bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classification of Pavement Climatic Regions through Unsupervised and Supervised Machine Learnings
Authors: Dong Qiao , Chen Xueqin , Dong Shi , Zhang Jun 
Published: February 2021

Abstract
This study extracted 16 climatic data variables including annual temperature, freeze thaw, precipitation, and snow fall conditions from the Long-term Pavement Performance (LTPP) program database to evaluate the climatic regionalization for pavement infrastructure. The effect and significance of climate change were firstly evaluated using time as the only predictor and t-test. It was found that both the temperature and humidity increased in most States. Three unsupervised machine learning including Principle Component Analysis (PCA), factor analysis and cluster analysis were conducted to identify the main component and common factors for climatic variables, and then to classify datasets into different groups. Then, two supervised machine learning methods including Fisher’s discriminant analysis and Artificial Neural Networks (ANN) were adopted to predict the climatic regions based on climatic data. Results of PCA and factor analysis show that temperature and humidity are the first two principle components and common factors, accounting for 71.6% of the variance. The 4-means clusters include wet no freeze, dry no freeze, dry freeze and snow freeze. The best k-mean clustering suggested 9 clusters with more temperature clusters. Both the Fisher’s linear discriminant analysis and ANN can effectively predict climatic regions with multiple climatic variables. ANN performs better with higher R square and low misclassification rate, especially for those with more layers and nodes.
Clinical Manifestations, Mutational Analysis, and Immunological Phenotype in Patients With RAG1/2 Mutations: First Cases Series From Mexico and Description of Two Novel Mutations.
Authors: Cruz-Munoz Mario Ernesto , Lugo-Reyes Saul Oswaldo , Pastor Nina , González-Serrano Edith , Yamazaki-Nakashimada Marco , Scheffer-Mendoza Selma , Berron-Ruiz Laura , Wakida Guillermo , Nuñez-Nuñez Maria Enriqueta , Macias-Robles Ana Paola , Staines-Boone Aide Tamara , Venegas-Montaya Edna , Alaez-Verson Carmen , Molina-Garay Carolina , Flores-Lagunes Luis Leonardo , Carrillo-Sánchez Karol , Niemela Julie , Rozensweig Sergio , Gaytan Paul , Yañez Jorge , Martinez-Duncker Ivan , Notarangelo Luigi , Espinosa-Padilla Sara 
Published: February 2021

Abstract
Mutations in Recombinase Activating Genes 1 and 2 (RAG1/2) results in human severe combined immunodeficiency (SCID). The products of these genes, are essential for V(D)J rearrangement of the antigen receptors during lymphocyte development. Nonsense mutations in RAG1 or RAG2 are associated with the most severe clinical and immunological phenotypes, whereas patients with missense mutations may develop leaky SCID or Omenn syndrome (OS). A group of non-previously recognized clinical phenotypes associated with granulomata and/or autoimmunity have been described as a consequence of hypomorphic mutations. Here we present six patients from unrelated families with missense variants in RAG1 or RAG2. Phenotypes observed in these patients ranged from OS to severe mycobacterial infections and granulomatous disease. Moreover, we report the first evidence of two previously unidentified variants as causative of pathological manifestations associated to immunodeficiency. This study represents the first case series of RAG1 or RAG2 deficient patients from Mexico and Latin America.
Application of Bioelectrochemical Technique in Energy Recovery and CH4 Control From Constructed Wetland (CW) and Associated Biochemical Mechanisms
Authors: Zhang Ke , Wu Xiangling , Wang Wei , Luo Hongbing , Chen Wei , Chen Jia 
Published: February 2021

