bluuebunny/crossref_metadata_2025 huggingface dataset:
An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Root Growth Regulation Mechanisms in Response to Nitrogen Availability
Authors: Xin Wei , Zhang Lina , Zhang Wenzhong , Gao Jiping , Yi Jun , Zhen Xiaoxi , Du Ming , Zhao Yanze , Chen Liqiang
Published: November 2019

Nitrogen is an essential nutrient for plant growth and basic metabolic processes. Root systems play an important role in the ability of plants to obtain nutrients from the soil, and are closely related to the growth and development of above-ground plants. Root morphology analysis showed that root growth was induced under low-nitrogen conditions and inhibited under high-nitrogen conditions. To better understand the molecular mechanisms and metabolic basis underlying the rice root response to nitrogen availability, an integrated analysis of the rice root transcriptome and metabolome under three environmental conditions (low-, control, and high-nitrogen conditions) was conducted. A total of 262 and 262 differentially level metabolites were identified under low- and high-nitrogen conditions, respectively. A total of 696 and 808 differentially expressed genes were identified under low- and high-nitrogen conditions, respectively. For both the differentially expressed genes and metabolites, KEGG pathway analysis indicated that amino acid metabolism, carbon and nitrogen metabolism, phenylpropanoid metabolism, and phytohormones’ signal transduction were significantly affected by nitrogen availability. Additionally, variable levels of 65 transcription factors (TFs) were identified in rice leaves exposed to high and low nitrogen, covering 22 TF families. These results also indicate that there is a significant difference in the transcriptional regulation mechanisms of rice roots between low and high nitrogen. In summary, our study provides new information for a further understanding of the response of rice roots to low-nitrogen and high-nitrogen conditions.
Promising Therapeutic Efficacy of GC1118, an Anti-EGFR Antibody, against KRAS Mutation-Driven Colorectal Cancer Patient-Derived Xenografts
Authors: Lee Hye , Son Eunju , Lee Kyoungmin , Lee Yeri , Kim Yejin , Lee Jae-Chul , Lim Yangmi , Hur Minkyu , Kim Donggeon , Nam Do-Hyun
Published: November 2019

Epidermal growth factor receptor (EGFR)-targeted monoclonal antibodies, including cetuximab and panitumumab, are used to treat metastatic colorectal cancer (mCRC). However, this treatment is only effective for a small subset of mCRC patients positive for the wild-type KRAS GTPase. GC1118 is a novel, fully humanized anti-EGFR IgG1 antibody that displays potent inhibitory effects on high-affinity EGFR ligand-induced signaling and enhanced antibody-mediated cytotoxicity. In this study, using 51 CRC patient-derived xenografts (PDXs), we showed that KRAS mutants expressed remarkably elevated autocrine levels of high-affinity EGFR ligands compared with wild-type KRAS. In three KRAS-mutant CRCPDXs, GC1118 was more effective than cetuximab, whereas the two agents demonstrated comparable efficacy against three wild-type KRAS PDXs. Persistent phosphatidylinositol-3-kinase (PI3K)/AKT signaling was thought to underlie resistance to GC1118. In support of these findings, a preliminary improved anti-cancer response was observed in a CRC PDX harboring mutated KRAS with intrinsically high AKT activity using GC1118 combined with the dual PI3K/mammalian target of rapamycin (mTOR)/AKT inhibitor BEZ-235, without observed toxicity. Taken together, the superior antitumor efficacy of GC1118 alone or in combination with PI3K/mTOR/AKT inhibitors shows great therapeutic potential for the treatment of KRAS-mutant mCRC with elevated ratios of high- to low-affinity EGFR ligands and PI3K-AKT pathway activation.
Glucose Transport and Transporters in the Endomembranes
Authors: Lizák Beáta , Szarka András , Kim Yejin , Choi Kyu-sung , Németh Csilla E. , Marcolongo Paola , Benedetti Angelo , Bánhegyi Gábor , Margittai Éva
Published: November 2019

