bergstrom Donald A. , Watters James , Casaletto Jessica B.
Published: July 2023

Supplementary Figure 2. Treatment with RLY-4008 is well-tolerated and leads to dose-dependent inhibition of FGFR2 and tumor regression in multiple FGFR2-altered tumor models.
Supplementary Appendix S1 from RLY-4008, the First Highly Selective FGFR2 Inhibitor with Activity across FGFR2 Alterations and Resistance Mutations
Authors: Subbiah Vivek , Sahai Vaibhav , Maglic Dejan , Bruderek Kamil , Touré B. Barry , Zhao Songping , Valverde Roberto , O'Hearn Patrick J. , Moustakas Demetri T. , Schönherr Heike , Gerami-Moayed Nastaran , Taylor Alexander M. , Hudson Brandi M. , Houde Damian J. , Pal Debjani , Foster Lindsey , Gunaydin Hakan , Ayaz Pelin , Sharon Dina A. , Goyal Lipika , Schram Alison M. , Kamath Suneel , Sherwin Cori Ann , Schmidt-Kittler Oleg , Jen Kai Yu , Ricard Fabien , Wolf Beni B. , Shaw David E. , Bergstrom Donald A. , Watters James , Casaletto Jessica B.
Published: July 2023

ReFocus entry criteria
Figure S5 from Distinct Assemblies of Heterodimeric Cytokine Receptors Govern Stemness Programs in Leukemia
Authors: Kan Winnie L. , Dhagat Urmi , Kaufmann Kerstin B. , Hercus Timothy R. , Nero Tracy L. , Zeng Andy G.X. , Toubia John , Barry Emma F. , Broughton Sophie E. , Gomez Guillermo A. , Benard Brooks A. , Dottore Mara , Cheung Tung Shing Karen S. , Boutzen Héléna , Samaraweera Saumya E. , Simpson Kaylene J. , Jin Liqing , Goodall Gregory J. , Begley C. Glenn , Thomas Daniel , Ekert Paul G. , Tvorogov Denis , D'Andrea Richard J. , Dick John E. , Parker Michael W. , Lopez Angel F.
Published: July 2023

Enrichment of the IL-3R hexamer versus dodecamer gene signature in primitive normal and leukemic stem cells.
Figure S4 from Distinct Assemblies of Heterodimeric Cytokine Receptors Govern Stemness Programs in Leukemia
Authors: Kan Winnie L. , Dhagat Urmi , Kaufmann Kerstin B. , Hercus Timothy R. , Nero Tracy L. , Zeng Andy G.X. , Toubia John , Barry Emma F. , Broughton Sophie E. , Gomez Guillermo A. , Benard Brooks A. , Dottore Mara , Cheung Tung Shing Karen S. , Boutzen Héléna , Samaraweera Saumya E. , Simpson Kaylene J. , Jin Liqing , Goodall Gregory J. , Begley C. Glenn , Thomas Daniel , Ekert Paul G. , Tvorogov Denis , D'Andrea Richard J. , Dick John E. , Parker Michael W. , Lopez Angel F.
Published: July 2023

The IL-3R dodecamer activates STAT1 to induce cell differentiation.
Figure S1 from Distinct Assemblies of Heterodimeric Cytokine Receptors Govern Stemness Programs in Leukemia
Authors: Kan Winnie L. , Dhagat Urmi , Kaufmann Kerstin B. , Hercus Timothy R. , Nero Tracy L. , Zeng Andy G.X. , Toubia John , Barry Emma F. , Broughton Sophie E. , Gomez Guillermo A. , Benard Brooks A. , Dottore Mara , Cheung Tung Shing Karen S. , Boutzen Héléna , Samaraweera Saumya E. , Simpson Kaylene J. , Jin Liqing , Goodall Gregory J. , Begley C. Glenn , Thomas Daniel , Ekert Paul G. , Tvorogov Denis , D'Andrea Richard J. , Dick John E. , Parker Michael W. , Lopez Angel F.
Published: July 2023

IL3Rα/βc transcript and protein expression ratio in AML patient samples.
Supplementary Table 2 from Enhancing CAR T-cell Therapy Using Fab-Based Constitutively Heterodimeric Cytokine Receptors
Authors: Righi Matteo , Gannon Isaac , Robson Matthew , Srivastava Saket , Kokalaki Evangelia , Grothier Thomas , Nannini Francesco , Allen Christopher , Bai Yuchen V. , Sillibourne James , Cordoba Shaun , Thomas Simon , Pule Martin
Published: July 2023

