bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Prognostic Risk Model for Necroptosis-associated Genes in Acute Lymphoblastic Leukemia
Authors: Liu Yueyao , Gou Lin , Ma Zhi-gui 
Published: January 2023

Abstract
Background
Acute lymphoblastic leukemia (ALL) is a hematological malignancy with high heterogeneity that develops in both children and adults. Necroptosis is a newly recognized form of cell death. Nevertheless, the prognostic significance and functions of necroptosis-related genes (NRGs) in ALL have not received sufficient attention. This study aimed to evaluate the association between NRGs levels and ALL prognosis using publicly available datasets.
Methods
RNA-sequencing (RNA-seq) data and clinical information for ALL patients were obtained from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. Univariate Cox and LASSO regression analyses were applied to select prognosis-related genes for the construction of a prognostic risk-scoring model. Internal and external validation proved the model efficient. Furthermore, we explored the correlation of the prognostic risk model with immune infiltration and drug resistance.
Results
A total of 7 necroptosis-related genes (NRGs), namely BIRC2, PKP3, MERTK, KL, ESR2, TLE6, and TET2, were used to construct a survival prognostic model. The model exhibited excellent performance in the TARGET cohort and validation group and had good prediction accuracy in screening out high-risk ALL patients. Functional analysis showed that tumor immune microenvironment and drug resistance differed between high- and low-risk groups.
Conclusion
Our NRGs risk score model is a promising strategy for the prediction of ALL patients’ prognosis.
Is it possible to derive a mathematical physical form for Euler’s formula in the reality of complex harmonic oscillator?
Authors: Sanduk Mohammed 
Published: January 2023

Abstract

Euler’s formula is a pure mathematical formula. In spite of its nonphysical nature, the form of this formula has a genuine fundamental role in quantum mechanics, but with no physical reason for this role. Philosophically, Heisenberg has proposed Kantian ideas in physics like “nature in itself”, unobservable nature, and “nature as appears”. He proposed a possibility of mathematical formulation for a system in nature in itself. In the present work, a mathematical model of rolling circles in real space has been proposed as a model for a system in nature in itself. Observation process acts as a transformation of the system to a model in observable nature. Partial observation transforms the real position vector of a point in that system to a form similar to the Euler’s formula. That causes the appearance of the imaginary unit. Interestingly, the transformed real kinematical forms exhibit similarity with the forms of relativistic quantum mechanics.
The impact of renewable energy consumption and technology progress on CO2 emissions in the long run: Evidence from Turkey
Authors: Mukhtarov Shahriyar 
Published: January 2023

Abstract
This paper analyzes the impact of renewable energy consumption, TFP as proxy of technology progress, income, imports and exports on consumption-based CO2 emissions for the Turkey from 1990 to 2019, utilizing the ARDL method. The findings indicated that use of renewable energy, TFP and exports have a negative influence on CO2 emissions. On the other hand, the positive impact of income and import on CO2 emissions were found. The negative impact of renewable energy consumption and TFP highlights the importance of implementing environmentally friendly measures in both the energy sector (in particular, raising the proportion of renewable energy in overall energy consumption) and technology innovation.
Management of Potato Brown Rot Disease by Chemically and Eco-Friendly Produced CuO-NPs, MgO-NPs
Authors: Rabea Amira , Naeem E. , Balabel Naglaa M. , Daigham Ghadir 
Published: January 2023