Glucose is a basic nutrient in most of the creatures; its transport through biological membranes is an absolute requirement of life. This role is fulfilled by glucose transporters, mediating the transport of glucose by facilitated diffusion or by secondary active transport. GLUT (glucose transporter) or SLC2A (Solute carrier 2A) families represent the main glucose transporters in mammalian cells, originally described as plasma membrane transporters. Glucose transport through intracellular membranes has not been elucidated yet; however, glucose is formed in the lumen of various organelles. The glucose-6-phosphatase system catalyzing the last common step of gluconeogenesis and glycogenolysis generates glucose within the lumen of the endoplasmic reticulum. Posttranslational processing of the oligosaccharide moiety of glycoproteins also results in intraluminal glucose formation in the endoplasmic reticulum (ER) and Golgi. Autophagic degradation of polysaccharides, glycoproteins, and glycolipids leads to glucose accumulation in lysosomes. Despite the obvious necessity, the mechanism of glucose transport and the molecular nature of mediating proteins in the endomembranes have been hardly elucidated for the last few years. However, recent studies revealed the intracellular localization and functional features of some glucose transporters; the aim of the present paper was to summarize the collected knowledge.
Profiling of RNAs from Human Islet-Derived Exosomes in a Model of Type 1 Diabetes
Authors: Krishnan Preethi , Syed Farooq , Jiyun Kang Nicole , G. Mirmira Raghavendra , Evans-Molina Carmella
Published: November 2019

Type 1 diabetes (T1D) is characterized by the immune-mediated destruction of insulin-producing islet β cells. Biomarkers capable of identifying T1D risk and dissecting disease-related heterogeneity represent an unmet clinical need. Toward the goal of informing T1D biomarker strategies, we profiled coding and noncoding RNAs in human islet-derived exosomes and identified RNAs that were differentially expressed under proinflammatory cytokine stress conditions. Human pancreatic islets were obtained from cadaveric donors and treated with/without IL-1β and IFN-γ. Total RNA and small RNA sequencing were performed from islet-derived exosomes to identify mRNAs, long noncoding RNAs, and small noncoding RNAs. RNAs with a fold change ≥1.3 and a p-value <0.05 were considered as differentially expressed. mRNAs and miRNAs represented the most abundant long and small RNA species, respectively. Each of the RNA species showed altered expression patterns with cytokine treatment, and differentially expressed RNAs were predicted to be involved in insulin secretion, calcium signaling, necrosis, and apoptosis. Taken together, our data identify RNAs that are dysregulated under cytokine stress in human islet-derived exosomes, providing a comprehensive catalog of protein coding and noncoding RNAs that may serve as potential circulating biomarkers in T1D.
Cannabidiol—from Plant to Human Body: A Promising Bioactive Molecule with Multi-Target Effects in Cancer
Authors: Kis Brigitta , Ifrim Feng Chen , Buda Valentina , Avram Stefana , Pavel Ioana Zinuca , Antal Diana , Paunescu Virgil , Dehelean Cristina Adriana , Ardelean Florina , Diaconeasa Zorita , Soica Codruta , Danciu Corina
Published: November 2019

Cannabis sativa L. is a plant long used for its textile fibers, seed oil, and oleoresin with medicinal and psychoactive properties. It is the main source of phytocannabinoids, with over 100 compounds detected so far. In recent years, a lot of attention has been given to the main phytochemicals present in Cannabis sativa L., namely, cannabidiol (CBD) and Δ9-tetrahydrocannabinol (THC). Compared to THC, CBD has non-psychoactive effects, an advantage for clinical applications of anti-tumor benefits. The review is designed to provide an update regarding the multi-target effects of CBD in different types of cancer. The main focus is on the latest in vitro and in vivo studies that present data regarding the anti-proliferative, pro-apoptotic, cytotoxic, anti-invasive, anti-antiangiogenic, anti-inflammatory, and immunomodulatory properties of CBD together with their mechanisms of action. The latest clinical evidence of the anticancer effects of CBD is also outlined. Moreover, the main aspects of the pharmacological and toxicological profiles are given.
Functional Analysis of the Soybean GmCDPK3 Gene Responding to Drought and Salt Stresses
Authors: Wang Dan , Liu Yuan-Xia , Yu Qian , Zhao Shu-Ping , Zhao Juan-Ying , Ru Jing-Na , Cao Xin-You , Fang Zheng-Wu , Chen Jun , Zhou Yong-Bin , Chen Ming , Ma You-Zhi , Xu Zhao-Shi , Lan Jin-Hao
Published: November 2019

