bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Immune-associated lncRNA Signature Predicts the Survival of Patients With Head and Neck Squamous Cell Carcinoma
Authors: Wang Jian , Bian Qinjiang , Liu Jialin , Du Lijuan , Moming Adili 
Published: August 2021

Abstract
BackgroundThe malignant progression and treatment resistance of head and neck squamous cell carcinoma are closely related to the tumor immune microenvironment. Long non-coding RNA (lncRNA) plays a regulatory role in this process and may be exploited as new signatures for head and neck squamous cell carcinoma(HNSCC) diagnosis, prognosis, and treatment.MethodsHNSCC transcriptome data was abstracted from the Cancer Genome Atlas (TCGA) data resource, and uncovered immune-linked lncRNA through co-expression analysis. Besides, univariate along with Lasso penalty regression were employed to determine immune-linked lncRNA pairs with different expressions. We then compared area under the curve, calculated the Akaike information criterion (AIC) value of the receiver operating characteristic curve for 5 years, determined cutoff points, and established an optimal predictive model for identifying high- and low-risk HNSCC patients. Then, we evaluated these patients with high- and low-risk HNSCC in terms of survival, clinic-pathological characteristics, tumor-infiltrating immune cells, chemotherapeutic efficacy, and immunosuppressed biomarkers.ResultsThis study included 545 samples. By co-expression analysis of known immune-linked genes and lncRNAs, a total of 809 immune-related lncRNAs were collected. 77 differentially expressed immune-related lncRNAs were identified (logFC>2,FDR<0.01). The identified differentially-expressed immune-linked lncRNAs were used to develop differential immune-linked lncRNA pairs. Univariate and modified Lasso regression analysis identified 40 differentially expressed immune linked lncRNAs pairs, 17 of which were incorporated in the Cox proportional hazard model by a stepwise approach. The signature could well predict the survival of patients, and the area under the receiver operating characteristic (ROC) of 17 lncRNA pairs predicted 1, 3, and 5-year survival rates (AUC) were all greater than 0.74. Kaplan-Meier analysis found that patients at low risk had longer survival than those in the high-risk group (p<.001). In addition, T stage, survival status, N stage, and clinical stage, were remarkably linked to the risk. The high- and low risk groups were correlated with tumor invading immune cells like macrophages, CD8+ T-cells, monocytes, along with CD4+ T-cells. ICI-related biomarker correlation analysis showed high risk scores were positively linked to high CDK8 expression (p<0.001) and negatively correlated with BTLA , LAG3 and PDCD1 (p<0.001). High-risk scores were correlated with lower IC50 for chemotherapeutics like Docetaxel (p<0.01), indicating that this model can predict chemotherapeutic efficacy.ConclusionsOur results offer promising prospects for identifying innovative molecular targets of immunotherapy and to improve therapeutic approaches for head and neck squamous cell carcinoma patients.
Measurements of the Planck length from a Ball-Clock without Knowledge of Newton’s Gravitational Constant G or the Planck Constant
Authors: haug espen 
Published: August 2021

Abstract
In this paper we show how one can extract the Planck length from ball with a built-in stopwatch with no knowledge of the Newtonian gravitational constant or the Planck constant. This is remarkable as until recently it has been assumed one cannot find the Planck length without knowledge of Newton’s gravitational constant. This method of measuring the Planck length should also be of great interest to not only physics researchers but also to physics teachers and students as it conveniently demonstrates that the Plank length is directly linked to gravitational phenomena, not only theoretically, but practically. To demonstrate that this is more than a theory we report 100 measurements of the Planck length using this simple approach. We will claim that, despite the mathematical and experimental simplicity, our findings could be of great importance in better understanding the Planck scale, as our findings strongly support the idea that to detect gravity is to detect the e↵ects from the Planck scale indirectly.
Computational Study of the Dissolution of Cellulose into Single Chains: the Role of the Solvent and Agitation
Authors: Bering Eivind , Torstensen Jonathan , Lervik Anders , de Wijn Astrid S. 
Published: August 2021