Abstract
Background: In terms of production and consumption, the potato crop is one of the major vegetables in Egypt. The brown rot disease causes enormous losses to the potato industry every year. To lower the risk of pesticide residues, this study focuses on the effective suppression of R. solanacearum, the agent responsible for brown rot disease in potatoes, both in vitro and in vivo with efficient, economical, and environmentally friendly medication CuO and MgO metal oxide nanoparticles.
Results: In the current study, CuO and MgO metal oxide nanoparticles were produced using a simple chemical process. Using UV-visible spectroscopy, TEM, the Zeta potential, X-ray diffraction (XRD), and Infrared spectroscopy using Fourier transform (FTIR), the average particle size, the morphology, and the structure of nanoparticles were investigated. Antibacterial effects against R. solanacearum's growth were strongly suppressed by CuO-NPs and MgO-NPs at 3 mg/mL; ZOI measured 19.3 mm, and 17 mm, respectively. The (MIC) stands for minimum inhibitory concentration while (MBC) stands for minimum bactericidal concentration for CuO-NPs and MgO-NPs, respectively, they were measured to be 0.5, 0.6, and 0.6, 0.75 mg/mL. As-prepared CuO-NPs and MgO-NPs at MIC concentrations considerably reduced the disease occurrence to 71.2% and 69.4%, respectively, as opposed to 43.0% and 39.5% persisted in the bulk CuSO4 and bulk MgSO4, according to in-vivo application verified by seed dressing with tuber soaking application. As compared to infected plants, the yield, total chlorophyll content, and enzyme efficiency of potatoes all increased significantly. After interactions with CuO-NPs and MgO-NPs, lipid peroxidation and ultrastructural investigations using transmission electron microscopy (TEM) demonstrated that the cytomembrane of bacteria was severely harmed by nanomechanical forces.
Conclusion: The promising CuO-NPs and MgO-NPs for use as intelligent substances for agriculture management of the plant pathogen since it paves the way for future investigations on the use of metal oxide nanoparticles as risk-free options to treat plant diseases that are the biggest challenges. Consequently, the notable increase in the yield of the potato crop, photosynthetic pigments, enzymatic activity, and total phenol promote resistance to the Ralstonia solanacearum compared to the infected control.
High expression of CXCL9 gene promotes immune invasion and improves the prognosis of patients with endometrial cancer
Authors: Zhang Meng , Li Ruiping , Zhang Shan , Wang Yunyun , Zhang Jiaxi , Guo Yuzhen 
Published: January 2023

Abstract
Objective: CXCL9 plays a key role in immune cell chemotaxis and inhibition of tumor angiogenesis. The aim of this study was to investigate the prognostic value of CXCL9 in endometrial cancer (EC) and the impact on the immune microenvironment.
Methods：RNA sequencing data for EC patients were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, while clinicopathological information for EC patients was obtained from the TCGA database. Cox univariate and multivariate analyses were used, followed by the construction and validation of nomograms. CXCL9 expression and survival analysis, gene correlation and immune infiltration correlation analysis, and pathway enrichment analysis were performed using UALCAN, Kaplan-Meier, GeneMANIA, STRING, TIMER, cBioPortal, muTarget, CIBERSORT, TISIDB, GO, KEGG and GSEA tools.
Results：CXCL9 was significantly upregulated in EC. Cox univariate and multivariate analysis showed that CXCL9 was an independent predictor of overall survival (OS), disease specific survival (DSS) and progression free interval (PFI) (P<0.05). However, increased CXCL9 expression predicted prolonged OS, DSS and PFI (P<0.05). In addition, CXCL9 was positively correlated with immune cell infiltration and correlated with marker genes of multiple immune pathways as well as marker genes of immune checkpoints. GSEA enrichment analysis suggests that high CXCL9 expression plays an important role in immune cell migration, activation and other functions.
Conclusion: The results of this study suggest that high CXCL9 expression was a predictor of good prognosis in patients with EC and may be associated with the recruitment of immune cells to the tumor microenvironment in the tumor tissue to function as an anti-tumor immune response.
Criticality of isolation valves in water distribution networks with hydraulics and topology
Authors: Wéber Richárd , Huzsvár Tamás , Déllei Ákos , Hős Csaba 
Published: January 2023

Abstract

Purpose:Occasional, random pipe bursts are inevitable in water distribution networks; thus, the proper operation of isolation valves is critical. The damaged segment is segregated using the neighbouring valves during shutdown, causing the smallest isolation possible. This study analyses the importance of isolation valves individually from the perspective of the demand shortfall increment.Methods:An in-house, open-source software called STACI performs demand-driven simulations to solve the hydraulic equations with pressure-dependent demand determining the nodal pressures, the volumetric flow rates, and the consumption loss. The system has an additional consumption loss if an isolation valve cannot be closed. The criticality of an isolation valve is the increment in the relative demand shortfall caused by its malfunction. Moreover, centrality indices from complex network theory are applied to estimate the criticality without the need for computationally expensive hydraulic simulations.Results:The distribution of criticality values follows a power-law trend, i.e. some of the isolation valves have significantly higher importance during a shutdown. Moreover, Spearman's rank correlation coefficients between the centrality and criticality values indicate limited applicability.Conclusion:The criticality analysis can highlight which isolation valves have higher importance during reconstruction planning or maintenance. The Katz and the Degree centrality show a moderate positive correlation to the criticality, i.e., if numerous hydraulic simulations are not feasible, these quantities give an acceptable estimation.
Improving reproductive health literacy of couples on the verge of marriage By using the FOCUS-PDCA model
Authors: Dabiri Fatemeh , Hajian Sepideh , Zayeri Farid , Teshnizi Saeed Hosseini , Fashami Mahta Abbasi 
Published: January 2023

