bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemical-free and scalable process for the fabrication of a uniform array of liquid-gated CNTFET, evaluated by KCl electrolyte
Authors: Agarwal Pankaj B. , Thakur Navneet Kumar , Sharma Rishi , Singh Parul , Joseph Joshy , Tripura Chaturvedula 
Published: February 2021

AbstractBiosensors based on liquid-gated carbon nanotubes field-effect transistors (LG-CNTFETs) have attracted considerable attention, as they offer high sensitivity and selectivity; quick response and label-free detection. However, their practical applications are limited due to the numerous fabrication challenges including resist-based lithography, in which after the lithography process, the resist leaves trace level contaminations over the CNTs that affect the performance of the fabricated biosensors. Here, we report the realization of LG-CNTFET devices using silicon shadow mask-based chemical-free lithography process on a 3-in. silicon wafer, yielding 21 sensor chips. Each sensor chip consists of 3 × 3 array of LG-CNTFET devices. Field emission scanning electron microscope (FESEM) and Raman mapping confirm the isolation of devices within the array chip having 9 individual devices. A reference electrode (Ag/AgCl) is used to demonstrate the uniformity of sensing performances among the fabricated LG-CNTFET devices in an array using different KCl molar solutions. The average threshold voltage (Vth) for all 9 devices varies from 0.46 to 0.19 V for 0.1 mM to 1 M KCl concentration range. This developed chemical-free process of LG-CNTFET array fabrication is simple, inexpensive, rapid having a commercial scope and thus opens a new realm of scalable realization of various biosensors.
A comparative study on the chloride effectiveness of synthetic rutile and natural rutile manufactured from ilmenite ore
Authors: Jung Eun Jin , Kim Jinyoung , Lee Ye Rin 
Published: February 2021

AbstractStudies on continuous and selective chlorination by using ilmenite have been actively conducted because the efficient removal of FeO from ilmenite(FeTiO3) ore using selective chlorination not only improves the reaction purity of TiCl4 but it also leads to price competitiveness compared to TiCl4 synthesized from natural rutile. The chlorination of synthetic rutile with FeO removed was compared with that of natural rutile to examine the reaction efficiency. The selective chlorination efficiency depends on the input amounts of coke and Cl2, as shown by thermodynamic calculation, when FeO is selectively removed. It was found that manufacturing of TiCl4 was easier by using the synthetic rutile, because it had greater porosity than natural rutile. Relatively greater pore volumes were found in the synthetic rutile than in natural rutile. It was confirmed that the reaction efficiency of chlorination for TiCl4 production was directly related to the difference in the porosity distribution between the titanium ores, as verified by a kinetic comparison of synthetic and natural rutiles.
Development and validation of a multiplex qPCR assay for detection and relative quantification of HPV16 and HPV18 E6 and E7 oncogenes
Authors: Bordigoni Alexia , Motte Anne , Tissot-Dupont Hervé , Colson Philippe , Desnues Christelle 
Published: February 2021

AbstractHuman papillomaviruses (HPV) play a key role in promoting human anogenital cancers. Current high-risk HPV screening or diagnosis tests involve cytological or molecular techniques mostly based on qualitative HPV DNA detection. Here, we describe the development of a rapid quantitative polymerase chain reaction (qPCR) detection test of HPV16 and HPV18 oncogenes (E6 and E7) normalized on human gene encoding GAPDH. Optimized qPCR parameters were defined, and analytical specificities were validated. The limit of detection was 101 for all genes tested. Assay performances were evaluated on clinical samples (n = 96). Concordance between the Xpert HPV assay and the triplex assay developed here was 93.44% for HPV16 and 73.58% for HPV18. HPV co-infections were detected in 15 samples. The systems developed in the present study can be used in complement to traditional HPV tests for specifically validating the presence of HPV16 and/or HPV18. It can also be used for the follow-up of patients with confirmed infection and at risk of developing lesions, through the quantification of E6 and E7 oncogene expression (mRNA) normalized on the GAPDH expression levels.
Automatic classification of canine thoracic radiographs using deep learning
Authors: Banzato Tommaso , Wodzinski Marek , Burti Silvia , Osti Valentina Longhin , Rossoni Valentina , Atzori Manfredo , Zotti Alessandro 
Published: February 2021