Abstract
We investigate the dissolution mechanism of cellulose using molecular dynamics simulations in both water and a mixture solvent consisting of water with Na + , OH - and urea. As a first computational study of its kind, we apply periodic external forces that mimic agitation of the suspension. Without the agitation, the bundles do not dissolve, neither in water nor solvent. In the solvent mixture the bundle swells up with significant amounts of urea entering the bundle, as well as more water than in the bundles subjected to pure water. We also find that the mixture solution stabilizes cellulose sheets, while in water these immediately collapse into bundles. Under agitation the bundles dissolve more easily in the solvent mixture than in water, where sheets of cellulose remain that are bound together through hydrophobic interactions. Our findings highlight the importance of urea in the solvent, as well as the hydrophobic interactions, and are consistent with experimental results.
Bioinformatic Modelling of SARS-CoV-2 Pandemic With a Focus on Country-Specific Dynamics
Authors: Liu Jakub , Suchocki Tomasz , Szyda Joanna 
Published: August 2021

Abstract
One of the seminal events since 2019 has been the outbreak of the SARS-CoV-2 pandemic. Countries have adopted various policies to deal with it, but they also differ in their socio-geographical characteristics and in the public health care facilities. The aim of our study was to investigate differences between epidemiological parameters across countries. The analysed data represents SARS-CoV-2 repository provided by the Johns Hopkins University. Separately for each country we estimated recovery and mortality rates using the SIRD model applied to the first 30, 60, 150 and 300 days of the pandemic. Moreover, a mixture of normal distributions was fitted to the number of confirmed cases and deaths during the first 300 days. The estimates of peaks’ means and variances were used to identify countries with outlying parameters. For the period of 300 days Belgium, Cyprus, France, the Netherlands, Serbia and the UK were classified as outliers by all three outlier detection methods. Yemen was classified as an outlier for each of the four considered timeframes, due to high mortality rates. During the first 300 days of the pandemic the majority of countries underwent three peaks in the number of confirmed cases, except Australia and Kazakhstan with two peaks.
Impact of Different Ventilation Strategies on Gas Exchanges and Circulation During Prolonged Mechanical Cardio-Pulmonary Resuscitation in a Porcine Model
Authors: FRITZ Caroline , JAEGER Deborah , LUO Yun , LARDENOIS Emilie , BADAT Bilal , ROQUET Florian Eric , RIGOLLOT Marceau , KIMMOUN Antoine , TRAN N'Guyen , RICHARD Jean-Christophe , CHOUIHED Tahar , LEVY Bruno 
Published: August 2021

Abstract
Background: Optimal ventilation during cardio-pulmonary resuscitation (CPR) is still controversial. Ventilation is expected to provide sufficient arterial oxygen content and adequate carbon dioxide removal, while minimizing the risk of circulatory impairment. The objective of the present study was to compare three ventilation strategies in a porcine model during mechanical continuous chest compressions (CCC) according to arterial oxygenation and hemodynamic impact. MethodVentricular fibrillation was induced and followed by five no-flow minutes and thirty low-flow minutes resuscitation with mechanical-CCC without vasopressive drugs administration. Three groups of eight Landras pig were randomized according to the ventilation strategy: i) Standard volume-control mode (SD-group); ii) bi-level pressure mode (CPV-group); iii) continuous insufflation with Boussignac Cardiac-Arrest Device (BC-group). We assessed i) arterial blood gases, ii) macro hemodynamics, iii) tissular cerebral macro and micro-circulation and iiii) airway pressure, minute ventilation at baseline and every five minutes during the protocol. Results: Arterial PaO2 level was higher at each measurement time in SD-group (>200mmHg) compare to CPV-group and BC-group (p<0.01). In BC-group, arterial PaCO2 level was significantly higher (>90mmHg) than in SD and CPV groups (p<0.01). There was no difference between groups concerning hemodynamic parameters, cerebral perfusion and microcirculation. Conclusion: Ventilation modalities in this porcine model of prolonged CPR influence oxygenation and decarboxylation without impairing circulation and cerebral perfusion.
The Spin-Dependent Properties of Silicon Carbide/Graphene Nanoribbons Junctions with Vacancy Defects
Authors: Khanlar Golnaz , Vishkayi Sahar Izadi , Soleimani H. Rahimpour 
Published: August 2021