Abstract
In the context of global warming, the bioelectrochemical method (microbial fuel cell MFC) was proposed for CH4 control from CWs. The main focus is to further explore the effect of plant roots location at the electrode, plant species on CH4 emissions, bioelectricity generation and the mechanism underlying competition between electrogenesis and methanogenesis at the anode. The results showed that the operation of MFC effectively reduced the CH4 emissions and promoted COD removal rates. CH4 emission was significantly higher in open circuit (6.2 mg m-2 h-1) than in closed circuit reactors (3.1 mg m-2 h-1). Plant roots at the cathode had the highest electricity generation and the lowest CH4 emissions. The highest power generation (0.49 V, 0.33 w m-3) and the lowest CH4 emissions (2.3 mg m-2 h-1) were observed in the reactors where Typha Orientalis was planted with plant roots at the cathode. The role of plants in strengthening electron acceptor was greater than that of plant rhizodeposits in strengthening electron donors. q-PCR and correlation analysis indicated that the mcrA genes and CH4 emissions were positively correlated (r=0.98, p<0.01), while no significant relationship between CH4 emissions and pmoA genes was observed. More nanowires, which are conductive to electron transfer, were found when plant roots were in cathode by scanning electron microscope (SEM). Illumina sequencing revealed that more abundant exoelectrogens and denitrifying bacteria (Geobacter, Desulfobulbu, Nitrospira and Anaerolinea) were observed when plant roots located in cathodes. Strictly acetotrophic archae (Methanosaetaceae) were likely main electron donor competitors with exoelectrogens. In addition, plant species played a more important role in CH4 emissions and electricity generation than the plant roots location at the electrode. Therefore, it is necessary to strengthen plant configuration to reduce CH4 emissions, so as to promote sustainable development of wastewater treatment.
Silica-coated Magnetic Nanoparticles Activate Microglia and Induce Neurotoxic D-Serine Secretion
Authors: Shin Tae Hwan , Lee Da Yeon , Manavalan Balachandran , Basith Shaherin , Na Yun-Cheol , Yoon Cheolho , Lee Hyeon-Seong , Paik Man Jeong , Lee Gwang 
Published: February 2021

Abstract
BackgroundNanoparticles have been studied for brain imaging, diagnosis, and drug delivery owing to their versatile properties due to their small sizes. However, there are growing concerns that nanoparticles may exert toxic effects in the brain. In this study, we assessed direct nanotoxicity on microglia, the resident macrophages of the central nervous system, and indirect toxicity on neuronal cells exerted by silica-coated magnetic nanoparticles containing rhodamine B isothiocyanate dye [MNPs@SiO2(RITC)]. MethodsWe investigated MNPs@SiO2(RITC)-induced biological changes in BV2 murine microglial cells via RNA-sequencing-based transcriptome analysis and gas chromatography-mass spectrometry-based intracellular and extracellular amino acid profiling. Morphological changes were analyzed by transmission electron microscopy. Indirect effects of MNPs@SiO2(RITC) on neuronal cells were assessed by Transwell-based coculture with MNPs@SiO2(RITC)-treated microglia. MNPs@SiO2(RITC)-induced biological changes in the mouse brain in vivo were examined by immunohistochemical analysis.ResultsBV2 murine microglial cells were morphologically activated and the expression of Iba1, an activation marker protein, was increased after MNPs@SiO2(RITC) treatment. transmission electron microscopy analysis revealed lysosomal accumulation of MNPs@SiO2(RITC) and the formation of vesicle-like structures in MNPs@SiO2(RITC)-treated BV2 cells. The expression of several genes related to metabolism and inflammation were altered in 0.1 µg/µl MNPs@SiO2(RITC)-treated microglia when compared with that in non-treated (control) and 0.01 µg/µl MNPs@SiO2(RITC)-treated microglia. Combined transcriptome and amino acid profiling analyses revealed that the transport of serine family amino acids, including glycine, cysteine, and serine, was enhanced. However, only serine was increased in the growth medium of activated microglia; especially, excitotoxic d-serine secretion from primary rat microglia was the most strongly enhanced. Activated primary microglia reduced intracellular ATP levels and proteasome activity in cocultured neuronal cells, especially in primary cortical neurons, via d-serine secretion. Moreover, ubiquitinated proteins accumulated and inclusion bodies were increased in primary dopaminergic and cortical neurons cocultured with activated primary microglia. In vivo, MNPs@SiO2(RITC), d-serine, and ubiquitin aggresomes were distributed in the MNPs@SiO2(RITC)-treated mouse brain. ConclusionsMNPs@SiO2(RITC)-induced activation of microglia triggers excitotoxicity in neurons via d-serine secretion, highlighting the importance of neurotoxicity mechanisms incurred by nanoparticle-induced microglial activation.
Visualization Analysis of Publication Trends and Research Hotspots on the Tumor Microenvironment of Pancreatic Cancer Between 2010 and 2020: a Bibliometric Study
Authors: Wu Kaiwen , Liu Ye , Liu Lei , Peng Yunlan , Pang Honglin , Sun Xiaobin , Xia Demeng 
Published: February 2021