Abstract
Background: Education and counseling during marriage is an opportunity to raise some issues needed by couples on the verge of marriage. This study was conducted with the aim of improving reproductive and sexual health literacy of couples on the verge of marriage.
Methods: The current study was participatory action research conducted based on the Find.Organize.Clarify.Understand.Select-Plan.Do.Check.Act (FOCUS-PDCA) model in 9 steps during 2019-2020 in the city of Bandar Abbas. According to the steps of this model, a qualitative study was conducted to examine the views of service providers and couples on the verge of marriage regarding the strengths and weaknesses of the training content and the way of providing the training. Then, the process of providing service to couples was designed, implemented, and evaluated based on the results. The Reproductive Health Literacy Scale and the Service Quality (SERVQUAL) Questionnaire were used to evaluate the interventions. Data were analyzed by SPSS version 26. A significance level of less than 0.05 was considered.
Results: The mean age of women and men participating in the quantitative part of the study was 21 ± 5 and 25.84 ± 3.9 years, respectively, which was similar to their counterparts in this part of the study, and the difference in the mean scores of reproductive health literacy before and after the changes in the program showed a significant difference (p>0.001). The study results showed that, except for the understanding dimension, most participants were at an insufficient level in other dimensions of reproductive health literacy. The result of measuring the satisfaction of service recipients indicated good satisfaction in the two dimensions of warranty and accountability, and there was a gap in empathy, assurance, and tangibility dimensions, which the biggest gap was related to the empathy dimension.
Conclusion: The changes made in improving the reproductive health literacy of couples were effective, which can be taken into consideration based on the added items in the current program of providing educational services in marriage preparation classes for couples.
Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry
Authors: Bai Nan , Adeshina Yusuf , Bychkov Igor , Xia Yan , Gowthaman Ragul , Miller Sven , Gupta Abhishek , Johnson David , Lan Lan , Golemis Erica , Makhov Peter , Xu Liang , Pillai Manoj , Boumber Yanis , Karanicolas John 
Published: January 2023

Abstract
RNA-binding proteins (RBPs) are key post-transcriptional regulators of gene expression, and thus underlie many important biological processes. Here, we developed a strategy that entails extracting a "hotspot pharmacophore" from the structure of a protein-RNA complex, to create a template for designing small-molecule inhibitors and for exploring the selectivity of the resulting inhibitors. We demonstrate this approach by designing inhibitors of Musashi proteins MSI1 and MSI2, key regulators of mRNA stability and translation that are upregulated in many cancers. We report this novel series of MSI1/MSI2 inhibitors is specific and active in biochemical, biophysical, and cellular assays. This study extends the paradigm of "hotspots" from protein-protein complexes to protein-RNA complexes, supports the "druggability" of RNA-binding protein surfaces, and represents one of the first rationally-designed inhibitors of non-enzymatic RNA-binding proteins. Owing to its simplicity and generality, we anticipate that this approach may also be used to develop inhibitors of many other RNA-binding proteins; we also consider the prospects of identifying potential off-target interactions by searching for other RBPs that recognize their cognate RNAs using similar interaction geometries. Beyond inhibitors, we also expect that compounds designed using this approach can serve as warheads for new PROTACs that selectively degrade RNA-binding proteins.
Structure of an endogenous mycobacterial MCE lipid transporter
Authors: Chen James , Fruhauf Alice , Fan Catherine , Ponce Jackeline , Ueberheide Beatrix , Bhabha Gira , Ekiert Damian 
Published: January 2023