Abstract
We have designed high-efficient spin-filtering junctions composed of graphene and silicon carbide nanoribbons. We have calculated the spin and charge transport in the junction by non-equilibrium Green’s function formalism combined with the density functional theory to find its spin-dependent electrical conductance, thermal conductance and Seebeck coefficient. In addition, the effect of Si and C atoms vacancies on the transport properties of the junction has been carefully investigated. The enhanced spin-filtering is clearly observed due to the edge and vacancy effects. On the other hand, vacancy defects increase the electrical and spin conductances of the junctions. The results show that the considered junctions are half-metal with reduced thermal conductance which makes them a suitable spin-dependent thermoelectric device. Our results predict the promising potential of the considered junctions for application in spintronic devices.
The Role of Anterior Bladder Flap Neourethra (ABFN) in Early Urinary Continence after Laparoscopic Radical Prostatectomy The Anterior Bladder Flap Neourethra (ABFN) in RP
Authors: Xu Zhibin , Guo MaoMao , Bian Hao , Li Zhenchi , Wang Chen , Hong Zengxu , Wang Jiangping 
Published: August 2021

Abstract
Purpose

To evaluate the impact of anterior bladder flap neourethra (ABFN) technique on early urinary continence after laparoscopic radical prostatectomy(RP).
Materials and Methods

Forty patients who underwent laparoscopic RP January 2019 to January 2021 were prospectively randomized into two groups: the ABFN group (n = 20) and the control group (n = 20). We compared continence rates and ICIQ-SF at 1d, 30 d, 90 d and 180 d after catheter removal. In addition, the urethral pressure of two groups, the length and thickness of neourethra in the ABFN group were measured at one week after catheter removal.
Results

The ABFN group had marked improvement incontinence rates at 1d, 30d and 90d after catheter removal vs the control group, while had the nearly same continence rate at 180 d. ICIQ-SF scores of the ABFN group were lower than the control group. Maximal urethral pressure (MUP), functional urethral length (FUL) and functional urethral area (UFA) for the ABFN group has significantly improvement than the control group. MRI showed that the neourethral length of the ABFN group was 13.7–16.2 mm, the thickness was 3.6–5.2 mm.
Conclusions

The ABFN technique markedly improved the early continence rate after laparoscopic RP.
Multi-Omics Analysis Defines 5-Fluorouracil Drug Resistance in 3D Hela Carcinoma Cell Model
Authors: Wang Lin , Wang Xueting , Wang Tong , Zhuang Yingping , WANG GUAN 
Published: August 2021

Abstract
Cervical cancer is a serious health problem in women around the globe, with 600 thousand new cases each year. However, the use of clinical drug is seriously dampened by the development of drug resistance, which has been evidenced to be associated with metabolic reprogramming and heterogeneity in tumor cells. Efficient in vitro tumor model is essential to improve the efficiency of drug screening and the accuracy of clinical application. Multicellular tumor spheroids (MTSs) can in a way recapitulates tumor traits in vivo, thereby representing a powerful transitional model between 2D monolayer culture and xenograft. In this study, based on the liquid overlay method, a protocol for rapid generation of the MTSs with uniform size and high reproducibility in a high-throughput manner was established. As expected, the cytotoxicity results showed that there was enhanced 5-FU resistance of HeLa carcinoma cells in 3D MTSs than 2D monolayer culture with a resistance index of 5.72. In the presence of both glucose and glutamine, HeLa carcinoma cells preferentially used glutamine as the bioenergetic substrate to support cell proliferation and maintenance under all conditions, while the ubiquitous by-product ammonium might be only recycled in the 3D MTSs. Furthermore, in order to obtain a holistic view of the molecular mechanisms that drive 5-FU resistance in 3D HeLa carcinoma cells, a multi-omics study was applied to discover hidden biological regularities. It was observed that in the 3D MTSs mitochondrial function-related proteins and the metabolites of the tricarboxylic acid cycle (TCA cycle) were significantly decreased, and the cellular metabolism was shifted towards glycolysis. The differences in the protein synthesis, processing, and transportation between 2D monolayer cultures and 3D MTSs was significant, mainly in the heat shock protein family, with the upregulation of protein folding function in endoplasmic reticulum (ER), which promoted the maintenance of ER homeostasis in the 3D MTSs. In addition, at the transcript and protein level, the expression of extracellular matrix (ECM) proteins (e.g., laminin and collagen) were up-regulated in the 3D MTSs, which enhanced the physical barrier of drug penetration. Summarizing, this study formulates a rapid, scalable and reproducible in vitro model of 3D MTS for drug screening purposes, and the findings establish a critical role of glycolytic metabolism, ER hemostasis and ECM proteins expression profiling in tumor chemoresistance of HeLa carcinoma cells towards 5-FU.
Degenerative Joint Disease Induced by Repeated Intra-Articular Injections of Monosodium Urate Crystals in Rats as Investigated by Translational Imaging
Authors: Accart Nathalie , Dawson Janet , Obrecht Michael , Lambert Christian , Flueckiger Manuela , Kreider Julie , Hatakeyama Shinji , Richards Peter , Beckmann Nicolau 
Published: August 2021