Plants have a series of response mechanisms to adapt when they are subjected to external stress. Calcium-dependent protein kinases (CDPKs) in plants function against a variety of abiotic stresses. We screened 17 CDPKs from drought- and salt-induced soybean transcriptome sequences. The phylogenetic tree divided CDPKs of rice, Arabidopsis and soybean into five groups (I–V). Cis-acting element analysis showed that the 17 CDPKs contained some elements associated with drought and salt stresses. Quantitative real-time PCR (qRT-PCR) analysis indicated that the 17 CDPKs were responsive after different degrees of induction under drought and salt stresses. GmCDPK3 was selected as a further research target due to its high relative expression. The subcellular localization experiment showed that GmCDPK3 was located on the membrane of Arabidopsis mesophyll protoplasts. Overexpression of GmCDPK3 improved drought and salt resistance in Arabidopsis. In the soybean hairy roots experiment, the leaves of GmCDPK3 hairy roots with RNA interference (GmCDPK3-RNAi) soybean lines were more wilted than those of GmCDPK3 overexpression (GmCDPK3-OE) soybean lines after drought and salt stresses. The trypan blue staining experiment further confirmed that cell membrane damage of GmCDPK3-RNAi soybean leaves was more severe than in GmCDPK3-OE soybean lines. In addition, proline (Pro) and chlorophyll contents were increased and malondialdehyde (MDA) content was decreased in GmCDPK3-OE soybean lines. On the contrary, GmCDPK3-RNAi soybean lines had decreased Pro and chlorophyll content and increased MDA. The results indicate that GmCDPK3 is essential in resisting drought and salt stresses.
Model Optimization and In Silico Analysis of Potential Dipeptidyl Peptidase IV Antagonists from GC-MS Identified Compounds in Nauclea latifolia Leaf Extracts
Authors: Iheagwam Franklyn Nonso , Ogunlana Olubanke Olujoke , Chinedu Shalom Nwodo
Published: November 2019

Dipeptidyl peptidase IV (DPP-IV) is a pharmacotherapeutic target in type 2 diabetes. Inhibitors of this enzyme constitute a new class of drugs used in the treatment and management of type 2 diabetes. In this study, phytocompounds in Nauclea latifolia (NL) leaf extracts, identified using gas chromatography–mass spectroscopy (GC-MS), were tested for potential antagonists of DPP-IV via in silico techniques. Phytocompounds present in N. latifolia aqueous (NLA) and ethanol (NLE) leaf extracts were identified using GC–MS. DPP-IV model optimization and molecular docking of the identified compounds/standard inhibitors in the binding pocket was simulated. Drug-likeness, pharmacokinetic and pharmacodynamic properties of promising docked leads were also predicted. Results showed the presence of 50 phytocompounds in NL extracts of which only 2-O-p-methylphenyl-1-thio-β-d-glucoside, 3-tosylsedoheptulose, 4-benzyloxy-6-hydroxymethyl-tetrahydropyran-2,3,5-triol and vitamin E exhibited comparable or better binding iGEMDOCK and AutoDock Vina scores than the clinically prescribed standards. These four compounds exhibited promising drug-likeness as well as absorption, distribution, metabolism, excretion and toxicity (ADMET) properties suggesting their candidature as novel leads for developing DPP-IV inhibitors.
McArdle Disease: New Insights into Its Underlying Molecular Mechanisms
Authors: Llavero Francisco , Arrazola Sastre Alazne , Luque Montoro Miriam , Gálvez Patricia , Lacerda Hadriano M , Parada Luis A. , Zugaza José Luis
Published: November 2019

McArdle disease, also known as glycogen storage disease type V (GSDV), is characterized by exercise intolerance, the second wind phenomenon, and high serum creatine kinase activity. Here, we recapitulate PYGM mutations in the population responsible for this disease. Traditionally, McArdle disease has been considered a metabolic myopathy caused by the lack of expression of the muscle isoform of the glycogen phosphorylase (PYGM). However, recent findings challenge this view, since it has been shown that PYGM is present in other tissues than the skeletal muscle. We review the latest studies about the molecular mechanism involved in glycogen phosphorylase activity regulation. Further, we summarize the expression and functional significance of PYGM in other tissues than skeletal muscle both in health and McArdle disease. Furthermore, we examine the different animal models that have served as the knowledge base for better understanding of McArdle disease. Finally, we give an overview of the latest state-of-the-art clinical trials currently being carried out and present an updated view of the current therapies.
The Precursor for Nerve Growth Factor (proNGF) in Thyroid Cancer Lymph Node Metastases: Correlation with Primary Tumour and Pathological Variables
Authors: Rowe Christopher W. , Dill Tony , Faulkner Sam , Gedye Craig , Paul Jonathan W. , Tolosa Jorge M. , Jones Mark , King Simon , Smith Roger , Hondermarck Hubert
Published: November 2019