Supplementary Table S2. Top 50 up-regulated GSEA pathways.
Data from Enhancing CAR T-cell Therapy Using Fab-Based Constitutively Heterodimeric Cytokine Receptors
Authors: Righi Matteo , Gannon Isaac , Robson Matthew , Srivastava Saket , Kokalaki Evangelia , Grothier Thomas , Nannini Francesco , Allen Christopher , Bai Yuchen V. , Sillibourne James , Cordoba Shaun , Thomas Simon , Pule Martin
Published: July 2023

Abstract
Adoptive T-cell therapy aims to achieve lasting tumor clearance, requiring enhanced engraftment and survival of the immune cells. Cytokines are paramount modulators of T-cell survival and proliferation. Cytokine receptors signal via ligand-induced dimerization, and this principle has been hijacked utilizing nonnative dimerization domains. A major limitation of current technologies resides in the absence of a module that recapitulates the natural cytokine receptor heterodimeric pairing. To circumvent this, we created a new engineered cytokine receptor able to constitutively recreate receptor-heterodimer utilizing the heterodimerization domain derived from the IgG1 antibody (dFab_CCR). We found that the signal delivered by the dFab_CCR-IL2 proficiently mimicked the cytokine receptor heterodimerization, with transcriptomic signatures like those obtained by activation of the native IL2 receptor. Moreover, we found that this dimerization structure was agnostic, efficiently activating signaling through four cytokine receptor families. Using a combination of in vivo and in vitro screening approaches, we characterized a library of 18 dFab_CCRs coexpressed with a clinically relevant solid tumor–specific GD2-specific chimeric antigen receptor (CAR). Based on this characterization, we suggest that the coexpression of either the common β-chain GMCSF or the IL18 dFab_CCRs is optimal to improve CAR T-cell expansion, engraftment, and efficacy. Our results demonstrate how Fab dimerization is efficient and versatile in recapitulating a cytokine receptor heterodimerization signal. This module could be applied for the enhancement of adoptive T-cell therapies, as well as therapies based on other immune cell types. Furthermore, these results provide a choice of cytokine signal to incorporate with adoptive T-cell therapies.
Supplementary Figure S4 from A Th1-like CD4+ T-cell Cluster That Predicts Disease-free Survival in Early-stage Lung Cancer
Authors: Yanagihara Akitoshi , Yamasaki Satoshi , Hashimoto Kosuke , Taguchi Ryo , Umesaki Tetsuya , Imai Hisao , Kaira Kyoichi , Nitanda Hiroyuki , Sakaguchi Hirozo , Ishida Hironori , Kobayashi Kunihiko , Horimoto Katsuhisa , Kagamu Hiroshi
Published: July 2023

Fig. S4. The percentages of CD8+ T-cell clusters in the peripheral blood were compared before and after surgical resection in patients with no recurrence and patients with recurrence. Differences were tested by paired Welch's t-test
FIGURE 5 from A Th1-like CD4+ T-cell Cluster That Predicts Disease-free Survival in Early-stage Lung Cancer
Authors: Yanagihara Akitoshi , Yamasaki Satoshi , Hashimoto Kosuke , Taguchi Ryo , Umesaki Tetsuya , Imai Hisao , Kaira Kyoichi , Nitanda Hiroyuki , Sakaguchi Hirozo , Ishida Hironori , Kobayashi Kunihiko , Horimoto Katsuhisa , Kagamu Hiroshi
Published: July 2023

CD8+ T-cell clusters in LNs. A, Representative cell-level molecular expression using tSNE figures by mass cytometry analysis of gated CD8+CD3+ draining LNs. B, FlowSOM annotation using CD45RA, CD62L, and CCR7 expression is shown.
Supplementary Figure 6 from Metronomic Administration of Topotecan Alone and in Combination with Docetaxel Inhibits Epithelial–mesenchymal Transition in Aggressive Variant Prostate Cancers
Authors: Mitra Ghosh Taraswi , Mazumder Suman , Davis Joshua , Yadav Jyoti , Akinpelu Ayuba , Alnaim Ahmed , Kumar Harish , Waliagha Razan , Church Bird Allison E. , Rais-Bahrami Soroush , Bird R. Curtis , Mistriotis Panagiotis , Mishra Amarjit , Yates Clayton C. , Mitra Amit K. , Arnold Robert D.
Published: July 2023

