bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of WWTR1 as an immune infiltration-correlated prognostic biomarker in colon cancer
Authors: Liu Xinnong , Ge Jianshun , Tian Linlin , Zhang Jie , wang Rui , Li Haining , Ding Yanbing , Lu Guotao , Yin Xudong 
Published: April 2022

Abstract
WWTR1, a gene related to the TGF-β signaling pathway, has been elucidated to be involved in oncogenesis in multiple studies. There is, however, no research on its link to immune infiltration in colon cancer. The TCGA database has identified WWTR1, a gene related to the TGF-β signaling pathway, which is lowly expressed in colon cancer patients compared to normal subjects. Meanwhile, with GEO and the TCGA database, we produced the Kapan-Meier curve, which revealed that colon cancer patients with high WWTR1 expression had a poor prognosis. We discovered that high expression of WWTR1 in colon cancer was associated with clinical stage, pathological T-stage, and lymphatic metastasis after examining the clinical characteristics of colon cancer patients. WWTR1 was found to be an independent predictive factor for colon cancer in a multivariate Cox regression study. Infiltration of immunological cells (B cells, CD8 + T cells, CD4 + T cells, Macrophage, Neutrophil, Dendritic cells) was linked to WWTR1 expression. In colon cancer, WWTR1 expression was also found to be favorably linked with major immune cell markers. WWTR1 expression levels were associated to ameboidal-type cell migration, focal adhesion, actin binding, Chemical carcinogenesis - reactive oxygen species, Non-alcoholic fatty liver disease, and Alzheimer disease, according to an analysis of WWTR1 differentially co-expressed genes (DCGs), GO, and KEGG enrichment analysis. These findings imply that WWTR1 is a prognostically valuable and important biomarker for colon cancer, and that its expression is strongly linked to colon cancer immune infiltration, making it a potential new target for colon cancer biotherapy.
Characterization of solution blow spun poly(lactic) acid based nanofibers containing sucuk spice mix essential oils
Authors: Ozcan Iklime , SARICAOĞLU Furkan Türker , Dagdelen Adnan Fatih , Cinar Aycan , Dundar Ayse Neslihan , Tosun Fatih 
Published: April 2022

Abstract
In this study, essential oil from sucuk spice mix was incorporated into poly(lactic) acid (PLA) and nanofibers were produced via solution blow spinning (SBS). Essential oil incorporation was performed at 0, 5, 10, 15, 20, 25 and 30% (v/w) of PLA. Scanning electron microscopy (SEM), atomic force microscopy (AFM), thermal properties, antioxidant capacity, and antibacterial activity against E. coli and S. aureus were characterized. Nanofibers were not soluble in water due to the hydrophobic nature of PLA. SEM images revealed that beadles and uniform nanofibers can be produced with SBS, and essential oil addition decreased the average fiber diameter. The surface topography of nanofibers was improved by increasing essential oil concentration. Melting and glass transition temperatures decreased and the thermal stability of nanofibers increased with essential oil addition. Nanofibers containing essential oil at 30% had the highest antioxidant capacity (40.02%). Nanofibers containing 20, 25, and 30% of essential oil had greater growth inhibition against Staphylococcus aureus and Escherichia coli. As a result, PLA-based nanofibers containing sucuk spice mix essential oil can be produced with SBS, and nanofibers containing 20, 25, and 30% essential oil could be a promising system not only in drug delivery systems but also in food packaging.
One-component delocalized nonlinear vibrational modes of square lattices
Authors: Ryabov D. S. , Chechin G. M. , Naumov E. K. , Semenov A. S. , Korznikova E. A. , Dmitriev Sergey V. 
Published: April 2022