Metastases in thyroid cancer are associated with aggressive disease and increased patient morbidity, but the factors driving metastatic progression are unclear. The precursor for nerve growth factor (proNGF) is increased in primary thyroid cancers, but its expression or significance in metastases is not known. In this study, we analysed the expression of proNGF in a retrospective cohort of thyroid cancer lymph node metastases (n = 56), linked with corresponding primary tumours, by automated immunohistochemistry and digital quantification. Potential associations of proNGF immunostaining with clinical and pathological parameters were investigated. ProNGF staining intensity (defined by the median h-score) was significantly higher in lymph node metastases (h-score 94, interquartile range (IQR) 50–147) than in corresponding primary tumours (57, IQR 42–84) (p = 0.002). There was a correlation between proNGF expression in primary tumours and corresponding metastases, where there was a 0.68 (95% CI 0 to 1.2) increase in metastatic tumour h-score for each unit increase in the primary tumour h-score. However, larger tumours (both primary and metastatic) had lower proNGF expression. In a multivariate model, proNGF expression in nodal metastases was negatively correlated with lateral neck disease and being male. In conclusion, ProNGF is expressed in locoregional metastases of thyroid cancer and is higher in lymph node metastases than in primary tumours, but is not associated with high-risk clinical features.
Therapeutic Effect of Iron Citrate in Blocking Calcium Deposition in High Pi-Calcified VSMC: Role of Autophagy and Apoptosis
Authors: Ciceri Paola , Falleni Monica , Tosi Delfina , Martinelli Carla , Cannizzo Stefania , Marchetti Giulia , D’Arminio Monforte Antonella , Bulfamante Gaetano , Block Geoffrey A , Messa Piergiorgio , Cozzolino Mario
Published: November 2019

In chronic kidney disease (CKD), the first cause of mortality is cardiovascular disease induced mainly by vascular calcification (VC). Recently, iron-based phosphate binders have been proposed in advanced CKD to treat hyperphosphatemia. We studied the effect of iron citrate (iron) on the progression of calcification in high-phosphate (Pi) calcified VSMC. Iron arrested further calcification when added on days 7–15 in the presence of high Pi (1.30 ± 0.03 vs 0.61 ± 0.02; OD/mg protein; day 15; Pi vs Pi + Fe, p < 0.01). We next investigated apoptosis and autophagy. Adding iron to high-Pi-treated VSMC, on days 7–11, decreased apoptotic cell number (17.3 ± 2.6 vs 11.6 ± 1.6; Annexin V; % positive cells; day 11; Pi vs Pi + Fe; p < 0.05). The result was confirmed thorough analysis of apoptotic nuclei both in VSMCs and aortic rings treated on days 7–15 (3.8 ± 0.2 vs 2.3 ± 0.3 and 4.0 ± 0.3 vs 2.2 ± 0.2; apoptotic nuclei; arbitrary score; day 15; Pi vs Pi + Fe; VSMCs and aortic rings; p < 0.05). Studying the prosurvival axis GAS6/AXL, we found that iron treatment on days 9–14 counteracted protein high-Pi-stimulated down-regulation and induced its de novo synthesis. Moreover, iron added on days 9–15 potentiated autophagy, as detected by an increased number of autophagosomes with damaged mitochondria and an increase in autophagic flux. Highlighting the effect of iron on apoptosis, we demonstrated its action in blocking the H2O2-induced increase in calcification added both before high Pi treatment and when the calcification was already exacerbated. In conclusion, we demonstrate that iron arrests further high Pi-induced calcium deposition through an anti-apoptotic action and the induction of autophagy on established calcified VSMC.
WY-14643 Regulates CYP1B1 Expression through Peroxisome Proliferator-Activated Receptor α-Mediated Signaling in Human Breast Cancer Cells
Authors: Hwang Yong Pil , Won Seong Su , Jin Sun Woo , Lee Gi Ho , Pham Thi Hoa , Choi Jae Ho , Kang Keon Wook , Jeong Hye Gwang
Published: November 2019