Supplementary Fig. 6 shows Cytotoxicity Profiling of ARLow/mCRPC/NEPC (PC-3 and PC-3M) and Taxane Resistance ARLow/mCRPC (DUTXR): PC-3, PC-3M and DUTXR cell lines were treated with CONV-TOPO, METRO-TOPO, CONV-DTX and combination (CONV-DTX+METRO-TOPO) treatment, and cell cytotoxicity and caspase3/7 levels ware assed A) Cytotoxicity profiling by MTT showed combination (CONV-DTX+METRO-TOPO) reduces highest cell survival compared with other treatments for all PCa cell lines, CONV-TOPO>CONV-DTX>METRO-TOPO B) Caspase3/7 activity showed combination (CONV-DTX+METRO-TOPO) treatment reduced apoptosis the greatest compared to other treatments in all cell lines. C) Cytation5 images showed treatment effects on the cell lines PC-3M and DUTXR. Results showed significantly higher cell death in METRO compared to CONV treatment for both the cell lines and combination (CONV-DTX+METRO-TOPO) treatment reduced cell death greater for both PCa cell lines. ImageJ analysis showed significant differences in cell density for CONV-TOPO, CONV-DTX, METRO-TOPO, and combination (CONV-DTX+METRO-TOPO) treatment in PC-3, PC-3M, and DUTXR cell lines. (*p ≤ 0.05).
Protective Effects of Oleoylethanolamine on Diabetic Nephropathy: Role of AMP-Activated Protein Kinase/Nuclear Factor-E2-Related Factor 2 Pathway
Authors: Wu Yong , Li Siyi , Liu Ying , Yang Liwen , Lin Weiping
Published: July 2023

This study aimed to investigate the protective effect of Oleoylethanolamine (OEA) on kidney injury in diabetic nephropathy (DN) mice. Sixty C57BL/6 mice were used, and 45 mice were induced with diabetes. Thirty diabetic mice were divided into OEA low-dose and high-dose treatment groups,
receiving 5 or 20 mg/kg OEA by gavage daily for 4 weeks. OEA treatment significantly improved general conditions, increased body weight, and reduced 24 h urine protein, urinary albumin, serum creatinine, and blood urea nitrogen levels. Inflammatory factors and renal inflammation were dramatically
reduced after OEA intervention. OEA also increased antioxidant enzyme activity and reduced the increase of reactive oxygen species and malondialdehyde content in kidney tissues. Western blot detection revealed that OEA intervention upregulated the expression of p-AMPK and n-Nrf2 proteins in
the AMPK/Nrf2 signaling pathway in renal tissue, effectively preventing the progression of DN. The study suggests that OEA’s protective effect on kidney injury in DN mice is related to the regulation of the AMPK/Nrf2 signaling pathway.
Feasibility and Safety of Regenerated Wild Antheraea pernyi Silk Fibroin/Polyvinyl Alcohol Scaffold in Repair of Calcaneal Tendon Defects
Authors: Cao Lihe , Tian Wenping , Li Baocheng , You Fuchao , Hang Ji , Hao Duan , He Donghuang
Published: July 2023

This research discussed the value of regenerated wild Antheraea pernyi silk fibroin (RWSF)/polyvinyl alcohol (PVA) nanofiber scaffold (NFS) in repairing the calcaneal tendon defect (CTD). RWSF was prepared by saturated salt solution (SSS) method, and then RWSF/PVA NFS was prepared
by electrospinning using RWSF and PVA as raw materials. Fourier transform infrared spectroscopy (FTIS) was applied to detect the characteristic absorption spectra of WSF, RWSF, and RWSF/PVA. The ultimate tensile strength (UTS) and elongation at break (BE) of RWSF/PVA NFS were analyzed by mechanical
tester. The cytotoxicity of RWSF/PVA NFS was determined by MTT assay. 18 SD rats were randomly rolled into an operation group, control group, and experimental group, with 6 rats in each. Meanwhile, 27 rats were randomly grouped into three: blank group, model group, and experimental group.
HE staining, Masson staining, and biomechanical properties of the regenerated fibers were analyzed in the calcaneal tendon tissues (CTTs) of rats in different groups. Expressions of tendon-related genes and inflammatory factors in CTTs in various groups were compared by RT-PCR. The results
revealed that the UTS and BE of PVA and RWSF/PVA were much higher than those of natural acellular tendon (P <0.01). On day 15 after operation, the hair in the incision area of rats in the Ope, Con, and Exp groups grew normally. The implanted RWSF/PVA NFS in the Exp group adhered
closely to the surrounding muscle tissue and degraded gradually, and there were still trace inflammatory cells at the junction. The tendon cross sectional area (CSA) in the Model group and RWSF/PVA group was greatly higher based on that in the Blank group (P <0.05), and the UTS in
of Model group was much higher than that in the Blank group but lower to the Model group, showing great differences with P <0.05. The Collagen I, Collagen III, TGF-β1, BGN, and TNMD in CTTs in the RWSF/PVA group were higher to the Model group 2 months ago (P <0.05);
while Collagen I, TGF-β1, BGN, and TNMD were still much higher 3 months later (P <0.01) but Collagen III was lower with an obvious difference (P <0.05). At 5 months, IL-1β and TNF-α in the RWSF/PVA group were greatly lower in contrast
to the model group, presenting extremely obvious differences (P <0.001). The results indicated that the RWSF/PVA NFS exhibited a good biocompatibility, can accelerate the collagen secretion, promote TGF-β1, inhibit IL-1β and TNF-α factors, thus
being conductive to repair of CTD. In conclusion, RWSF/PVA NFS possessed a good biocompatibility, can promote collagen secretion, elevate the TGF-β1, and inhibit IL-1β and TNF-α factors to participate in calcaneal CTD repair, showing a high value in repair
of CTD.
Recombinant Human Interferon α-2b Nanoparticles in the Treatment of Human Papillomavirus Infection Model and Detection of LMX 1A Expression in Cervical Exhumation Cells
Authors: Shi Zhina , Zhao Tian , Zhang Jing , Zhang Shen , Wu Yinglei , Jia Yanan , Yang Hua , Yuan Yaohui
Published: July 2023

