bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of lncRNAs and immune-related prognostic genes as thyroid cancer microenvironment biomarkers
Authors: Xia Zhongbin , Huang Haiyue , Gao Feng , Han Guangyu , Hu Yuzhe , Yu Peng , Shen Shaochen 
Published: October 2022

Abstract
Although thyroid cancer is a frequent clinical tumor, it mostly affects young individuals, with an average age of around 40 years old, in contrast to the features of general cancer in the elderly. The outcomes of patients with undifferentiated THCA are still quite bad, despite the fact that full surgical resection and radiation have greatly increased the survival rate of patients with THCA. Therefore, improved patient prognostic interventions may be made by the discovery of the immune-related prognostic gene and long noncoding RNA (lncRNA) biomarker connected to the thyroid cancer microenvironment. The research obtained mRNA and lncRNA data from the TCGA database ( https://portal.gdc.cancer.gov ) for THCA patients, and it downloaded IRGs data from Import Shared Data ( https://www.Immport.org ). Then, a weighted gene co-expression network was constructed in order to identify the main modules connected to THCA. To determine the prognosis of THCA, immune-related long non-coding RNA (IR-lncRNA) and 11 mRNA classifiers were produced after univariate Cox regression analysis of all IRGs in the core module. Furthermore, the sample was split into two groups: high-risk and low-risk groups based on the classifier's risk score calculation. Through the use of the ESTIMATE and CIBERSORT algorithms in comparison to the two groups, we investigated more closely at the THCA samples' tumor microenvironment. Finally, we discovered three small molecules that may be useful therapeutically treating THCA patients with high risk. And our findings indicate IRG and IR-lncRNA-based classifiers may serve as trustworthy prognostic indicators for THCA survival.
Flavivirus prM interacts with MDA5 and MAVS to inhibit RLR antiviral signaling
Authors: Sui Liyan , Zhao Yinghua , Wang Wenfang , Chi Hongmiao , Tian Tian , Zhang Jinlong , Zhao Yicheng , Hou Zhijun , Wei Zheng-Kai , Zhou Guoqiang , Wang Guoqing , Wang Zedong , Liu Quan 
Published: October 2022

Abstract
Background: Vector-borne flaviviruses, including tick-borne encephalitis virus (TBEV), Zika virus (ZIKA), West Nile virus (WNV), yellow fever virus (YFV), dengue virus (DENV), and Japanese encephalitis virus (JEV), pose a growing threat to public health worldwide, and have evolved complex mechanisms to overcome host antiviral innate immunity. However, the underlying mechanisms of flavivirus structural proteins to evade host immune response remain elusive.
Results: We show that TBEV structural protein, pre-membrane (prM) protein, could inhibit type I interferon (IFN-I) production. Mechanically, TBEV prM interacted with both MDA5 and MAVS and interfered with the formation of MDA5-MAVS complex, thereby impeding the nuclear translocation and dimerization of IRF3 to inhibit RLR antiviral signaling. ZIKA and WNV prM was also demonstrated to interact with both MDA5 and MAVS, while dengue virus serotype 2 (DENV2) and YFV prM associated only with MDA5 or MAVS to suppress IFN-I production. In contrast, JEV prM could not suppress IFN-I production. Overexpression of TBEV and ZIKA prM significantly promoted the replication of TBEV and Sendai virus. Conclusion: Our findings reveal the immune evasion mechanisms of flavivirus prM, which may contribute to understanding flavivirus pathogenicity, therapeutic intervention and vaccine development.
Sulfated endospermic nanocellulose crystals prevent the transmission of SARS-CoV-2 and HIV-1
Authors: Barriga Enrique Javier Carvajal , Fitzgerald Wendy , Dimitriadis Emilios K. , Margolis Leonid , Fields R. Douglas 
Published: October 2022