Human cytochrome P450 1B1 (CYP1B1)-mediated biotransformation of endobiotics and xenobiotics plays an important role in the progression of human breast cancer. In this study, we investigated the effects of WY-14643, a peroxisome proliferator-activated receptor α (PPARα) agonist, on CYP1B1 expression and the related mechanism in MCF7 breast cancer cells. We performed quantitative reverse transcription-polymerase chain reaction, transient transfection, and chromatin immunoprecipitation to evaluate the effects of PPARα on peroxisome proliferator response element (PPRE)-mediated transcription. WY-14643 increased the protein and mRNA levels of CYP1B1, as well as promoter activity, in MCF-7 cells. Moreover, WY-14643 plus GW6471, a PPARα antagonist, significantly inhibited the WY-14643-mediated increase in CYP1B1 expression. PPARα knockdown by a small interfering RNA markedly suppressed the induction of CYP1B1 expression by WY-14643, suggesting that WY-14643 induces CYP1B1 expression via a PPARα-dependent mechanism. Bioinformatics analysis identified putative PPREs (−833/−813) within the promoter region of the CYP1B1 gene. Inactivation of these putative PPREs by deletion mutagenesis suppressed the WY-14643-mediated induction of CYP1B1 promoter activation. Furthermore, WY-14643 induced PPARα to assume a form capable of binding specifically to the PPRE-binding site in the CYP1B1 promoter. Our findings suggest that WY-14643 induces the expression of CYP1B1 through activation of PPARα.
Influence of the Sense of Coherence, the Doctor–Patient Relationship, Optimism and Non-Haematological Adverse Reactions on Health-Related Quality of Life in Patients with Breast Cancer
Authors: Prieto-Callejero Blanca , Rivera Francisco , Andrés-Villas Montserrat , Gómez-Salgado Juan
Published: November 2019

Breast cancer is the most common malignant tumour in women around the world. The objective of this study was to quantify the number of non-haematological adverse reactions associated with chemotherapy, as well as to assess the effect of the sense of coherence, optimism–pessimism and the quality of the doctor–patient relationship on the quality of life of breast cancer patients. To this end, a cross-sectional descriptive study was conducted involving 110 breast cancer patients who were treated with docetaxel, epirubicin, and cyclophosphamide during the period 2012–2014. The difference in the quality of life in patients who have five or fewer toxicities compared to those with more than six is highlighted. This difference is not as important when comparing patients with 6 to 10 toxicities and those with more than 10. The multivariate model used in this study corroborates the direct implication of the sense of coherence on the quality of life and adds the number of adverse reactions as a new construct. This has virtually the same impact on the quality of life of these patients, but in reverse. In conclusion, to improve the quality of life of breast cancer patients it would be necessary to have an impact on the number of adverse reactions involved in chemotherapeutic treatment, as well as on psychological interventions, with the sense of coherence as a possible starting point.
Survivability of Anhydrobiotic Cyanobacteria in Salty Ice: Implications for the Habitability of Icy Worlds
Authors: Cosciotti Barbara , Balbi Amedeo , Ceccarelli Alessandra , Fagliarone Claudia , Mattei Elisabetta , Lauro Sebastian Emanuel , Di Paolo Federico , Pettinelli Elena , Billi Daniela
Published: November 2019

Two anhydrobiotic strains of the cyanobacterium Chroococcidiopsis, namely CCMEE 029 and CCMEE 171, isolated from the Negev Desert in Israel and from the Dry Valleys in Antarctica, were exposed to salty-ice simulations. The aim of the experiment was to investigate the cyanobacterial capability to survive under sub-freezing temperatures in samples simulating the environment of icy worlds. The two strains were mixed with liquid solutions having sub-eutectic concentration of Na2SO4, MgSO4 and NaCl, then frozen down to different final temperatures (258 K, 233 K and 203 K) in various experimental runs. Both strains survived the exposure to 258 K in NaCl solution, probably as they migrated in the liquid veins between ice grain boundaries. However, they also survived at 258 K in Na2SO4 and MgSO4-salty-ice samples—that is, a temperature well below the eutectic temperature of the solutions, where liquid veins should not exist anymore. Moreover, both strains survived the exposure at 233 K in each salty-ice sample, with CCMEE 171 showing an enhanced survivability, whereas there were no survivors at 203 K. The survival limit at low temperature was further extended when both strains were exposed to 193 K as air-dried cells. The results suggest that vitrification might be a strategy for microbial life forms to survive in potentially habitable icy moons, for example in Europa’s icy crust. By entering a dried, frozen state, they could be transported from niches, which became non-habitable to new habitable ones, and possibly return to metabolic activity.
Fucoidan from Undaria pinnatifida Ameliorates Epidermal Barrier Disruption via Keratinocyte Differentiation and CaSR Level Regulation
Authors: Chen Yu , Li Xuenan , Gan Xiaoshuang , Qi Junmei , Che Biao , Tai Meiling , Gao Shuang , Zhao Wengang , Xu Nuo , Hu Zhenlin
Published: November 2019