Interferon (INF) is a kind of multifunctional and highly active protein-like cytokines produced by animal cells after stimulation, which exerts the broad-spectrum antiviral, anti-tumor, and immunomodulatory effects. Preparing the nanoparticles (NPs) loaded drug can improve the stability
of protein polypeptides in vivo, prolong the biological half-life period, and improve the bioavailability. In this research, recombinant human interferon (RHUINF) α-2b NPs were prepared to explore their therapeutic effect on human papillomavirus (HPV) infection model. Firstly,
the RHUINF α-2b poly (lactic acid-glycolic acid) copolymer (PLGA) of composite bioactive glass was prepared by electrostatic spray technology. The in vitro quality, stability, and pharmacokinetic characteristics in vivo of the NPs were measured. Then, a mouse model
infected with HPV16 pseudovirus infection (NC group) was prepared. Next, they were treated by painting imiquimod (IMQ) (IMQ group), intramuscularly injecting the RHUINF α-2b (Intron A), intramuscularly injecting the RHUINF α-2b-Plga NP suspension (Intra/PLGA), and
intramuscularly injecting the RHUINF α-2B-bioactive glass-PLGA NP suspension (Intron A/BAG/PLGA), respectively. In addition, the differences in serum inflammatory cytokines, vaginal biofluorescence activity (VBA), HPV load, and LMX 1A expressions in cervical exhumation cells (CECs)
were analyzed. The average particle sizes (PSs) of Intron A/PLGA and Intron A/BAG/PLGA NPs were 352.3 nm and 385.1 nm, respectively, and no great differences were observed in encapsulation rate (ER), drug loading (DL), and in vivo release (IVR). The maximum peak times (MPTs) of Intron
A, Intron A/PLGA, and Intron A/BAG/PLGA were 1.3 h, 6.2 h, and 6.5 h, respectively, and their maintenance durations were 5.5 h, 120.7 h, and 245.6 h, respectively. Based on the NC group, IFN-γ, IL-2, and TNF-α in the IMQ group, Intron A group, Intron A/PLGA group,
Intron A/PLGA group, and Intron A/BAG/PLGA group were decreased, VBA and HPV load were decreased, and mRNA of LMX 1A in ECEs was increased (p < 0.05). Based on the Intron A group, the Intron A/PLGA and Intron A/BAG/PLGA groups exhibited decreased serum inflammatory factors (IFFs),
VBA, HPV load, and LMX 1A mRNA in the CECs were increased (p < 0.05). By taking the Intron A/PLGA group as reference, the Intron A/BAG/PLGA group showed greatly reduced serum IFFs, VBA, HPV load, and LMX 1A mRNA expression in CECs (p<0.05). Preparing RHUINF α-2b
NPs could prolong the half-life period of RHUINF α-2b in vivo, reduce the inflammatory response and load of HPV-DNA in HPV infection models, and upregulate LMX 1A in CECs. In addition, RHUINF α-2b NPs could improve the therapeutic effect of RHUINF α-2b.
Sirt3 improves monosodium urate crystal-induced inflammation by suppressing Acod1 expression
Authors: Lv Linxi , Jiang Hui , Song Dianze , Zhou Xiaoqin , Chen Feng , Ren Long , Xie Yongen , Zeng Mei
Published: July 2023

Background

Previous studies have revealed that Sirt3 deficiency is associated with several inflammatory responses. The purpose of this study is to investigate the role and potential molecular mechanisms of Sirt3 in the inflammation induced by monosodium urate (MSU) crystals.