Abstract
Effects of repeated injection of monosodium urate (MSU) crystals, in combination with lipopolysaccharide (LPS), into rat knee joints every two weeks for a maximum of five administrations were investigated. Joint swelling, nociception and hard/soft tissue changes were assessed longitudinally by non-invasive imaging. MSU crystals induced joint swelling, synovial membrane thickening, fibrosis of the infrapatellar fat pad, tidemark breaching, and cartilage invasion by inflammatory cells. Several inflammatory proteins were present in synovial fluid. A higher sensitivity to mechanical stimulus was detected in paws of limbs receiving MSU/LPS compared to saline-injected limbs. In MSU/LPS-challenged joints, magnetic resonance imaging (MRI) revealed increased synovial fluid volume in the posterior region of the joint, alterations in the infrapatellar fat pad reflecting a progressive decrease of fat volume and fibrosis formation, and a significant increase in the relaxation time T2 in femoral cartilage, consistent with a reduction of proteoglycan content. MRI also showed cyst formation in the tibia, femur remodeling, and T2 reductions in extensor muscles consistent with fibrosis development. Repeated intra-articular MSU/LPS injections in the rat knee joint induced pathology in multiple tissues and may be a useful means to investigate the relationship between urate crystal deposition and the development of degenerative joint disease.
Surface Quality Analysis of AZ31B Mg Alloy Sheet in Ultrasonic-Assisted Warm Single-Point Incremental Forming
Authors: Liao Juan , Zeng Xiangshou , Xue Xin 
Published: August 2021

Abstract
With a view to improving the surface quality of the magnesium (Mg) alloy at a warm temperature, the ultrasonic-assisted warm single point incremental forming (SPIF) is proposed. The surface quality of the Mg alloy during the warm SPIF is primarily affected by two parts: the orange peel patterns of the non-contact surface and the scratches and adhesive wear of the contact surface. In this work, the surface quality of the AZ31B Mg alloy sheet parts at different forming temperatures and ultrasonic amplitudes is evaluated by examining the surface roughness and topography. The results show that the generation of orange peel patterns is significantly affected by temperature. In addition, scratches and adhesive wear of the contact surface increase with the rising temperature. After applying the ultrasonic vibration (UV), the quality of both the non-contact and the contact surfaces of the parts are significantly improved, but too large ultrasonic amplitude slightly reduces the surface quality. Moreover, the microstructural examination results show that UV has a great effect on dynamic recrystallization and grain refinement, which positively affects surface quality improvement.
RETRACTED: A new method for layout layer optimization of long horizontal borehole for gas extraction in overlying strata: a case study in Guhanshan coalmine, China
Authors: Guo Wenbing , Guo Mingjie , Yuan Ruifu , Zhao Gaobo , Li Guofu , Tan Yi , Bai Erhu , Ma Zhibao 
Published: August 2021

Abstract

The authors have requested that this preprint be removed from Research Square.
Identification of novel candidate factor SNX5 specific for pregnancy failure in Holstein heifers
Authors: Kusama Kazuya , Bai Rulan , Matsuno Yuta , Ideta Atsushi , Sakurai Toshihiro , Nagaoka Kentaro , Hori Masatoshi , Imakawa Kazuhiko 
Published: August 2021