The epidermal barrier acts as a line of defense against external agents as well as helps to maintain body homeostasis. The calcium concentration gradient across the epidermal barrier is closely related to the proliferation and differentiation of keratinocytes (KCs), and the regulation of these two processes is the key to the repair of epidermal barrier disruption. In the present study, we found that fucoidan from Undaria pinnatifida (UPF) could promote the repair of epidermal barrier disruption in mice. The mechanistic study demonstrated that UPF could promote HaCaT cell differentiation under low calcium condition by up-regulating the expression of calcium-sensing receptor (CaSR), which could then lead to the activation of the Catenin/PLCγ1 pathway. Further, UPF could increase the expression of CaSR through activate the ERK and p38 pathway. These findings reveal the molecular mechanism of UPF in the repair of the epidermal barrier and provide a basis for the development of UPF into an agent for the repair of epidermal barrier repair.
Antiviral Activity of Germacrone against Pseudorabies Virus in Vitro
Authors: He Wanting , Zhai Xiaofeng , Su Jingyin , Ye Rui , Zheng Yuna , Su Shuo
Published: November 2019

Pseudorabies virus (PRV), a member of the Herpesviridae, is the causative agent of an acute infectious disease in a variety of animals. The emergence of a novel variant strain brought huge economic losses to the pig industry since classical vaccine strains were not completely effective against variant strains. Therefore, the development of new anti-pseudorabies virus drugs and vaccines is of great significance for the treatment and prevention of pseudorabies. In this study, we found that germacrone, one of the major components of the essential oils extracted from Rhizoma Curcuma, was able to effectively inhibit PRV replication in a dose-dependent manner in vitro. Germacrone showed antiviral activity against PRV in the early phase of the viral replication cycle. Moreover, we found that germacrone does not directly kill the virus, nor does it affect the expression of the PRV receptor protein nectin-1, nectin-2, and CD155. Our results suggest germacrone could be used as an efficient microbicide or immunomodulatory agent in the control of the emerging variant PRV.
Comparative Analysis of the YABBY Gene Family of Bienertia sinuspersici, a Single-Cell C4 Plant
Authors: Soundararajan Prabhakaran , Won So Youn , Park Dong Suk , Lee Yeon-Hee , Kim Jung Sun
Published: November 2019

The emergence and expression of the YABBY gene family (YGF) coincided with the evolution of leaves in seed plants, and was integral to the early evidence of lamina followed by reproductive development. YGF contains six subclasses, i.e., CRC, INO, FIL, YAB2, YAB3, and YAB5. This study aims to extract the genome sequences of the YGF in Bienertia sinuspersici, an important model plant for single-cell C4 (SCC4), non-Kranz photosynthesis. A comparative genomic analysis was undertaken with Vitis vinefera, Arabidopsis thaliana, Brassica rapa, and Chenopodium quinoa. Six copies of YGF were present in B. sinuspersici and A. thaliana with a single copy of each YGF subgroup. V. vinefera possessed seven copies of YGF with duplicates in FIL and YAB2 subgroups, but no YAB3. B. rapa and C. quinoa after whole genome duplication contained additional copies of YGF. The gene structure and conserved motifs were analyzed among the YGF. In addition, the relative quantification of YGF was analyzed in the leaves, reproductive developmental stages such as the bud, and the pre-anthesis and anthesis stages in B. sinuspersici, A. thaliana, and B. rapa. CRC and INO possessed conserved floral-specific expression. Temporal and perpetual changes in the expression of YGF orthologs were observed in the leaves and reproductive developmental stages. The results of this study provide an overview of YGF evolution, copy number, and its differential expression in B. sinuspersici. Further studies are required to shed light on the roles of YABBY genes in the evolution of SCC4 plants and their distinct physiologies.
Yoga Posture Recognition and Quantitative Evaluation with Wearable Sensors Based on Two-Stage Classifier and Prior Bayesian Network
Authors: Wu Ze , Zhang Jiwen , Chen Ken , Fu Chenglong
Published: November 2019