Abstract
To replicate inside human macrophages and cause the disease tuberculosis, Mycobacterium tuberculosis (Mtb) must scavenge a variety of nutrients from the host1,2. The Mammalian Cell Entry (MCE) proteins are important virulence factors in Mtb1,3, where they are encoded in large gene clusters and have been implicated in the transport of fatty acids4–7 and cholesterol1,4,8 across the impermeable mycobacterial cell envelope. Very little is known about how cargos are transported across this barrier, and how the ~10 proteins encoded in a mycobacterial mce gene cluster might assemble to transport cargo across the cell envelope remains unknown. Here we report the cryo-EM structure of the endogenous Mce1 fatty acid import machine from Mycobacterium smegmatis, a non-pathogenic relative of Mtb. The structure reveals how the proteins of the Mce1 system assemble to form an elongated ABC transporter complex, long enough to span the cell envelope. The Mce1 complex is dominated by a curved, needle-like domain that appears to be unrelated to previously described protein structures, and creates a protected hydrophobic pathway for lipid transport across the periplasm. Unexpectedly, our structural data revealed the presence of a previously unknown subunit of the Mce1 complex, which we identified using a combination of cryo-EM and AlphaFold2, and name LucB. Our data lead to a structural model for Mce1-mediated fatty acid import across the mycobacterial cell envelope.
Prognostic nutritional index as a potential prognostic marker for pancreatic cancer after distal pancreatectomy: A single-center, retrospective cohort study
Authors: Zhou Enliang , Zhao Chongyu , Li Xiaohui , Cui Bokang 
Published: January 2023

Abstract
Background
Inflammation plays a crucial role in tumorigenesis, angiogenesis, and metastasis. Although many nutrition–inflammation markers have been identified as potential prognostic factors for various cancers, the role of these markers in predicting the prognosis and recurrence of pancreatic body and tail cancer (PBTC) after distal pancreatectomy remains unclear.
Methods
A total of 102 patients diagnosed with PBTC after surgical resection were enrolled in this study. The prognostic nutritional index (PNI), neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR), lymphocyte-to-C-reactive protein ratio (LCR), systemic immune-inflammation index (SII), and platelet-to-lymphocyte ratio (PLR) were evaluated to identify a suitable nutrition–inflammation marker. A multivariate Cox regression model was used to analyze the predictive factors of overall survival (OS) and progression-free survival (PFS). Time-dependent receiver operating characteristic curves were plotted to compare the predictive ability of the abovementioned nutrition–inflammation markers.
Results
Multivariate analysis revealed that PNI was the only independent predictor of OS (P = 0.039) and PFS (P = 0.001) in patients with PBTC after surgical resection. The predictive accuracy of PNI was superior to that of other nutrition–inflammation markers. Additionally, perineural invasion and R0 resection were identified as independent predictive factors for OS (P = 0.002, P = 0.006, respectively) and PFS (P = 0.001, P < 0.001, respectively), and NLR (P = 0.003), T stage (P = 0.038), and lymph node metastasis (P = 0.046) were identified as independent predictive factors for PFS.
Conclusion
PNI is an efficient nutrition–inflammation marker for predicting the prognosis and recurrence of PBTC after surgical resection. Patients should be stratified based on PNI before resection. Compared with patients with higher PNI values, those with lower PNI values require more frequent postoperative surveillance.
Chemoenzymatic indican for sustainable light-driven denim dyeing
Authors: Bidart Gonzalo , Teze David , Jansen Charlotte , Pasutto Eleonora , Putkaradze Natalia , Sesay Anna-Mamusu , Fredslund Folmer , Leggio Leila Lo , Ögmundarson Olafur , Sukumara Sumesh , Qvortrup Katrine , Welner Ditte 
Published: January 2023

Abstract

Blue denim, a billion-dollar industry, is currently dyed with indigo in an unsustainable process requiring harsh reducing and alkaline chemicals. Several innovations aim to replace the damaging chemicals and processes with ecologically attractive alternatives, but the economic and social aspects of sustainability are often overlooked, resulting in poor implementation. Forming indigo directly in the yarn through indican (indoxyl-β-glucoside) is a promising route with mild conditions. However, a sustainable source of indican is missing. We employed enzyme and process engineering guided by techno-economic analyses to develop an economically viable drop-in indican synthesis technology. Engineering of PtUGT1, a glycosyltransferase from the indigo plant, alleviated the severe substrate inactivation observed at the titers needed for bulk production. We further discovered a mild, light-driven dyeing process. Techno-economic, social sustainability, and comparative life-cycle assessments showed that these novel technologies have the potential to significantly reduce dyeing impacts.
Hepatocellular carcinoma (HCC) Tumor microenvironment is more suppressive than colorectal cancer liver metastasis (CRLM) Tumor microenvironment.
Authors: Santagata Sara , Castaldo Daniela , Rea Giuseppina , Napolitano Maria , Capiluongo Anna , D'Alterio Crescenzo , Trotta Anna Maria , Ieranò Caterina , Portella Luigi , Tatangelo Fabiana , Albino Vittorio , Guarino Rita , Cutolo Carmen , Izzo Francesco , Scala Stefania 
Published: January 2023