AbstractThe interpretation of thoracic radiographs is a challenging and error-prone task for veterinarians. Despite recent advancements in machine learning and computer vision, the development of computer-aided diagnostic systems for radiographs remains a challenging and unsolved problem, particularly in the context of veterinary medicine. In this study, a novel method, based on multi-label deep convolutional neural network (CNN), for the classification of thoracic radiographs in dogs was developed. All the thoracic radiographs of dogs performed between 2010 and 2020 in the institution were retrospectively collected. Radiographs were taken with two different radiograph acquisition systems and were divided into two data sets accordingly. One data set (Data Set 1) was used for training and testing and another data set (Data Set 2) was used to test the generalization ability of the CNNs. Radiographic findings used as non mutually exclusive labels to train the CNNs were: unremarkable, cardiomegaly, alveolar pattern, bronchial pattern, interstitial pattern, mass, pleural effusion, pneumothorax, and megaesophagus. Two different CNNs, based on ResNet-50 and DenseNet-121 architectures respectively, were developed and tested. The CNN based on ResNet-50 had an Area Under the Receive-Operator Curve (AUC) above 0.8 for all the included radiographic findings except for bronchial and interstitial patterns both on Data Set 1 and Data Set 2. The CNN based on DenseNet-121 had a lower overall performance. Statistically significant differences in the generalization ability between the two CNNs were evident, with the CNN based on ResNet-50 showing better performance for alveolar pattern, interstitial pattern, megaesophagus, and pneumothorax.
Crosstalk between auxin and gibberellin during stalk elongation in flowering Chinese cabbage
Authors: Kou Erfeng , Huang Xinmin , Zhu Yunna , Su Wei , Liu Houcheng , Sun Guangwen , Chen Riyuan , Hao Yanwei , Song Shiwei 
Published: February 2021

AbstractPlant growth and development are tightly regulated by phytohormones. However, little is known about the interaction between auxin and gibberellin acid (GA) during flower stalk elongation and how it is directly related to organ formation. Therefore, the effects of indole acetic acid (IAA) and GA3 treatments and their interaction on flower stalk elongation in flowering Chinese cabbage were investigated. The growth of flowering Chinese cabbage is regulated by IAA and GA3, and the opposite results were observed after treatments with uniconazole (GA synthesis inhibitor) and N-1-naphthylphthalamic acid (NPA) (auxin transport inhibitor). Anatomical analysis of the pith region in stalks revealed that IAA promoted expansion via signal transduction and transport pathways. GA3 regulated the elongation of flower stalks by controlling GA synthesis and partially controlling the IAA signaling pathway. GA3 also had a stronger effect on stalk elongation than IAA. The results of qRT-PCR and histological analysis revealed that GA3 and IAA induced the expansion of cell walls by activating the expression of genes encoding cell wall structural proteins such as Expansin (EXP). These findings provide new insights into the mechanism of stalk formation regulated by the combination of IAA and GA3.
Comparative analysis of the alveolar microbiome in COPD, ECOPD, Sarcoidosis, and ILD patients to identify respiratory illnesses specific microbial signatures
Authors: Gupta Shashank , Shariff Malini , Chaturvedi Gaura , Sharma Agrima , Goel Nitin , Yadav Monika , Mortensen Martin S. , Sørensen Søren J. , Mukerji Mitali , Chauhan Nar Singh 
Published: February 2021

AbstractStudying respiratory illness-specific microbial signatures and their interaction with other micro-residents could provide a better understanding of lung microbial ecology. Each respiratory illness has a specific disease etiology, however, so far no study has revealed disease—specific microbial markers. The present study was designed to determine disease-specific microbial features and their interactions with other residents in chronic obstructive pulmonary diseases (stable and exacerbated), sarcoidosis, and interstitial lung diseases. Broncho-alveolar lavage samples (n = 43) were analyzed by SSU rRNA gene sequencing to study the alveolar microbiome in these diseases. A predominance of Proteobacteria followed by Firmicutes, Bacteroidetes, Actinobacteria, and Fusobacteria was observed in all the disease subsets. Shannon diversity was significantly higher in stable COPD when compared to exacerbated chronic obstructive pulmonary disease (ECOPD) (p = 0.0061), and ILD patient samples (p = 0.037). The lung microbiome of the patients with stable COPD was more diverse in comparison to ECOPD and ILD patients (p < 0.001). Lefse analysis identified 40 disease—differentiating microbial features (LDA score (log10) > 4). Species network analysis indicated a significant correlation (p < 0.05) of diseases specific microbial signature with other lung microbiome members. The current study strengthens the proposed hypothesis that each respiratory illness has unique microbial signatures. These microbial signatures could be used as diagnostic markers to differentiate among various respiratory illnesses.
Electrocatalytic hydrogen evolution on the noble metal-free MoS2/carbon nanotube heterostructure: a theoretical study
Authors: Keivanimehr Farhad , Habibzadeh Sajjad , Baghban Alireza , Esmaeili Amin , Mohaddespour Ahmad , Mashhadzadeh Amin Hamed , Ganjali Mohammad Reza , Saeb Mohammad Reza , Fierro Vanessa , Celzard Alain 
Published: February 2021