Abstract
Biomaterials with antimicrobial activity are gaining attention due to their biodegradability and efficacy in interacting with a wide range of microorganisms. A new cellulose nano-biomaterial, endospermic nanocellulose crystals (ENC) obtained from parenchymal tissue of ivory nut endosperm, has a natural capacity as a universal binder. This feature is enhanced when it is chemically functionalized, and can be exploited in the fight against microbes.
We tested the ability of sulfated ENC in aqueous suspension to encapsulate viruses through a crosslinking reaction mediated by cations. 0.25% w/v ENC suspensions efficiently encapsulated spike (S) protein, preventing its interaction with ACE2 receptor. ENC was further able to encapsulate SARS-CoV-2 pseudoviruses and prevent infection of 293T-ACE2 cells. ENC also suppressed infection of MT-4 cells with HIV-1LAI.04. This antiviral activity of sulfated ENC is due to the irreversible interaction of ENC with viral particles mediated by crosslinking, as antiviral activity was less effective in the absence of cations. Additionally, ENC was used as a matrix to immobilize recombinant ACE2 receptors and anti-S IgG, creating molecular lures that efficiently inhibited SARS-CoV-2 infections in vitro. These results show that sulfated ENC from ivory nuts can be used as an efficient antiviral material.
Concurrently mapping quantitative trait loci associations from multiple subspecies within hybrid populations
Authors: Warburton Christie , Costilla Roy , Engle Bailey , Moore Stephen , Corbet Nicholas , Fordyce Geoffry , McGowan Michael , Hayes Ben 
Published: October 2022

Abstract
Many of the world’s agriculturally important plant and animal populations consist of hybrids of subspecies. Cattle in tropical and sub-tropical regions for example, originate from two genetically distinct subspecies, Bos indicus and Bos taurus. Methods to derive the underlying genetic architecture for these two subspecies are essential to develop accurate genomic predictions in these hybrid populations. We propose a novel method to achieve this. First, we use haplotypes to assign single nucleotide polymorphism (SNP) alleles to ancestral subspecies-of-origin in a multi-breed and multi-subspecies population. Then we use a BayesR framework to allow SNP alleles originating from the different subspecies to have different effects (unequal variances). Applying this method in a composite population of B. indicus and B. taurus hybrids, our results show that there are underlying genomic differences between the two subspecies, and these effects are not identified in multi-breed genomic evaluations that do not account for subspecies-of-origin effects. The method slightly improved the accuracy of genomic prediction. More significantly, by allocating SNP alleles to ancestral subspecies-of-origin, we were able to identify four SNP with high posterior probabilities of inclusion that have not been previously associated with cattle fertility and were very close to genes associated with fertility in other species. These results show that haplotypes can be used to trace subspecies-of-origin through the genome of this hybrid population and, in conjunction with our novel Bayesian analysis, subspecies SNP allele allocation can be used to increase the accuracy of quantitative trait loci (QTL) association mapping in genetically diverse populations.
Diffusion-free Valve for Pre-programmed Immunoassay With Capillary Microfluidics
Authors: Cabot Joan , Azizian Pooya , Casals-Terré Jasmina , Ricart Jordi 
Published: October 2022

Abstract
By manipulating the geometry of the microfluidic channels and their surface chemistry, capillary-driven microfluidics can move and stop fluids spontaneously without the need for external instrumentation. Furthermore, complex microfluidic circuits can be pre-programmed by synchronizing the capillary pressures and encoding the surface tension of the microfluidic chips. One of the key components of these systems is the capillary valve. However, the main concern for these valves is the presence of unwanted diffusion during the valve loading and activation steps that can cause cross-contamination. In this study, we designed and validated a novel diffusion-free capillary valve, the π-valve. This valve consists of a 3D structure and a void area. The void acts as a spacer between two fluids to avoid direct contact. When the valve is triggered, the air trapped within the void is displaced by a pneumatic suction induced from the capillary flow of the downstream. The proposed design eliminates any diffusion between fluids. Numerical simulation was used to design and improve the architecture of the π-valve, and 3D printing was used to fabricate either the mold or the microfluidic chip. The comparison with a conventional valve (based on a constriction-expansion valve) demonstrated that the π-valve eliminated possible backflow into the valve and reduced the mixing and diffusion during the loading and trigger steps. It was multiplexed successfully, achieving the sequential release of 3 solutions in a 3D printed microfluidic chip without the need for any external instrumentation. Overall, the π-valve prevents cross-contamination, minimizes sample use, and facilitates a sophisticated pre-programmed release of fluids, offering a promising tool for carrying out automated immunoassays at the point-of-care testing.
Statistical analysis and automation through machine learning of resonant ultrasound spectroscopy data from tests performed on complex additively manufactured parts
Authors: Obaton Anne-Françoise , Fallahi Nasim , Tanich Anis , Lafon Louis-Ferdinand , Weaver Gregory 
Published: October 2022