Abstract
Background and purpose: HCC is inflammation-associated cancer and develops on chronic inflamed liver while CRLM develop on permissive healthy liver microenvironment. To evaluate the immune aspects of these two different environments, peripheral blood-(PB), peritumoral-(PT) and tumoral tissues-(TT) from HCC and CRLM patients were evaluated.
Methods: 40 HCC and 34 CRLM were enrolled and freshly TT, PT and PB were collected at the surgery. PB-, PT- and TT-derived CD4+CD25+ Tregs and PB-derived CD4+CD25− Teffector cells (Teffs) were isolated and characterized for phenotype and function. Tregs function was evaluated in the presence of Peptide-R29, AMD3100 or anti-PD-1. RNA was extracted from PB/PT/TT-tissues and tested for FOXP3, CXCL12, CXCR4, CCL5, IL-15, CXCL5, Arg-1, N-cad, Vim, CXCL8, TGFb and VEGF-A expression.
Results: In HCC/CRLM-PB higher number of functional Tregs, CD4+CD25hiFOXP3+ were detected, although PB-HCC Tregs exert a more suppressive function as compared to CRLM-Tregs. In HCC/CRLM-TT Tregs were highly represented with Activated/ENTPD-1+Tregs prevalent in HCC. As compared to CRLM, HCC overexpressed CXCR4 and N-cadherin/Vimentin in a contest rich of arginase and CCL5. Monocytic-MDSCs were highly represented in HCC/CRLM while high Polymorphonuclear-MDSCs were detected only in HCC. Interestingly, CXCR4-PB-Tregs inhibition, through the inhibitor-R29, impaired Tregs function in HCC/CRLM.
Conclusion: in HCC and CRLM, peripheral blood, peritumoral and tumoral tissues-Tregs are highly represented and functional. Nevertheless, HCC display a more immunosuppressive TME due to Tregs, MDSCs, intrinsic tumor features (CXCR4, CCL5, arginase) and the contest in which it develops. As CXCR4 is overexpressed in HCC/CRLM tumor/TME cells, CXCR4 inhibitors may be considered for double hits therapy in liver cancer patients.
To investigate the crystalline grain size, morphological structure and microwave properties of PANI/PbO composite materials
Authors:   Nagajyoti1, B Manjunatha ,   B T Vijaykumar3, Lagashetty Arunkumar , shetty Aparna , Kalayne Sangshetty 
Published: January 2023

Abstract

PANI/PbO was prepared by with the help of chemical oxidative polymerisation method and hcl acts as an oxidant agent. The above prepared composite material were characterised by the structural properties carried out X-ray diffraction (XRD), morphological properties by (SEM) and also microwave properties.
Gut microbiota and diet matrix modulate the effects of the flavonoid quercetin on atherosclerosis
Authors: Rey Federico , Kasahara Kazuyuki , Kerby Robert , Cross Tzu-Wen , Everhart Jessica , Kay Colin , Bolling Bradley , Bäckhed Fredrik 
Published: January 2023

Abstract

Gut bacterial metabolism of dietary flavonoids results in the production of a variety of phenolic acids, whose contributions to health remain poorly understood. Here, we show that supplementation with the commonly consumed flavonoid quercetin impacted gut microbiome composition and resulted in a significant reduction in atherosclerosis burden in conventionally-raised (ConvR) Apolipoprotein E (ApoE) knockout (KO) mice fed a high- MAC (microbiota-accessible carbohydrates) diet. However, this effect was not observed in animals consuming a defined diet containing low levels of MAC. Furthermore, we found that the effect of quercetin on atherosclerosis required gut microbes, as supplementation of this flavonoid to germ-free (GF) ApoE KO mice consuming the high-MAC diet did not affect the development of atherosclerosis. Metabolomic analysis revealed that consumption of quercetin significantly increased plasma levels of benzoylglutamic acid and protocatechuic acid in ConvR mice exposed to the high-MAC diet, while these increases were not observed in GF mice or conventional animals consuming the low- MAC diet supplemented with the flavonoid. Furthermore, levels of these metabolites were negatively associated with atherosclerosis burden. Altogether, these results suggest that the beneficial effects of quercetin on atherosclerosis are influenced by gut microbes and dietary MAC.