AbstractMolybdenum disulfide (MoS2) is considered as a promising noble-metal-free electrocatalyst for the Hydrogen Evolution Reaction (HER). However, to effectively employ such material in the HER process, the corresponding electrocatalytic activity should be comparable or even higher than that of Pt-based materials. Thus, efforts in structural design of MoS2 electrocatalyst should be taken to enhance the respective physico-chemical properties, particularly, the electronic properties. Indeed, no report has yet appeared about the possibility of an HER electrocatalytic association between the MoS2 and carbon nanotubes (CNT). Hence, this paper investigates the synergistic electrocatalytic activity of MoS2/ CNT heterostructure for HER by Density Functional Theory simulations. The characteristics of the heterostructure, including density of states, binding energies, charge transfer, bandgap structure and minimum-energy path for the HER process were discussed. It was found that regardless of its configuration, CNT is bound to MoS2 with an atomic interlayer gap of 3.37 Å and binding energy of 0.467 eV per carbon atom, suggesting a weak interaction between CNT and MoS2. In addition, the energy barrier of HER process was calculated lower in MoS2/CNT, 0.024 eV, than in the MoS2 monolayer, 0.067 eV. Thus, the study elaborately predicts that the proposed heterostructure improves the intrinsic electrocatalytic activity of MoS2.
Electronic structure of vertically coupled quantum dot-ring heterostructures under applied electromagnetic probes. A finite-element approach
Authors: Mora-Ramos M. E. , Vinasco J. A. , Laroze D. , Radu A. , Restrepo R. L. , Heyn Christian , Tulupenko V. , Hieu Nguyen N. , Phuc Huynh V. , Ojeda J. H. , Morales A. L. , Duque C. A. 
Published: February 2021

AbstractWe theoretically investigate the electron and hole states in a semiconductor quantum dot-quantum ring coupled structure, inspired by the recent experimental report by Elborg and collaborators (2017). The finite element method constitutes the numerical technique used to solve the three-dimensional effective mass equation within the parabolic band approximation, including the effects of externally applied electric and magnetic fields. Initially, the features of conduction electron states in the proposed system appear discussed in detail, under different geometrical configurations and values of the intensity of the aforementioned electromagnetic probes. In the second part, the properties of an electron-hole pair confined within the very kind of structure reported in the reference above are investigated via a model that tries to reproduce as close as possible the developed profile. In accordance, we report on the energies of confined electron and hole, affected by the influence of an external electric field, revealing the possibility of field-induced separate spatial localization, which may result in an indirect exciton configuration. In relation with this fact, we present a preliminary analysis of such phenomenon via the calculation of the Coulomb integral.
A single-centre, retrospective study of the incidence of invasive fungal infections during 85 years of autopsy service in Brazil
Authors: Dantas Kátia Cristina , Mauad Thais , de André Carmen D. Saldiva , Bierrenbach Ana Luiza , Saldiva Paulo Hilário Nascimento 
Published: February 2021