Abstract
Additive manufacturing brings inspection issues for quality assurance of final parts because non-destructive testing methods are faced with shape complexity, size, and high surface roughness. Thus, to drive additive manufacturing forward, advanced non-destructive testing methods are required. Methods based on resonant ultrasound spectroscopy (RUS) can take on all the challenges that come with additive manufacturing. Indeed, these full body inspection methods are adapted to shape complexity, to nearly any size, and to high degrees of surface roughness. Furthermore, they are easy to implement, fast and low cost. In this paper, we present the benefit of a resonant ultrasound spectroscopy method, combined with a statistical analysis through Z score implementation, to classify supposedly identical parts, from a batch. We also demonstrate that the inspection can be further accelerated and automated, to make the analysis operator independent, whether the analysis of the resonant ultrasound spectroscopy data is performed supervised or unsupervised with machine learning algorithms.
SNX3 aggravates pathological cardiac hypertrophy via targeting ATG5-dependent autophagy
Authors: Hu Yuehuai , Wang Panxia , Chen Jianxing , Liu Cui , Yu Wenjing , Wu Zhongkai , Lu Jing , Liu Peiqing 
Published: October 2022

Abstract

Autophagy is an intracellular lysosomal degradation pathway that plays a critical role in maintaining cardiac homeostasis. Disordered autophagy is closely related to the pathological process of many heart diseases, including cardiac hypertrophy. However, mechanisms regulating cardiac autophagy remained unclear. Previously, we found that overexpression of SNX3 induces cardiac hypertrophy in mice. In this study, a reduced autophagy was observed in SNX3 transgenic mice. Therefore, the objective of our study was to determine whether SNX3 regulates pathological cardiac hypertrophy by regulating autophagy process. A decreased level of autophagy-related protein LC3 was detected in failing hearts from human patients and mouse models. To explore the role of SNX3 in cardiac autophagy, we generated cardiac-specific SNX3 transgenic mice and infected neonatal rat cardiomyocytes (NRCMs) with adenovirus encoding SNX3 (Ad-SNX3). Bothin vivoandin vitrostudies suggested that overexpression of SNX3 inhibited cardiomyocytes autophagy. Overexpression of SNX3in vitrofurther reduced ISO-induced autophagic flux through inhibiting autophagic formation. Rapamycin, an autophagy inducer, could effectively reversed SNX3-induced cardiac hypertrophy and autophagy inhibition bothin vitroandin vivo. Immunofluorescent staining and co-immunoprecipitation results revealed an interaction between SNX3 and autophagy related gene 5 (ATG5). We discovered that the stability of ATG5 was impaired by SNX3.
Development novel collision approach for particulate flows
Authors: Adamczyk Wojciech , Widuch Agata , Morkisz Pawel , Myohanen Kari , Klimanek Adam , Pawlak Sebastian 
Published: October 2022

Abstract
With technology development, there is a growing need for an accurate simulation tools, allowing the best possible representation of the reality. Developed model found not only application in prototyping process but can provide significant knowledge into the artificial intelligent model extending their comprehension. Computational performance and accuracy of the numerical model, dedicated for granular flows are mostly a function of mathematical model that track the mutual interaction between particles. Currently the kinetic theory of granular flow or soft- and hard-sphere collision models are used for modeling particle interactions. Each of them suffers from some imperfection that often limit the problem sizes. The purpose of this work is building new mathematical approach, not only fast, but also accurate regarding predicting collisions and determining particle trajectories by application of machine learning technique.
Responses of aroma related metabolic attributes of Opisthopappus longilobus flowers to environmental changes
Authors: Liu ZhiXia , Lan Yafei , Zhang Hao , Hao Weili , He Shan , Liu Li , Feng Xiaolong , Qie Qiyang , Chai Min , Sun Genlou , Wang Yiling 
Published: October 2022