Abstract
All possible one-component delocalized nonlinear vibrational modes (DNVMs) in a square lattice are analyzed. DNVMs are obtained taking into account exclusively the symmetry of a square lattice, and therefore they exist regardless of the type of interactions between particles. In this work, the interactions of the nearest and next nearest neighbors are described by the β-FPU potential. For each DNVM, frequency, kinetic and potential energies are described as functions of amplitude. The mechanical stresses caused by DNVMs and the effect of DNVMs on the stiffness constants of the lattice are presented. DNVMs with higher vibration frequencies have a stronger effect on the mechanical properties of the lattice. Examples of analytical analysis of DNVMs are given. It is found that two of the sixteen one-component DNVMs can have frequencies above the phonon band in the entire range of their amplitudes. These DNVMs can be used to construct discrete breathers by applying localizing functions.
Bridging archaeology and marine conservation in the Neotropics
Authors: Fossile Thiago , Herbst Dannieli Firme , McGrath Krista , Toso Alice , Giannini Paulo César Fonseca , Milheira Rafael Guedes , Gilson Simon-Pierre , Ferreira Jessica , Bandeira Dione da Rocha , Haimovici Manuel , Ceretta Bruna , Bender Mariana G. , Colonese André Carlo 
Published: April 2022

Abstract
Anthropogenic impacts on tropical and subtropical coastal environments are increasing at an alarming rate compromising ecosystem function, structure and services. Understanding the scale of marine population decline and diversity loss requires a long-term perspective that incorporates information from a range of sources. The Southern Atlantic Ocean, however, represents a major gap in our understanding of pre-industrial marine species composition. Here we contribute to fill this gap by performing an extensive review of the published data on Middle and Late Holocene marine fish composition along the southern coast of Brazil. This region preserves archaeological sites that are unique archives of past socio-ecological systems and of pre-European biological diversity. We assessed snapshots of species compositions and relative abundances spanning the last 5000 years, and modelled differences in species’ functional traits between archaeological and modern fisheries. We found evidence for both generalist and specialist fishing practices in pre-European times, with large body size and body mass caught regularly over hundreds of years. Comparison with modern catches revealed a significant decline in these functional traits, possibly associated with overfishing and the escalating human impacts in recent times.
Characterization of rectal cancer: Whole-tumour histogram analysis of diffusion kurtosis imaging at 3 T
Authors: Sun Yiqun , Wang Yueming , Li Jianwen , Fu Caixia , Xin Chao , Cai Sanjun , Tong Tong , Gu Yajia 
Published: April 2022

Abstract
Purpose: This study aimed to explore the performance of whole-tumour histogram analysis of diffusion kurtosis imaging (DKI) in the characterization of rectal cancer.Methods: Forty-two rectal cancer patients were retrospectively enrolled. Histogram analysis of D, K and the conventional apparent diffusion coefficient (ADC) were calculated. Student’s t test or the Mann–Whitney U test and receiver operating characteristic (ROC) curves were used for statistical analysis.Results: The ADCSD and ADCkurtosis were significantly higher in N (+) patients than in N0 patients (p<0.05). The ADCSD, DSD and Kkurtosis were significantly higher in PNI-positive patients than in PNI-negative patients (p<0.05). Dskewness was significantly higher in KRAS mutation-type patients than in KRAS wild-type patients (p<0.05). The area under the curve (AUC) of the multiparametric ADCSD and ADCkurtosis values for the detection of metastatic lymph nodes was 0.816 (p<0.001); the sensitivity and specificity were 81.0% and 76.2%, respectively. The AUC of the multiparametric ADCSD, DSD, and Kkurtosis values for the detection of PNI was 0.830 (p<0.001); the sensitivity and specificity were 80% and 88.9%, respectively. Dskewness can be used to determine the KRAS status; the cut-off value, AUC, sensitivity and specificity were 0.465, 0.732 (p=0.010), 78.3%, and 73.7%, respectively. Conclusion: Whole-tumour histogram analysis of DKI could be used to identify both pathological and genetic characteristics of rectal cancer.
Nanometric cutting mechanism of cerium-lanthanum alloy
Authors: Zhao Chen-Yu , Lai Min , Fang Feng-Zhou 
Published: April 2022