AbstractAutopsy continues to play an essential role in monitoring opportunistic fungal infections. However, few studies have analysed the historical trends of fungal infections in autopsies. Here, we analyse available data on fungal infections obtained from autopsy reports during 85 years of autopsies performed by the largest autopsy service in Brazil. All invasive fungal infections presented in autopsy reports between 1930 and 2015 were included. Of the 158,404 autopsy reports analysed, 1096 involved invasive fungal infections. In general, paracoccidioidomycosis (24%) was the most frequent infection, followed by candidiasis (18%), pneumocystosis (11.7%), cryptococcosis (11%), aspergillosis (11%) and histoplasmosis (3.8%). Paracoccidioidomycosis decreased after the 1950s, whereas opportunistic fungal infections increased steadily after the 1980s during the peak of the AIDS pandemic. The lung was the most frequently affected organ (73%). Disseminated infection was present in 64.5% of cases. In 26% of the 513 cases for which clinical charts were available for review, the diagnosis of opportunistic fungal infections was performed only at autopsy. Our unique 85-year history of autopsies showed a transition from endemic to opportunistic fungal infections in São Paulo, Brazil, reflecting increased urbanization, the appearance of novel diseases, such as AIDS in the 1980s, and advances in medical care over time.
MYD88 signals induce tumour-initiating cell generation through the NF-κB-HIF-1α activation cascade
Authors: Tanimura Atsuko , Nakazato Akane , Tanaka Nobuyuki 
Published: February 2021

AbstractTumour-promoting inflammation is a hallmark of cancer, and chronic inflammatory disease increases the risk of cancer. In this context, MYD88, a downstream signalling molecule of Toll-like receptors that initiates inflammatory signalling cascades, has a critical role in tumour development in mice and its gene mutation was found in human cancers. In inflammation-induced colon cancer, tumour suppressor p53 mutations have also been detected with high frequency as early events. However, the molecular mechanism of MYD88-induced cancer development is poorly understood. Here, we demonstrated that MYD88 induced the protein accumulation of the transcription factor HIF-1α through NF-κB in p53-deficient cells. HIF-1α accumulation was not caused by enhanced protein stability but by NF-κB-mediated transcriptional activation, the enhanced translation of HIF-1α and JNK activation. In contrast, MYD88-induced mRNA expressions of HIF-1α and HIF-1-target genes were attenuated in the presence of p53. Furthermore, constitutively active forms of MYD88 induced tumour-initiating cell (TIC) generation in p53-deficient cells, as determined by tumour xenografts in nude mice. TIC generating activity was diminished by the suppression of NF-κB or HIF-1α. These results indicate that MYD88 signals induce the generation of TICs through the NF-κB-HIF-1α activation cascade in p53-deficient cells and suggest this molecular mechanism underlies inflammation-induced cancer development.
Evaluation on maturity and stability of organic fertilisers in semi-arid Ethiopian Rift Valley
Authors: Mukai Shiro , Oyanagi Wataru 
Published: February 2021

AbstractCase studies that have comprehensively examined local organic fertilisers (OFs) for their maturity and stability are rare in sub-Saharan Africa. Farmers in the semi-arid Ethiopian Rift Valley use indigenous compost (kosi) and household wastes for OFs. With the entry of fast compost that was introduced by the administration, maturity and stability of these OFs were assessed. Their maturity was assessed by: monitoring pile temperature and volume, pH, organic matter and total nitrogen contents, and carbon to nitrogen ratio; determination of NO3– to NH4+ ratio; and respirometric measurement of CO2 evolution. Their stability was assessed by weed seed germination tests and phytotoxicity bioassays. Weed seeds that were originally contained in the feedstock of the kosi and fast compost samples became inactive during the composting process. The CO2 evolution tests and phytotoxicity bioassays indicated a probable presence of some phytotoxic compounds in the kosi. Mature kosi and immature kosi in a kosi pile should be mixed before the field application. Some samples (15%) of the household wastes contained weed seeds. The combination of several assessment methods used in this study and determination methods for nitrogen components using RQ-flex is considered to be effective for on-site quality assessment of OFs in sub-Saharan Africa.
Poor CD4/CD8 ratio recovery in HBcAb-positive HIV patients with worse immune status is associated with significantly higher CD8 cell numbers
Authors: Malagnino Vincenzo , Cerva Carlotta , Teti Elisabetta , Campogiani Laura , Compagno Mirko , Foroghi Biland Luca , Saderi Laura , Armenia Daniele , Salpini Romina , Svicher Valentina , Sotgiu Giovanni , Iannetta Marco , Andreoni Massimo , Sarmati Loredana 
Published: February 2021