Methods

The Sirt3 expression level in the peripheral blood mononuclear cells (PBMCs) of patients with gout was measured. Function and molecular mechanism of Sirt3 in MSU crystal-induced inflammation were investigated in bone marrow-derived macrophages (BMDMs), C57BL/6 mouse, and Sirt3−/− mouse.

Results

Sirt3 expression was decreased in the PBMCs of patients with gout. Sirt3 agonist (Viniferin) inhibited the acetylation levels of mitochondrial proteins including the SOD2 protein. RNA sequencing, bio-informatics analysis, RT-PCR, and Western blot demonstrated that Sirt3 could suppress the expression of Acod1 (Irg1), which plays an important role in gout. In BMDMs treated with palmitic acid (C16:0) plus MSU crystals, Acod1 knockdown repressed mitochondrial reactive oxygen species (mtROS) over-production, macrophage migration, and mitochondrial fragmentation, and Acod1 improved AMPK activity. The over-expression of Acod1 did not significantly affect the level of itaconic acid, but greatly decreased the levels of some important intermediate metabolites of the tricarboxylic acid (TCA) cycle. These data indicate that Acod1 exerts a pro-inflammatory role in MSU crystal-induced inflammation and is independent of the metabolic level of itaconic acid. Sirt3 deficiency exacerbates inflammatory response induced by MSU crystals in vitro and in vivo.

Conclusion

The current study has shown that Sirt3 can alleviate the MSU crystal-induced inflammation by inhibiting the expression of Acod1.
Kultura w przekładzie – tłumacz wobec kultury: O monografii Michała Gąski pt. Elementy trzeciej kultury w procesie tłumaczenia prozy Holenderskich Indii Wschodnich na języki polski i niemiecki, Wydawnictwo Universitas, Kraków 2021, 276 stron
Authors: Pankanin Emilia
Published: July 2023

Niniejszy artykuł jest próbą krytycznej analizy głównych założeń i wniosków zawartych w monografii Michała Gąski pt. „Elementy trzeciej kultury w procesie tłumaczenia prozy Holenderskich Indii Wschodnich na języki polski i niemiecki”. Szczególną uwagę poświęcono relacji tłumacz-kultura, odnosząc się do kompetencji interkulturowej tłumacza i stosowanych przez niego technik tłumaczeniowych oraz zwracając uwagę na wzmocnienie kształcenia tej kompetencji u tłumaczy.
Screening the anthelmintic effects of leaves and fruits extracts from various Acacia species as a potential feed for small-ruminant animals
Authors: HANDAYANTA EKA , HADI RENDI FATHONI
Published: July 2023

Abstract. Handayanta E, Hadi RF. 2023. Screening the anthelmintic effects of leaves and fruits extracts from various Acacia species as a potential feed for small-ruminant animals. Biodiversitas 24: 3140-3144. This study aimed to determine the anthelmintic properties of leaves and fruits obtained from various Acaciaspecies against Haemonchus contortus Rudolphi, 1803. Both leaf and fruit samples were allocated into five different groups: negative control (NC), 0.9% of NaCl solution; positive control (PC), albendazole solution; and solutions containing 12% concentration of each Acacia auriculiformis A.Cunn. ex Benth.(AA), Acacia mangium Willd.(AM), and Acacia crassicarpa A.Cunn. ex Benth.(AC) powder. The added concentration was set at 12%, and each treatment group was brought to incubation in 6 different time parameters (1, 2, 3, 4, 5, and 6 hours) against H. contortus. Each Acacia leaves extract did not significantly differ in eliminating H. contortus, unless for AM under 4 hours of incubation (p<0.05), wherein at the final incubation time, all Acacia-treated samples displayed complete mortality. Meanwhile, treatment with Acacia fruits during 6-hour incubations led to a removal of 76.66-83.33 % H. contortus population, in which Albendazole-treated groups showed complete mortality. Thus, this study suggested the leaves from Acacia are a potential animal feed as anthelmintic against H. contortus parasites. However, further studies investigating the potential mechanism by which various Acacia species present anthelmintic activity are necessary.
It’s a Sin: Introduction to a Special Issue
Authors: Bollas Angelos
Published: July 2023

This introduction to the journal’s Special Issue on the 2021 seriesIt’s a Singives a brief overview of the show’s significance in popular culture and the rationale behind the selection of contributors.
The Use of Motivational Strategies in the EFL Classroom
Authors: Kouraichi Bochra
Published: July 2023