Abstract
Molecular dynamics (MD) simulation is an effective approach to reveal the atomic-scale details of the material removal mechanism in nanometric cutting. In this study, through a MD simulation, we analyze the effects of cutting speed and cutting depth on cutting force and subsurface deformation of the cerium–lanthanum alloy during nanometric cutting. The results illustrate that the dislocations, stacking faults, and phase transitions occur on the material subsurface during the cutting process. The dislocations are mainly Shockley partial dislocation, and increasing the temperature and pressure during the cutting process leads to the transformation of γ-Ce (FCC) into β-Ce (HCP) and δ-Ce (BCC). β-Ce is mainly distributed in the stacking fault area, while δ-Ce is distributed in the boundary area between the dislocation atoms and γ-Ce atoms. The cutting speed and cutting depth are important factors affecting the distribution of subsurface damage. A thicker subsurface deformed layer on the machined surface, comprising dislocations, stacking faults, and lattice defects, is generated with an increase in the cutting speed and cutting depth. Simultaneously, the cutting speed and cutting depth significantly affect the cutting force, material removal rate, and generated subsurface state. The fluctuations in the cutting force are related to the generation and disappearance of dislocations. The higher the cutting speed and the deeper the cutting depth, the more phase-transition atoms on the subsurface.
GATA2 as an outcome signature: promoting bladder cancer migration and inhibiting PD-L1 expression
Authors: Sun Siqing , Bi Jianbin 
Published: April 2022

Abstract
BackgroundEmbryonic development is regulated by stem cells, and epithelial-to-mesenchymal transition (EMT) is associated with cell stemness ; nevertheless, the EMT regulation by embryonic development-related genes has not been studied. Immune checkpoints exert an essential effect in tumor treatment ; however, their regulatory mechanisms have not been fully elucidated. MethodsWe obtained clinicopathological and transcriptome data from The Cancer Genome Atlas. Embryonic development- associated genes were obtained from The Human Gene Database. We identified genes using univariate Cox regression analysis and identified various subtypes using consensus clustering analysis. Immunoassays were performed using the CIBERSORT package and Estimation of Stromal and Immune cells in the Malignant Tumor tissues using an expression data algorithm. The least absolute shrinkage and selection operator algorithm and multivariate Cox regression analysis were adopted to generate the prognostic model. We used the OCLR and TIDE algorithms. We conducted functional experiments.ResultsTwenty-two embryonic development-associated genes were risk factors for bladder cancer, and their expression levels significantly correlated with the TNM stage. We assessed the extent of immune infiltration, regulation of immune checkpoints, and responses to immune checkpoint blockade based on these genes. These risk genes were associated with EMT and modulated immune checkpoints. Cellular experiments demonstrated that EVC2 and GATA2 drive BLCA invasion and migration. GATA2 regulated the PD-L1 expression.ConclusionWe identified three critical genes: RUNX2, GATA2 and EVC2. These three genes are related to EMT and immune cell infiltration and are independent prognostic elements for BLCA.
Prognostic value of serum cytokeratin 19 fragments in esophageal cancer: a systematic review and meta-analysis
Authors: Zhou Jianfeng , Fang Pinhao , Li Xiaokun , Luan Siyuan , Xiao Xin , Shang Qixin , Zhang Hanlu , Yang Yushang , Zeng Xiaoxi , yuan Yong 
Published: April 2022

Abstract
Background
Growing number of evidence has shown that cytokeratin 19 fragment (cyfra21–1), one of the vital tumor biomarkers, was commonly utilized in diagnosing and predicting the prognosis of esophageal cancer (EC). The purpose of this systematic and meta-analysis was to quantitatively evaluate the association between cyfra21–1 and EC prognosis.
Methods
Relevant literature was retrieved from databases of PubMed, Web of Science, Cochrane library, and Embase. Meta-analysis was conducted using hazard ratio (HR) and 95% confidence intervals (CI) of survival outcomes as effect size to quantitatively summarize.
Results
Totally 2568 patients from 11 studies were included in this meta-analysis. The pooled HR showed that elevated cyfra21–1 serum level was associated with poorer overall survival (OS), with the pooled HR being 1.37 (95%CI: 1.21–1.56, P < 0.001). Subgroup analysis showed that evaluated cyfra21–1 serum level was also associated with a poorer prognosis. The pooled HR was 1.31 (95%CI: 1.14–1.51, P < 0.001) for those patients who had been treated with surgery and 1.65 (95%CI: 1.23–2.21, P < 0.001) for patients treated with non-surgery.
Conclusion
This meta-analysis elucidated that cyfra21–1 was a robust prognostic biomarker in EC patients. A high serum level of cyfra21–1 was associated with poorer OS in EC, indicating that cyfra21–1 may involve in the mechanism of tumor progression.
Global, neuronal, and beta-cell specific deletion of insulin inhibitory receptor (incep-tor) improves glucose homeostasis in diet-induced obese mice
Authors: Grandl Gerald , Colldén Gustav , Ansarullah Ansarullah , Xu Weiwei , Far Fataneh Fathi , Gruber Tim , Bastidas-Ponce Aimée , Zhang Qian , Novikoff Aaron , Garcia-Caceres Cristina , Tschöp Matthias , Lickert Heiko , Müller Timo 
Published: April 2022