Abstract
Various metabolic processes are activated in response to environmental changes. Opisthopappus longilobus (Opisthopappus) and its descendant species, Opisthopappus taihangensis commonly thrive on the Taihang Mountains of China. Being typical cliff plants, both O. longilobus and O. taihangensis release unique aromatics. We investigated whether these aromatics might be differentiated and inherently adaptive attributes. To determine the potential differentiation and environmental response patterns between O. longilobus and O. taihangensis, comparative metabolic analysis was performed on O. longilobus wild flower (CLW), O. longilobus reciprocal transplant flower (CLT), and O. taihangensis wild flower (TH) groups. Significant differences in the metabolic profiles between O. longilobus and O. taihangensis flowers were observed, and 29 substances related to their scents were obtained (two alkenes, two aldehydes, three esters, eight phenols, three acids, three ketones, three alcohols, and five flavonoids) of which eugenol and chlorogenic were the primary aromatictic molecules. The chlorogenic content of TH was significantly higher than that of CLW and CLT, while the eugenol content was highest in CLT followed by TH, and both metabolites were enriched in the phenylpropane pathway. In addition, the aromatic related compounds were significantly correlated with the lowest temperatures in October and in December. The results above indicated that phenylpropane, particularly eugenol and chlorogenic, played important roles in the responses of O. longilobus species to environmental changes.
Long-term atmosphere surveillance (2016-2021) of PM2.5-bound polycyclic aromatic hydrocarbons and health risk assessment in Yangtze River delta, China
Authors: Wu Keqin , Yao Yuyang , Meng Yuanhua , Zhang Xuhui , Zhou Run , Liu Wenwei , Ding Xinliang 
Published: October 2022

Abstract
Long-term atmospheric quality monitoring of PM2.5 and PM2.5-bound polycyclic aromatic hydrocarbons (PAHs) was performed in Wuxi from 2016 to 2021. A total of 504 atmospheric PM2.5 samples were collected, and PM2.5-bound 16 PAHs were detected. The PM2.5 and ∑PAHs level decreased annually from 2016–2021, from 64.3 to 34.0 μg/m3 and 5.27 to 4.22 ng/m3, respectively. The benzo[a]pyrene (BaP) of 42% of the monitoring days in 2017 exceeded the recommended health-based standard of the European Union (EU) at 1ng/m3. Five- and six-ring PAHs, including benz[a]anthracene (Baa), benzo[k] fluoranthene (Bkf), BaP, and benzo[g,h,i]perylene (Bghi), were the dominant components, indicating a prominent petroleum, biomass, and coal combustion contribution by molecular diagnostic ratios and positive matrix factorization analysis. Statistically significant temporal and spatial distribution differences of PM2.5, and ∑PAHs were also found. The toxicity equivalent concentration (TEQ) was 0.70 for total PAHs and the TEQ of BaP (0.178) was the highest, followed by Bkf (0.090), dibenz[a,h]anthracene (Dah) (0.048), and indeno[1,2,3-cd]pyrene (Ind) (0.034). The medians of the incremental lifetime cancer risk (ILCR) for long-term exposure to PAHs were 2.74E-8, 1.98E-8, and 1.71E-7 for children, teenagers, and adults, respectively, indicating that the carcinogenic risk of PAHs pollution in air was acceptable to local residents in this area. Sensitivity analysis showed that BaP, Bkf, and Dah significantly contributed to carcinogenic toxicity. This research supplies comprehensive statistics on the local air persistent organic pollutants profile, helps to identify the principle pollution source and compounds, and contributes to the prevention of regional air pollution.
Zn-containing Wollastonite with Well-defined Microstructural and Good Antifungal Activity
Authors: Mardin Sutrisnawati , Hamzawy Esmat , El-Aty Abeer A. Abd , El-Bassyouni Gehan T. 
Published: October 2022

Abstract
Antimicrobial and antifungal materials we prepared from Zn-containing wollastonite set by wet precipitation method. Wollastonite, hardystonite, willemite and very little quartz were developed after sintering at 1100°C/2h, however, the Raman spectroscopy approved the later phases by their characteristic Raman shift bands. The microstructure exhibited accumulated rounded to irregular clusters containing nano-size particles (< 500nm) developed in all sintered samples. Zeta potential; exposed negative values for all powdered samples from − 2.64 to -17.6 mV (i.e., for Zn-free to highest Zn-containing samples). It can be easily noticed that the lowest ZnO-content exhibits a varied range of antibacterial activities in contrast to Gram-negative (E. coli) and Gram-positive (S. aureus & B. subtilis). Correspondingly, the CZS5 exhibits good inhibitory effect against the filamentous pathogenic fungus (A. niger).
Leucine-rich repeat kinase 2 negatively regulates glucose tolerance via regulation of membrane translocation of Glucose transporter type 4 in adipocytes
Authors: Kawakami Fumitaka , Imai Motoki , Isaka Yuki , Cookson Mark , Maruyama Hiroko , Kubo Makoto , Farrer Matthew J. , Kanzaki Makoto , Tamaki Shun , Kawashima Rei , Maekawa Tatsunori , Kurosaki Yoshifumi , Kojima Fumiaki , Ichikawa Takafumi 
Published: October 2022