Abstract
Background: Pancreatic cancer (PC) is a serious disease with high mortality. The tumor microenvironment plays a key role in the occurrence and development of PC. The purpose of this study is to analyze the trends by year, country, institution, journal, and keywords in publications on the PC microenvironment and to predict the future hotspots.Methods: The Web of Science Core Collection was used to search for and download publications. We analyzed the contributions of various countries/regions, institutes, and authors and discerned the research hotspots and promising future trends by using the CiteSpace and VOSviewer programs. We also summarized relevant completed clinical trials.Results: A total of 1,766 papers on the PC microenvironment published between 2010 and 2020 were included in the study. The average number of citations per article was 28.7. The United States had the most publications, followed by China, and a total of five influential articles were identified through co-citation analysis. Clustering analysis revealed three clusters of keywords: carcinogenesis of PC, stroma of PC, and therapy of PC. The research hotspots included cancer-associated fibroblasts, exosomes, FOLFIRINOX [FOL – folinic acid (also called leucovorin, calcium folinate, or FA), F – fluorouracil (also called 5-FU), Irin – irinotecan, Ox – oxaliplatin], and immunotherapy.Conclusion: The number of publications and the research enthusiasm generally showed an upward trend, and the United States has made prominent contributions to the field of the tumor microenvironment of PC. The current research hotspots are mainly cancer-associated fibroblasts, exosomes, and the treatment of pancreatic cancer, which might be the directions of future research.
Longitudinal Analysis of Inflammatory Response to SARS-CoV-2 in the Upper Respiratory Tract Reveals an Association With Viral Load, Independent of Symptoms
Authors: Didierlaurent Arnaud , Diem-Lan Vu , Murillo Paola Martinez , Pigny Fiona , Vono Maria , Meyer Benjamin , Eberhardt Christiane S , Lemeille Sylvain , Dach Elodie Von , Blanchard-Rohner Geraldine , Eckerle Isabella , Huttner Angela , Siegrist Claire-Anne , Kaiser Laurent 
Published: February 2021

Abstract
BackgroundSARS-CoV-2 infection leads to high viral loads in the upper respiratory tract that may be determinant in virus dissemination. The extent of intranasal antiviral response in relation to symptoms is unknown. Understanding how local innate responses control virus is key in the development of therapeutic approaches.MethodsSARS-CoV-2-infected patients were enrolled in an observational study conducted at the Geneva University Hospitals, Switzerland, investigating virological and immunological characteristics. Nasal-wash and serum specimens from a subset of patients were collected to measure viral load and a cytokine panel at different time points after infection; cytokine levels were analyzed in relation to symptoms.ResultsSamples from 13 SARS-CoV-2-infected patients and six controls were analyzed. We found an increase in CXCL10 and IL-6, whose levels remained elevated for up to 3 weeks after symptom onset. SARS-CoV-2 infection also induced CCL2 and GM-CSF, suggesting local recruitment and activation of myeloid cells. Local cytokine levels correlated with viral load but not with serum cytokine levels, nor with specific symptoms, including anosmia.ConclusionsThe nasal epithelium is an active site of cytokine response against SARS-CoV-2 that can last more than 2 weeks; in this cohort, anosmia was not associated with increases in any locally produced cytokines.
Performance Investigation of Carbon Nanotube Based Temperature Compensated Piezoresistive Pressure Sensor
Authors: DEVI REKHA , Gill Sandeep Singh 
Published: February 2021

Abstract
In silicon-based piezoresistive pressure sensor, the accuracy of the sensor is affected mainly by thermal drift and the sensitivity of the sensor varies with the rise in temperature. Here, the temperature effects on the desired representation of the sensor are analysed .Use of smart material Carbon nanotubes ( CNT) and a few effective temperature compensation techniques are presented in this study to reduce the temperature effect on the accuracy of the sensor. Resistive compensation employed extra piezoresistors with Negative Temperature Coefficient of Resistivity (TCR) for temperature compensation. The attainment of the desired compensation techniques is highly compatible with the MEMS device fabrication. The compensated pressure sensor is supremacy for pressure measurement with temperature variations. Though various techniques have been suggested and put into actuality with successful attainment, the techniques featuring easy implementation and perfect compatibility with existing schemes are still blooming demanded to design a piezoresistive pressure sensor with perfect comprehensive performance. In this paper, CNT piezoresistive material has been employed as sensing elements for pressure sensor and compared with silicon in terms of output voltage and sensor performance degradation at higher temperature. Pressure sensors using CNT and silicon piezo resistive sensing materials were simulated on silicon (100) diaphragm by ANYSIS. Based on simulation results, silicon and CNT both pressure sensor also shows better results at near room temperature. With the increasing temperature it is observed that silicon pressure output underestimated by 23%.
Analysis of tumor microenvironment characteristics in bladder cancer: implications for immune checkpoint inhibitor therapy
Authors: Chen Xingyu , Chen Haotian , He Dong , Cheng YaXing , Zhu Yuxing , Xiao Mengqing , Lan Hua , Wang Zhanwang , Cao Ke 
Published: February 2021