Abstract
Our data support the hypothesis that inhibition of inceptor to sensitize INSR/IGF1R action may be a promising pharmacological target in the context of diet-induced impairments of glucose homeostasis, with the potential to avoid 𝛽-cell failure and to slow diabetes progression.
Detection of Interstitial Pneumonia with Autoimmune Features and Idiopathic Pulmonary Fibrosis Are Enhanced by Involvement of Matrix Metalloproteinases Levels and Clinical diagnosis
Authors: Sun Baoqing , Liu Mingtao , Xue Mingshan , Lin Runpei , Zeng Yifeng , Zhang Teng , Guo Baojun , Chen Youpeng , Cheng Zhangkai J. 
Published: April 2022

Abstract
Background: Higher detection of interstitial pneumonia with autoimmune features (IPAF), idiopathic pulmonary fibrosis (IPF) has significant diagnostic and therapeutic implications. Some MMPs have been reliable diagnostic biomarkers in IPAF and IPF in previous studies, yet relevant reliability remains to be recognized. Material and Methods: 36 ILD patients, including 31 IPAF patients (Mean ± SD, 50.20 ± 5.10 years; 16 (51.6%) females) and 5 IPF patients (Mean ± SD, 61.20 ± 6.73 years; 1 (20.0%) females) were retrospectively enrolled. Serial serum samples were collected from corresponding patients between January 2019 and December 2020. Notably, Serum MMPs levels were measured by U-PLEX Biomarker Group 1(Human) Multiplex Assays (MSD, USA). Results: A combination of MMPs, combinatorial biomarkers and was strongly associated with the above clinical subjects (AUC, 0.597 for Stability vs. Improvement and 0.756 for Stability vs. Exacerbation). Importantly, the AUC of MMP-12 reaches 0.730 (P<0.05, Stability AUC vs. Improvement AUC) while MMP-13 reaches 0.741 (P<0.05, Stability AUC vs. Exacerbation AUC) showed better academic performance than other MMPs in two comparisons. Conclusions: Clinical risk factors and MMPs are strongly associated with either stratification of the degree of disease of progression of IPAF or in two IPAF and IPF independent cohorts. To our knowledge, this is the first to illustrate that MMP-12 and MMP-13 may be expected to become typical promising biomarkers in Improvement - IPAF and Exacerbation - IPAF, respectively.
Non-coding RNAs in drug and radiation resistance of bone and soft tissue sarcoma: A systematic review
Authors: Chen Huan-Huan , Zhang Tie-Ning , Zhang Fang-Yuan , Zhang Tao 
Published: April 2022

Abstract
Background: Sarcomas comprise approximately 1% of all human malignancies, and treatment resistance is one of the main reasons for poor prognosis. Accumulating evidence suggests that non-coding RNAs, including microRNAs, long non-coding RNAs, and circular RNAs, are important molecules involved in the crosstalk between resistance to chemotherapy, targeted therapy, and radiotherapy via various pathways.Methods: We searched PubMed (MEDLINE) databases for articles on non-coding RNAs relevant to sarcoma from inception to November 30, 2021. Studies investigating the roles of host-derived microRNAs, long non-coding RNAs, and circular RNAs in sarcoma were included. Data on the roles of ncRNAs in therapeutic regulation and their applicability as biomarkers of sarcomas were extracted. Two independent researchers assessed the quality of the studies using modified guidelines from the Systematic Review Center for Laboratory Animal Experimentation (SYRCLE), a tool based on the Cochrane Collaboration Risk of Bias tool.Results: Observational studies revealed ectopic expression of non-coding RNAs in sarcoma patients with different responses to antitumor treatments. Experimental studies have confirmed crosstalk between cellular pathways pertinent to chemotherapy, targeted therapy, and radiotherapy resistance. Of the included studies, the SYRCLE scores ranged from 3 to 6 (average score = 4.51). This finding suggested a moderate risk of bias. Of the ten articles that investigated non-coding RNAs as biomarkers, none included a validation cohort. Selective reporting of the sensitivity, specificity, and receiver operating curves was common.Conclusion: Although non-coding RNAs appear to be good candidates as biomarkers and therapeutics for sarcoma, their differential expression across tissues complicates their application. Further investigation of the potential for inhibition or activation of these regulatory molecules to reverse treatment resistance may be useful.
Synoptic Climatology of Pre-Monsoon Severe Lightning Events in Bangladesh
Authors: Farukh Murad , Islam Md. Azharul , Uddin Md. Nasir 
Published: April 2022