Abstract
Epidemiological studies have shown that abnormalities of glucose metabolism are involved in leucine-rich repeat kinase 2 (LRRK2)-associated Parkinson's disease (PD). However, the physiological significance of this association is unclear. In the present study, we investigated the effect of the LRRK2 on high-fat diet induced glucose intolerance using Lrrk2-knock-out (Lrrk2-KO) mice. We found for the first time that high-fat (HFD) fed Lrrk2-KO mice display improved glucose tolerance and homeostatic model assessment of insulin resistance compared to their wild type (WT) counterparts. We found that Lrrk2 is highly expressed in adipose tissues compared with to other tissues that are thought to be important in glucose tolerance, including skeletal muscle, liver, and pancreas. Lrrk2 expression and phosphorylation of its kinase substrates Rab8a and Rab10 were significantly elevated after HFD treatment in WT mice. Conversely, treatment with a LRRK2 kinase inhibitor stimulated insulin-dependent membrane translocation of insulin-dependent glucose transporter (GLUT4) in 3T3-L1 adipocytes. We conclude that increased LRRK2 kinase activity in adipose tissue exacerbates glucose intolerance by suppressing Rab8- and Rab10-mediated GLUT4 membrane translocation.
Whole-brain tracking of addictive and natural rewards processing
Authors: Beroun Anna , Bijoch Łukasz , Klos Joanna , Pawlowska Monika , Wiśniewska Justyna , Legutko Diana , Szachowicz Urszula , Kaczmarek Leszek 
Published: October 2022

Abstract

Natural rewards, such as food, and sex are appetitive stimuli available for animals in their natural environment. Similarly, addictive rewards such as drugs of abuse possess strong, positive valence, but their action relies on their pharmacological properties. Nevertheless, it is believed that both of these kinds of rewards activate similar brain circuitry. The present study aimed to discover which parts of the brain process the experience of natural and addictive rewards. To holistically address this question, we used a single-cell whole-brain imaging approach to find patterns of activation for acute and prolonged sucrose and cocaine exposure. We analyzed almost 400 brain structures and created a brain-wide map of specific, c-Fos-positive neurons engaged by these rewards. Acute but not prolonged sucrose exposure triggered a massive c-Fos expression throughout the brain. Cocaine exposure on the other hand potentiated c-Fos expression with prolonged use, engaging more structures than sucrose treatment. The functional connectivity analysis unraveled an increase in brain modularity after exposure to both types of rewards. This modularity stabilized during prolonged sucrose, but not cocaine, intake. To check whether discrepancies between the processing of both types of rewards can be found on a cellular level, we further studied the nucleus accumbens, one of the most strongly activated brain structures by both sucrose and cocaine experience. We found a high overlap between natural and addictive rewards on the level of c-Fos expression. Electrophysiological measurements of cellular correlates of synaptic plasticity revealed that natural and addictive rewards alike induce the accumulation of silent synapses. These results strengthen the hypothesis that in the nucleus accumbens drugs of abuse cause maladaptive neuronal plasticity in the circuitry that typically processes natural rewards.
Assessment of Knowledge, Attitude and Practice of Residents towards Civil Registration and Vital Statistics in Gurage Zone, Ethiopia
Authors: Chernet Ayele Gebeyehu , Trueha Kassahun , Muanenda Sebsib , Cherie Kebadu Tadesse , Lentiro Kifle 
Published: October 2022

Abstract
Background: Even if the Government of Ethiopia has given great emphasis to strengthen CRVS system throughout the country, the system is still in its infancy stage. Therefore, this research aimed to examine knowledge, attitude and practice of people towards CRVS in Gurage Zone, Ethiopia.
Methods: About 439 household from three districts and two cities administrative were selected using a multi-stage random sampling technique. Well-structured questionnaire on Knowledge, attitude and practice was prepared and information was collected and analyzed from the household head from December 15-20, 2020.
Result: The result revealed that most of the residents have enough knowledge and good attitude about CRVS. But only 22.6% up to 39% of them know the official registration time and the practice of vital event registration was found to be very low.
Conclusion: The result showed that the residents have good knowledge and attitude towards CRVS while the practice is very low. Hence, improving the practice of registering vital events by eliminating obstacles is expected from the local and national administrative.