Keller (2010) ARCS-modellje a második nyelvi motivációs elméletek és az osztálytermi gyakorlat közötti szakadékkal foglalkozik, melyben a motiváció négy kategóriájára összpontosít: figyelem, relevancia, bizalom és elégedettség. Jelen kutatás célja, hogy betekintést adjon a tunéziai egyetemi tanárok motivációs stratégiáiba, melyeket a tantermi oktatás során alkalmaznak (MotS) (Dörnyei 2001). Továbbá, arról is szót ejtek, hogy a diákok mennyire tartják ezeket a stratégiákat hatékonynak. A tanulmány célja továbbá még annak a feltárása, hogy milyen kapcsolat van a hallgatók önértékelése és a tanáraik által alkalmazott MotS-ek között. Ezen kívül rávilágít minden olyan hasonlóságra vagy különbségre, amely a MotS használatáról beszámoló tanárok és a tényleges motivációs gyakorlatuk között mutatkozik. A kutatási kérdések megválaszolásához és az adatgyűjtéshez a következő eszközöket használtam: (a) az IMMS kérdőívet (Keller 2010), (b) az L2MSS kérdőívet (Dörnyei 2009), és (c) a MOLT osztálytermi megfigyelési sémát (Guilloteaux és Dörnyei 2008). Az adatok elemzéséhez kvantitatív és kvalitatív módszereket alkalmaztam. Statisztikai elemzéseket végeztem a négy MotS-kategória leíró statisztikáinak kiszámítására mind a diákok, mind a tanárok esetében. Ezután független mintás t-próbát végeztünk, hogy megállapítsuk, van-e szignifikáns különbség a diákok és a tanárok MotS-ről alkotott felfogása között. Korrelációs elemzéseket is végeztem, hogy az L2MSS-modellen keresztül azonosítsam az alkalmazott MotS hatását a diákok jövőbeli önképére. A megfigyelési eredményeket először kvalitatív módon elemeztem a MOLT sémát követve. Az eredmények azt mutatják, hogy jelentős különbség van a tanárok és a diákok visszajelzésében, ami a MotS-ot illeti. A diákok eredményeit az órai megfigyelések során megerősítették. Ezen túlmenően az L2MSS és az IMMS kategóriák közötti összefüggések a kérdőíves eredmények fényében voltak megmagyarázhatóak.
Praktik Tahfiz Al-Qur’an selama Masa Pandemi COVID-19 (Studi Living Qur’an di SD Islam Al Azhar 17 Bintaro)
Authors: Yusuf Muhammad , Isnawati Isnawati
Published: July 2023

This study describes the practice of tahfiz Al-Qur'an during the pandemic period at SD Islam Al Azhar 17 Bintaro. This research is qualitative research using field research data collection methods. The primary data source was the Learning Syllabus for Tahfiz Al-Qur'an at SD Islam Al Azhar 17 Bintaro, the results of observations, interviews, and findings during the research. The secondary source is authoritative literature which examines the tahfiz program during the pandemic. This research shows that during the pandemic, the daily agenda and supporting activities for the practice of reciting the Qur'an at SD Islam Al Azhar 17 Bintaro continued to run well, even with changes and adjustments. The talaqqi pattern, which was originally carried out in person, changed to virtual through the Zoom application and WhatsApp video calls. In implementing tahfiz with the Distance Learning (PJJ) system, teachers and schools must be able to establish good synergy with parents, because the role of parents has a significant impact on the achievement of student memorization.
The Director – a Leading Social Actor in the Inspection of Bulgarian Education Quality
Authors: Hadzhigeorgieva Tsetska
Published: July 2023

Inspecting the quality of education is an innovative social phenomenon in the Bulgarian education system and presents the director with the challenges of two opposite roles: "assessed" and "assessing", as in the leading role of a participant in quality management. The article analyzes the social roles of the director of the educational institution, as well as some of the methods, concepts and tools of the evaluation of the quality of education. They are presented through the variety of social processes, and activities and interactions in the main stages of the inspection: preparatory, actual and final, which the director must know as a leading participant in the process of inspecting the quality of education. Under the social spotlight, the changes in the duties and responsibilities of the director as the main social actor in the society of the educational institution in planning, organizing, facilitating the inspection in the complex compilation of the social roles performed by him/her, of evaluator, evaluated, self-evaluator and finally, together with the inspection team, a direct participant in the quality management of the educational institution.
Understanding Cross-Sectional Variability in Equity Returns Using a Conditional Asset Pricing Model
Authors: CANDEMIR Işıl
Published: July 2023