Currently, with the satisfaction of people’s material life, sports, like yoga and tai chi, have become essential activities in people’s daily life. For most yoga amateurs, they could only learn yoga by self-study, like mechanically imitating from yoga video. They could not know whether they performed standardly without feedback and guidance. In this paper, we proposed a full-body posture modeling and quantitative evaluation method to recognize and evaluate yoga postures to provide guidance to the learner. Back propagation artificial neural network (BP-ANN) was adopted as the first classifier to divide yoga postures into different categories, and fuzzy C-means (FCM) was utilized as the second classifier to classify the postures in a category. The posture data on each body part was regarded as a multidimensional Gaussian variable to build a Bayesian network. The conditional probability of the Gaussian variable corresponding to each body part relative to the Gaussian variable corresponding to the connected body part was used as criterion to quantitatively evaluate the standard degree of body parts. The angular differences between nonstandard parts and the standard model could be calculated to provide guidance with an easily-accepted language, such as “lift up your left arm”, “straighten your right forearm”. To evaluate our method, a wearable device with 11 inertial measurement units (IMUs) fixed onto the body was designed to measure yoga posture data with quaternion format, and the posture database with a total of 211,643 data frames and 1831 posture instances was collected from 11 subjects. Both the posture recognition test and evaluation test were conducted. In the recognition test, 30% data was randomly picked from the database to train BP-ANN and FCM classifiers, and the recognition accuracy of the remaining 70% data was 95.39%, which is highly competitive with previous posture recognition approaches. In the evaluation test, 30% data were picked randomly from subject three, subject four, and subject six, to train the Bayesian network. The probabilities of nonstandard parts were almost all smaller than 0.3, while the probabilities of standard parts were almost all greater than 0.5, and thus the nonstandard parts of body posture could be effectively separated and picked for guidance. We also tested separately the trainers’ yoga posture performance in the condition of without and with guidance provided by our proposed method. The results showed that with guidance, the joint angle errors significantly decreased.
Infrared Spectroscopy with a Fiber-Coupled Quantum Cascade Laser for Attenuated Total Reflection Measurements Towards Biomedical Applications
Authors: Jernelv Ine L. , Strøm Karina , Hjelme Dag Roar , Aksnes Astrid
Published: November 2019

The development of rapid and accurate biomedical laser spectroscopy systems in the mid-infrared has been enabled by the commercial availability of external-cavity quantum cascade lasers (EC-QCLs). EC-QCLs are a preferable alternative to benchtop instruments such as Fourier transform infrared spectrometers for sensor development as they are small and have high spectral power density. They also allow for the investigation of multiple analytes due to their broad tuneability and through the use of multivariate analysis. This article presents an in vitro investigation with two fiber-coupled measurement setups based on attenuated total reflection spectroscopy and direct transmission spectroscopy for sensing. A pulsed EC-QCL (1200–900 cm − 1 ) was used for measurements of glucose and albumin in aqueous solutions, with lactate and urea as interferents. This analyte composition was chosen as an example of a complex aqueous solution with relevance for biomedical sensors. Glucose concentrations were determined in both setup types with root-mean-square error of cross-validation (RMSECV) of less than 20 mg/dL using partial least-squares (PLS) regression. These results demonstrate accurate analyte measurements, and are promising for further development of fiber-coupled, miniaturised in vivo sensors based on mid-infrared spectroscopy.
Absolute Distance Measurement Using Frequency-Scanning Interferometry Based on Hilbert Phase Subdivision
Authors: Jiang Shuo , Liu Bo , Wang Huachuang , Zhao Bin
Published: November 2019

In order to eliminate the influence of laser frequency nonlinearity, the frequency-scanning interferometry (FSI) often uses the beat signal of an auxiliary interferometer as the external clock. The time points at every amplitude peaks and bottoms of the auxiliary beat signal are selected as the sampling time points for the main interferometer signal. To satisfy the Nyquist sampling requirement, the optical path difference (OPD) of the delay fiber in auxiliary interferometer should be at least twice longer than the measurement distance. In this paper, we proposed a method to shorten the length of delay fiber. The Hilbert transform was used to extract the phase of the auxiliary interference signal and calculate the time points corresponding to subdivided phase intervals. Then, the main interference signal was resampled at these moments, and the fast Fourier transform was performed on the resampled signal. The experimental results showed that the target at the distance of about 5 m was measured when the OPD of the auxiliary interferometer was about 4.5 m. The standard deviation of the distance measurement results could reach 4.64 μm.
Nanoparticles as Emerging Labels in Electrochemical Immunosensors
Authors: Iglesias-Mayor Alba , Amor-Gutiérrez Olaya , Costa-García Agustín , de la Escosura-Muñiz Alfredo
Published: November 2019