Abstract
In Bangladesh, 1073 lightning deaths are reported only in May from 2010 to 2021 that accounts 34% of the total lightning death. The mean thunderstorm days are the maximum in Sylhet that accounts 9.46, 19.27, and 21.67 from March through May with the mean lightning frequency of 29.11, 70.50, and 82.55. Seasonal average temperature difference between winter and pre-monsoon in the country is quite high (7.8ºC) with a sharp jump from February to March (4.5ºC), whilst the maximum temperature peak in April (36.49ºC) indicates pre-monsoon instability. The 700hPa temperature shows a moderate correlation of 0.62 and 0.66 with lightning frequency and thunderstorm days, respectively. A strong SLP ridge from the northwest and 500hPa GpH ridge over northwest to south-eastern Bangladesh favors thunderstorm mediated severe pre-monsoon lightning. The low pressure trough over the Gangetic plains of India towards Bangladesh is a very unique characteristics for convective activities in May. The pre-monsoon lightning activity is also attributed by very strong temperature anomaly whilst the associated convective precipitation system is triggered by topographic forcing of the Shillong Plateau and Chittagong hill tracts. Southerly to south-westerly low level jet assist moisture transport from Bay of Bengal (BoB) in pre-monsoon. North to north-westerly subtropical jet stream provides conditions conducive to the development of pre-monsoon thunderstorms and resultant lightning activity. Moreover, CAPE all over the country in May destabilizes the country’s atmosphere with lots of thunderstorms. The precise information of pre-monsoon climatological anomaly can be beneficial for the management of direct-death related lightning disaster in Bangladesh.
Using the Collaborative Cross to identify the role of host genetics in defining the murine gut microbiome
Authors: Nagarajan Aravindh , Scoggin Kristin , Gupta Jyotsana , Threadgill David W. , Andrews-Polymenis Helene L. 
Published: April 2022

Abstract
Background: The human gut microbiota is a complex community comprised of trillions of bacteria and is critical for the digestion and absorption of nutrients. Bacterial communities of the intestinal microbiota influence the development of several conditions and diseases. We studied the effect of host genetics on gut microbial composition using Collaborative Cross (CC) mice, a panel of genetically diverse mouse strains. CC mice are genetically diverse across strains, but genetically identical within a given strain allowing for repetition and deeper analysis than is possible with other collections of genetically diverse mice. Results: 16S rRNA from the feces of 167 mice from 28 different CC strains was sequenced and analyzed using the Qiime2 pipeline. We observed large variance in the bacterial composition across CC strains starting at the phylum level. Using bacterial composition data, we identified 26 significant Quantitative Trait Locus (QTL) linked to 23 genera on 15 different mouse chromosomes. Genes within these intervals were analyzed for significant association with pathways and the previously known human GWAS database using Enrichr and DAVID analysis. Multiple host genes involved in obesity, glucose homeostasis, immunity, neurological diseases, and many other protein-coding genes located in these regions may play roles in determining the composition of the gut microbiota. After the collection of feces used for sequencing, a subset of CC mice was infected with Salmonella Typhimurium. Using the infection outcome data, we correlated the increase in abundance of Genus Lachnospiraceae and decrease in Genus Parasutterella to positive health outcomes after infection. Machine learning classifiers accurately predicted the CC strain and the infection outcome using pre-infection bacterial composition data from the feces. Conclusion: Our study supports the hypothesis that multiple host genes influence the gut microbiome composition and homeostasis, and that certain organisms may influence health outcomes after S. Typhimurium infection.