Abstract
Background

The tumor microenvironment (TME) has a significant influence on prognosis and immunotherapy. There are no studies on the systematic analysis of bladder cancer TME and its effect on immune checkpoint inhibitor therapy.
Methods

We comprehensively evaluated the TME infiltration pattern of bladder cancer in 1,889 patients and conducted extensive immunogenomic analysis to explore the heterogeneity and prognostic significance of the TME of bladder cancer. The principal component analysis algorithm was used to calculate the immune cell (IC)score to quantify the level of IC infiltration. We used the receiver operating characteristic (ROC) curve, Tumor Immune Dysfunction and Exclusion (TIDE), and Subnetwork Mappings in Alignment of Pathways (SubMAP) algorithms to evaluate whether the ICscore can predict the benefits of immune checkpoint inhibitors in bladder cancer patients.
Results

We identified three different TME phenotypes using unsupervised clustering methods. To explore the potential biological pathways that drive the formation of these microenvironmental phenotypes, we demonstrated the clinical and pathological characteristics, biological signaling pathways, cancer immune circulation, copy number, and somatic mutation differences among the different subtypes. In addition, univariate and multivariate Cox regression analyses showed that the ICscore is a reliable and independent prognostic marker. The ICscore can also predict immune checkpoint inhibitor responsiveness as patients with higher ICscores showed a significant therapeutic advantage in immunotherapy.
Conclusions

This study increases our understanding of the characteristics of TME infiltration in bladder cancer and provides guidance on more effective personalized immunotherapeutic strategies.
ALK-Negative Lung Inflammatory Myofibroblastic Tumor in a Young Adult: a Case Report and Literature Review of Molecular Alterations
Authors: Debonis Silvia Angela , Bongiovanni Alberto , Pieri Federica , Fausti Valentina , Vita Alessandro De , Riva Nada , Gurrieri Lorena , Vanni Silvia , Diano Danila , Mercatali Laura , Ibrahim Toni 
Published: February 2021

Abstract
Background: Inflammatory myofibroblastic tumor (IMT) is a rare mesenchymal tumor and is prevalent among children and adolescents. Surgery is the most important therapeutic approach for IMT and complete resection is recommended. Although 50% of IMTs present anaplastic lymphoma kinase (ALK) rearrangements, an efficacy has been shown by the use of Crizotinib . However the genetic landscape of this tumor is not fully understood and the therapeutic options are limited in particular for the remaining percentage of negative ALK tumors. Case presentation: In our case, we detail the clinical history of 18-year-old female patient diagnosed with pulmonary IMT negative for ALK, subjected to surgery and subsequently to follow-up. The initial pathology report oriented for a salivary gland lung cancer. Afterwards due to a second look by another pathologist an ALK negative IMT of the lung was diagnosed. We also perform a literature review based on IMT and other kinase fusions found in addition to ALK such as ROS proto-oncogene 1 (ROS1), rearranged during transfection (RET), neurotrophic receptor tyrosine kinases (NTRKs) and platelet derived growth factor receptor (PDGFR beta). Conclusions: IMT is a very rare disease involving children and adolescents. Little is known about the clinical and molecular characteristics, pathological diagnosis, prognosis and optimal management strategy of IMT. Since there is no "standard of care" therapy for IMT, identifying feasible genomic alterations could redefine the management of patients with negative ALK disease.
Ethanol and cocaine increases microtubule stability and decreases [11C]MPC-6827 uptake in SH-SY5Y cells
Authors: Damuka Naresh , Orr Miranda E , Czoty Paul W , Weiner Jeffrey L , Martin Thomas J , Nader Michael A , Bansode Avinash H , Pathirannahel Buddhika S Liyana , Mintz Akiva , Macauley Shannon L , Craft Suzanne , Sai Kiran Kumar Solingapuram 
Published: February 2021