A common practice in the literature examining Turkish equity premia involves the application of time-invariant models that assume the constancy of parameters across time. The present study examines whether the cross-sectional variability among equity returns can be explained by market, size, value and momentum factors and whether the parameters are time varying, utilizing a conditional asset pricing model formulated by Ferson and Harvey (1999). The study yields four main findings. Firstly, I find that the market dividend yield has a positive and significant effect on portfolio returns over the period from July 1989 to May 2021. Secondly, I reject the time-invariance in betas, while not rejecting it for alpha. Thirdly, none of the factors I examined have been priced, indicating that the four-asset pricing model is not sufficient to explain time-varying premia. Finally, the results are sensitive to the methodology employed for portfolio construction.
Państwo wpisane w depozyt religii. Przeobrażenia struktury terytorialno-religijno-etnicznej Izraela w kontekście oddziaływań międzynarodowych
Authors: Rykała Andrzej
Published: July 2023

Izrael należy do tych państw, których położenie ma „wartość polityczną”. Znaczenie przypisywane obszarowi, który zajmuje, związane jest przede wszystkim z genezą i historią narodu żydowskiego oraz jego religią, w depozyt której Erec Israel została wpisana na trwałe i na zasadzie centralnego miejsca. Swoją „wartość geopolityczną” obszar ten zmienił wraz z pojawieniem się ludności arabsko-muzułmańskiej. Jej osiedlenie się stanowiło zwrot kulturowy w historii regionu. W artykule dokonano: 1) próby określenia relacji zachodzących między judaizmem a przestrzenią życia jego wyznawców, 2) przedstawienia geograficzno-politycznych i religijnych uwarunkowań życia Żydów w diasporze w kontekście odbudowy ich siedziby narodowej, 3) analizy przyczyn, przebiegu i konsekwencji zmian usytuowania geopolitycznego Izraela w powiązaniu z przeobrażeniami jego struktury terytorialno-religijno-narodowej, 4) określenia wpływu tych przeobrażeń na zachowanie uczestników stosunków międzynarodowych.
Ficus Carica Latex Modulates Immunity-linked Gene Expression in Human Papillomavirus Positive Cervical Cancer Cell Lines: Evidence From RNA Seq Transcriptome Analysis
Authors: Cakir Muharrem Okan , Bilge Ugur , Naughton Declan , Ashrafi G Hossein
Published: July 2023

Cervical carcinogenesis is the leading cause of cancer related death in women and the role of high-risk human papillomavirus (HR-HPV) as a possible risk factor in the development of this cancer is well recognised. Despite the availability of multi-therapeutic approaches, there is still a major concern regarding the prevention of metastatic dissemination and excessive tissue injuries. Therefore, it is imperative to develop a safer and more efficient treatment modality. Ficus Carica, a natural plant, has shown potential therapeutic properties through its fruit latex when applied to HPV-positive cervical cancer cell lines. However, the mechanisms of action of Ficus Carica (fig) latex are not well understood. This study aims to provide a deeper insight into the biological activities of fig latex on human cervical cancer cell lines expressing high-risk HPV types 16 and 18. The data obtained from this study reveals that fig latex influences the expression of genes in-volved in "Class I MHC-mediated antigen presentation" as well as "Antigen processing: Ubiquitination and Proteasome degradation." These genes play a crucial role in host immune surveillance and the resolution of infection. Findings from this study suggest that fig latex may enhance T cell responses against oncogenic HPV, which could be beneficial for the clearance of early-stage cancer.
Analysis of Hematological Predictors via Explainable Artificial Intelligence in Prediction of Acute Heart Failure: A Retrospective Study
Authors: Yilmaz Rustem , Yagin Fatma Hilal , Colak Cemil , Toprak Kenan , Samee Nagwan Abdel , Mahmoud Noha F.
Published: July 2023