Abstract
Pregnancy loss predominantly occurs during periods between blastocyst hatching and conceptus (embryo plus extraembryonic membranes) implantation to the endometrium in cattle. Insufficient biochemical communication between conceptus and endometrium has been suspected as the primary cause for early embryonic losses. If molecules regulating this communication were identified, molecular mechanisms associated with early pregnancy success or loss could be better understood. To identify novel factors as detection markers of non-pregnant or females undergoing embryonic loss, blood sera from embryo-transferred heifers on day 7 (day 0 = day of estrus) were collected on day 17, 20, or 22, which were subjected to metabolome and global proteome iTRAQ analyses. On each sample, the metabolome analysis partly divided serum components into pregnant or not. In the iTRAQ analysis, heatmap analysis with 25 unique proteins separated into pregnant or not on day 20 or 22. Furthermore, receiver operating characteristic curve (ROC) analysis identified five candidate proteins detecting non-pregnant heifers, of which SNX5 in day 22 sera had the highest area under the curve (AUC), 0.983. We also detected SNX5 in day 22 sera from non-pregnant heifers using western blotting. These results suggest that high SNX5 in day 22 sera could predict early pregnancy loss in heifers.
iTRAQ Based Protein Profile Analysis Revealed Key Proteins Involved in Regulation of Drought-Tolerance During Seed Germination in Adzuki Bean
Authors: Han Xuesong , Yang Fangwen , Zhao Yongguo , Chen Hongwei , Wan Zhenghuang , Li Li , Sun Longqing , Liu Liangjun , Jiao chunhai , Liu Changyan , Sha Aihua 
Published: August 2021

Abstract
Adzuki bean is famous as its high-quality protein, fiber, vitamins, minerals as well as rich bioactive substances. However, it is vulnerable to drought at the germination stage. Up to date, little information is available about the genetic controls of drought tolerance during seed germination in adzuki bean. In this study, differential expression proteins（DEPs）were identified based on iTRAQ technology during seed germination between the drought-tolerant variety 17235 and drought-sensitive variety 17033 in adzuki bean. A total of 2834 proteins were identified in the two adzuki bean in the germinating seeds. Eighty-seven and eighty DEPs were increased and decreased accumulation in variety 17235 compared to 17033 under drought, respectively. Meanwhile, 132/205 and 144/123 DEPs were up- or down-regulated in 17235 and 17033 under drought compared to the control, respectively. GO, KEGG, and PPI analysis revealed that the proteins related to carbohydrate metabolism and energy production showed abundantly increase in response to drought stresses. Ectopic overexpression of one candidate encoding V-ATPase in tobacco enhanced the drought tolerance of plants. The results provide valuable insights into adzuki bean response to drought stress, and the DEPs might be applied to develop drought tolerant adzuki bean in breeding programs.
MAFB is a biomarker for cancer severity, prognostic marker, and a potential target for cancer immunotherapy
Authors: Omar Samir , Kobayashi Naohiro , Siyam Mennatullah , Yadav Manoj , Inoue Yuri , Takahashi Satoru , hamada Michito 
Published: August 2021

Abstract
MAFB is a transcription factor specifically expressed in macrophages. Using in vitro and in vivo in mouse tumor models, our previous study suggested that MAFB could be a suitable marker for tumor-associated macrophages (TAMs), besides MAFB is expressed in anti-inflammatory alternatively activated M2 macrophages in vitro. TAMs play a key role in the tumor microenvironment (TME) by inducing immunosuppression, angiogenesis, tumor invasion, and metastasis. However, finding a suitable specific biomarker and target for TAMs is challenging. Here, we demonstrated that MAFB could be used as a biomarker for TAMs and consequently, for severity in various human cancers, including lung, liver, colon, and pancreatic cancers, according to the immunohistochemical analysis of the expression of MAFB, CD68, and CD204.
Moreover, In a cohort of lung adenocarcinomas patients (n = 120), increased MAFB expression was related to increased tendency towards metastasis and poor overall survival rate. Further, we showed that MAFB expression was positively correlated to the expression of CD204 and CD68 in both human hepatocarcinoma and colon cancers. Our findings indicate that MAFB as a specific biomarker can be used as prognostic marker for Metastasis potential in Lung adenocarcinomas patients and also a biomarker for the severe Liver, Colon and pancreatic cancers. In addition, we showed that MAFB was expressed in Tumor associated macrophages expressing Programmed cell death protein-1 and/or Programmed cell death ligand 1 (TAM PD-1+ and TAM PD-L1+) cells in both human lung adenocarcinomas and Lewis lung carcinoma (LLC) mouse model. These findings indicate that MAFB can be a potential target for drug development against TAM PD-1+ and TAM PD-L1+ cells. In summary, transcriptional factor MAFB can be used as a specific biomarker, prognostic marker and a potential target for cancer immunotherapy against TAMs.