AbstractLow CD4+ cell count in patients with human immunodeficiency virus (HIV) and hepatitis B virus (HBV) coinfection during combination antiretroviral therapy (cART) has been described; however, notably few studies have investigated coinfected patients positive for antibodies to the HBV c antigen (HBcAb). An observational retrospective study enrolling 190 patients was conducted by grouping patients with respect to HBV status and recording CD4+ T cell counts and percentages (CD4%), CD8+ T cell counts and percentages (CD8%), and the CD4+ to CD8+ T cell ratio (CD4/CD8) at the time of HIV diagnosis, at the start of treatment and at months 1, 2, 3, 4, 5, 6, 12, and 24 after beginning cART. One hundred and twenty patients (63.2%) were negative for previous HBV infection, while 70 (36.8%) were HBcAb-positive. A significant increase in the CD4/CD8 ratio was recorded in HIV monoinfected subjects compared to HBV coinfected patients from months 4 to 12 from the beginning of cART (p value = 0.02 at month 4, p value = 0.005 at month 5, p value = 0.006 at month 6, and p value = 0.008 at month 12). A significant increase in the absolute count of CD8+ T lymphocytes was described from months 2 to 24 from the start of cART in the subgroup of HBV coinfected patients with an AIDS event at the onset of HIV infection. The presence of HBcAb was observed to be associated with reduced CD4/CD8 ratio growth and a significantly higher proportion of subjects with CD4/CD8 < 0.45 in the HIV/HBV coinfected group. A significant increase in the CD8 T cell count was shown up to 24 months after the initiation of effective cART in the subgroup of patients with the worst immune status.
Identification of novel cell glycolysis related gene signature predicting survival in patients with breast cancer
Authors: Jiang Feng , Wu Chuyan , Wang Ming , Wei Ke , Wang Jimei 
Published: February 2021

AbstractOne of the most frequently identified tumors and a contributing cause of death in women is breast cancer (BC). Many biomarkers associated with survival and prognosis were identified in previous studies through database mining. Nevertheless, the predictive capabilities of single-gene biomarkers are not accurate enough. Genetic signatures can be an enhanced prediction method. This research analyzed data from The Cancer Genome Atlas (TCGA) for the detection of a new genetic signature to predict BC prognosis. Profiling of mRNA expression was carried out in samples of patients with TCGA BC (n = 1222). Gene set enrichment research has been undertaken to classify gene sets that vary greatly between BC tissues and normal tissues. Cox models for additive hazards regression were used to classify genes that were strongly linked to overall survival. A subsequent Cox regression multivariate analysis was used to construct a predictive risk parameter model. Kaplan–Meier survival predictions and log-rank validation have been used to verify the value of risk prediction parameters. Seven genes (PGK1, CACNA1H, IL13RA1, SDC1, AK3, NUP43, SDC3) correlated with glycolysis were shown to be strongly linked to overall survival. Depending on the 7-gene-signature, 1222 BC patients were classified into subgroups of high/low-risk. Certain variables have not impaired the prognostic potential of the seven-gene signature. A seven-gene signature correlated with cellular glycolysis was developed to predict the survival of BC patients. The results include insight into cellular glycolysis mechanisms and the detection of patients with poor BC prognosis.
The Aurora kinase/β-catenin axis contributes to dexamethasone resistance in leukemia
Authors: Shah Kinjal , Ahmed Mehreen , Kazi Julhash U. 
Published: February 2021

AbstractGlucocorticoids, such as dexamethasone and prednisolone, are widely used in cancer treatment. Different hematological malignancies respond differently to this treatment which, as could be expected, correlates with treatment outcome. In this study, we have used a glucocorticoid-induced gene signature to develop a deep learning model that can predict dexamethasone sensitivity. By combining gene expression data from cell lines and patients with acute lymphoblastic leukemia, we observed that the model is useful for the classification of patients. Predicted samples have been used to detect deregulated pathways that lead to dexamethasone resistance. Gene set enrichment analysis, peptide substrate-based kinase profiling assay, and western blot analysis identified Aurora kinase, S6K, p38, and β-catenin as key signaling proteins involved in dexamethasone resistance. Deep learning-enabled drug synergy prediction followed by in vitro drug synergy analysis identified kinase inhibitors against Aurora kinase, JAK, S6K, and mTOR that displayed synergy with dexamethasone. Combining pathway enrichment, kinase regulation, and kinase inhibition data, we propose that Aurora kinase or its several direct or indirect downstream kinase effectors such as mTOR, S6K, p38, and JAK may be involved in β-catenin stabilization through phosphorylation-dependent inactivation of GSK-3β. Collectively, our data suggest that activation of the Aurora kinase/β-catenin axis during dexamethasone treatment may contribute to cell survival signaling which is possibly maintained in patients who are resistant to dexamethasone.