Background: Acute heart failure (AHF) is a serious medical problem that necessitates hospitalisation and often results in death. Patients hospitalised to the emergency department (ED) should therefore receive an immediate diagnosis and treatment. Unfortunately, there is not yet a fast and accurate laboratory test for identifying AHF. The purpose of this research is to apply the principles of explainable artificial intelligence (XAI) to the analysis of hematological predictors for AHF. Methods: In this retrospective analysis, 425 patients with AHF and 430 healthy individuals served as assessments. Patients' demographic and hematological information was analyzed to determine AHF. Important risk variables for AHF diagnosis were identified using LASSO feature selection. To test the efficacy of the suggested prediction model (XGBoost), a 10-fold cross-validation procedure was implemented. The area under the receiver operating characteristic curve (AUC), F1 score, Brier score, and Positive Predictive Value (PPV) and Negative Predictive Value (NPV) were all computed to evaluate the model's efficacy. Permutation-based analysis and SHAP, were used to assess the importance and influence of the model's incorporated risk factors. Results: White blood cell (WBC), monocytes, neutrophils, neutrophil-lymphocyte ratio (NLR), red cell distribution width-standard deviation (RDW-SD), RDW-coefficient of variation (RDW-CV), and platelet distribution width (PDW) values were significantly higher than the healthy group (p<0.05). On the other hand, erythrocyte, hemoglobin, basophil, lymphocyte, mean platelet volume (MPV), platelet, hematocrit, mean erythrocyte hemoglobin (MCH) and procalcitonin (PCT) values were found to be significantly lower in AHF patients compared to healthy controls (p <0.05). When XGBoost was used in conjunction with LASSO to estimate AHF, the resulting model had an AUC of 87.9%, an F1 score of 87.4%, a Brier score of 0.036, and an F1 score of 87.4%. PDW, age, RDW-SD, and PLT were identified as the most crucial risk factors in differentiating AHF. Conclusions: The XGBoost model demonstrated exceptional performance in accurately estimating Acute Heart Failure, and the application of Explainable Artificial Intelligence effectively provided intuitive explanations for the model's estimations. The suggested interpretable model holds potential for the identification of patients at high risk, thereby facilitating the optimization of treatment and planning for follow-up in cases of AHF.
Considerations, Advances, and Challenges Associated with the Use of Specific Emitter Identification in the Security of Internet of Things Deployments: A Survey
Authors: Tyler Joshua H. , Fadul Mohamed K.M. , Reising Donald R.
Published: July 2023

Initially introduced almost thirty years ago for the express purpose of providing electronic warfare systems the capabilities to detect, characterize, and identify radar emitters, Specific Emitter Identification (SEI) has recently received a lot of attention within the research community as a physical layer technique for securing Internet of Things (IoT) deployments. This attention is due in large part to SEI’s demonstrated success in passively and uniquely identifying wireless emitters using traditional machine learning and the success of Deep Learning (DL) within the natural language processing and computer vision areas. SEI exploits distinct and unintentional features present within an emitter’s transmitted signals. The existence of these distinctive and unintentional features is attributed to slight manufacturing and assembly variations that exist within and between the components, sub-systems, and systems that comprise an emitter’s Radio Frequency (RF) front end. Although sufficient to facilitate SEI, these features do not hinder normal operations such as detection, channel estimation, timing, and demodulation. However, despite the plethora of SEI publications, it has remained largely a focus of academic endeavors that primarily focus on proof-of-concept demonstration and little to no use in operational networks for various reasons. The focus of this survey is a review of SEI publications from the perspective of its use as a practical, effective, and usable IoT security mechanism, thus we use IoT requirements and constraints (e.g., wireless standard, nature of their deployment) as a lens through which each reviewed paper is analyzed. Previous surveys have not taken such an approach and have only used IoT as motivation, a setting, or a context. In this survey, we consider operating conditions, SEI threats, SEI at scale, publicly available data sets, and SEI considerations that are dictated by the fact that it is to be employed by IoT devices or IoT infrastructure.
On the Use of Artificial Intelligence in Predicting the Compressive Strength of Various Cardboard Packaging
Authors: Gajewski Tomasz , Grabski Jakub K. , Cornaggia Aram , Garbowski Tomasz
Published: July 2023

Artificial intelligence is increasingly used in various branches of engineering. In this article, artificial neural networks are used to predict the crush resistance of corrugated packaging. Among the analysed packages were boxes with ventilation openings, packages with perforations, and typical flap boxes, which makes the proposed estimation method very universal. Typical shallow feedforward networks were used, which are perfect for regression problems, mainly when the set of input and output parameters is small, so no complicated architecture or advanced learning techniques are required. The input parameters of the neural networks are selected so as to take into account not only the material used for the production of the packaging, but also the dimensions of the box and the impact of ventilation holes and perforations on the load capacity of individual walls of the packaging. In order to maximize the effectiveness of neural network training process, the group of input parameters was changed so as to eliminate those to which the sensitivity of the model was the lowest. This allowed the selection of the optimal configuration of training pairs for which the estimation error was on the acceptable level. Finally, models of neural networks were selected, for which the training and testing error did not exceed 10%. The demonstrated effectiveness allows to conclude that the proposed set of universal input parameters is suitable for efficient training of a single neural network model capable of predicting the compressive strength of various types of corrugated packaging.