Abstract
Microtubules (MTs) are structural units in the cytoskeleton. In brain cells they are responsible for axonal transport, information processing, and signaling mechanisms. Proper function of these processes is critical for healthy brain functions. Alcohol and substance use disorders (AUD/SUDs) affects the function and organization of MTs in the brain, making them a potential neuroimaging marker to study the resulting impairment of overall neurobehavioral and cognitive processes. Our lab reported the first brain-penetrant MT-tracking Positron Emission Tomography (PET) ligand [11C]MPC-6827 and demonstrated its in vivo utility in rodents and non-human primates. To further explore the in vivo imaging potential of [11C]MPC-6827, we need to investigate its mechanism of action. Here, we report preliminary in vitro binding results in SH-SY5Y neuroblastoma cells exposed to ethanol (EtOH) or cocaine in combination with multiple agents that alter MT stability. EtOH and cocaine treatments increased MT stability and decreased free tubulin monomers. Our initial cell-binding assay demonstrated that [11C]MPC-6827 selectively bound to free/unbound tubulin units. Consistent with this mechanism of action, we observed lower [11C]MPC-6827 uptake in SH-SY5Y cells after EtOH and cocaine treatments (e.g., fewer free tubulin monomers). We are currently performing in vivo PET imaging and ex vivo biodistribution studies in rodent and nonhuman primate models of AUD and SUDs.
Ecological contacts and host specificity promote replacement of nutritional endosymbionts in ticks
Authors: Buysse Marie , Binetruy Florian , Leibson Raz , Gottlieb Yuval , Duron Olivier 
Published: February 2021

Abstract
Symbiosis with vitamin-provisioning microbes is essential for the nutrition of animals with specialized feeding habits. While coevolution stabilizes the interactions between symbiotic partners, their associations are not necessarily permanent: Recently acquired symbionts can replace ancestral symbionts. In this study, we demonstrate successful replacement dynamics of Francisella-Like Endosymbionts (-LE), a group of invasive B-vitamin-provisioning endosymbionts, across tick communities driven by a complex web of horizontal transfers. Using a broad collection of Francisella-LE-infected tick species, we determined the diversity of Francisella-LE haplotypes through a multi-locus strain typing approach, and further characterized their phylogenetic relationships and their association with biological traits of their tick hosts. The patterns observed showed that Francisella-LE commonly transfer through similar ecological networks and geographic distributions shared among different tick species, and, in certain cases, through preferential shuffling across congeneric tick species. Altogether, these findings reveal the importance of both routes in shaping the invasive pattern in which new nutritional symbioses are initiated.
Limits of Temperature Adaptation and Thermopreferendum
Authors: Aslanidi Konstantin Borisovich , Kharakoz Dmitry Petrovich 
Published: February 2021

Abstract
Background Managing the limits of temperature adaptation is relevant both in medicine and in biotechnology. There are numerous scattered publications on the identification of the temperature limits of existence for various organisms and using different methods. It was shown earlier that each cycle of synaptic exocytosis includes reversible phase transitions of lipids of the presynaptic membrane due to the entry and subsequent removal of calcium ions from the synaptic terminal. Violation of cyclic changes in membrane fluidity caused by a sharp increase or decrease in ambient temperatures will lead to the termination of synaptic transmission, which can be recorded by the loss of righting reflex.Results The viability polygon for Danio rerio was determined by the minimum temperature of cold shock (about 6 o C), maximum temperature of heat shock (about 43 o C), and thermopreferendum temperature (about 27 o C). The ratio of the temperature range of cold shock to the temperature range of heat shock was about 1.3. Conclusions The experimental values of the temperatures of cold shock and heat shock and the temperature of the thermal preferendum correspond to the temperatures of phase transitions of the lipid-protein composition of the synaptic membrane between the liquid and solid states. The viability range for zebrafish coincides with the temperature range, over which enzymes function effectively and also coincides with the viability polygons for the vast majority of organisms. The boundaries of the viability polygon are characteristic biological constants. The viability polygon of a particular organism is determined not only by the genome, but also by the physicochemical properties of lipids that make up the membrane structures of synaptic endings. The limits of temperature adaptation of any biological species are determined by the temperature range of the functioning of its nervous system.