This review shows recent trends in the use of nanoparticles as labels for electrochemical immunosensing applications. Some general considerations on the principles of both the direct detection based on redox properties and indirect detection through electrocatalytic properties, before focusing on the applications for mainly proteins detection, are given. Emerging use as blocking tags in nanochannels-based immunosensing systems is also covered in this review. Finally, aspects related to the analytical performance of the developed devices together with prospects for future improvements and applications are discussed.
Overview of the Evolution of Silica-Based Chromo-Fluorogenic Nanosensors
Authors: Pla Luis , Lozano-Torres Beatriz , Martínez-Máñez Ramón , Sancenón Félix , Ros-Lis Jose V.
Published: November 2019

This review includes examples of silica-based, chromo-fluorogenic nanosensors with the aim of illustrating the evolution of the discipline in recent decades through relevant research developed in our group. Examples have been grouped according to the sensing strategies. A clear evolution from simply functionalized materials to new protocols involving molecular gates and the use of highly selective biomolecules such as antibodies and oligonucleotides is reported. Some final examples related to the evolution of chromogenic arrays and the possible use of nanoparticles to communicate with other nanoparticles or cells are also included. A total of 64 articles have been summarized, highlighting different sensing mechanisms.
Anti-Clutter Gaussian Inverse Wishart PHD Filter for Extended Target Tracking
Authors: Huang Yuan , Wang Liping , Wang Xueying , An Wei
Published: November 2019

The extended target Gaussian inverse Wishart probability hypothesis density (ET-GIW-PHD) filter overestimates the number of targets under high clutter density. The reason for this is that the source of measurements cannot be determined correctly if only the number of measurements is used. To address this problem, we proposed an anti-clutter filter with hypothesis testing, we take into account the number of measurements in cells, the target state and spatial distribution of clutter to decide whether the measurements in cell are clutter. Specifically, the hypothesis testing method is adopted to determine the origination of the measurements. Then, the likelihood functions of targets and clutter are deduced based on the information mentioned above, resulting in the likelihood ratio test statistic. Next, the likelihood ratio test statistic is proved to be subject to a chi-square distribution and a threshold corresponding to the confidence coefficient is introduced and the measurements below this threshold are considered as clutter. Then the correction step of ET-GIW-PHD is revised based on hypothesis testing results. Extensive experiments have demonstrated the significant performance improvement of our proposed method.
Wearable-Sensor-Based Detection and Prediction of Freezing of Gait in Parkinson’s Disease: A Review
Authors: Pardoel Scott , Kofman Jonathan , Nantel Julie , Lemaire Edward D.
Published: November 2019

Freezing of gait (FOG) is a serious gait disturbance, common in mid- and late-stage Parkinson’s disease, that affects mobility and increases fall risk. Wearable sensors have been used to detect and predict FOG with the ultimate aim of preventing freezes or reducing their effect using gait monitoring and assistive devices. This review presents and assesses the state of the art of FOG detection and prediction using wearable sensors, with the intention of providing guidance on current knowledge, and identifying knowledge gaps that need to be filled and challenges to be considered in future studies. This review searched the Scopus, PubMed, and Web of Science databases to identify studies that used wearable sensors to detect or predict FOG episodes in Parkinson’s disease. Following screening, 74 publications were included, comprising 68 publications detecting FOG, seven predicting FOG, and one in both categories. Details were extracted regarding participants, walking task, sensor type and body location, detection or prediction approach, feature extraction and selection, classification method, and detection and prediction performance. The results showed that increasingly complex machine-learning algorithms combined with diverse feature sets improved FOG detection. The lack of large FOG datasets and highly person-specific FOG manifestation were common challenges. Transfer learning and semi-supervised learning were promising for FOG detection and prediction since they provided person-specific tuning while preserving model generalization.
Validation of Novel Relative Orientation and Inertial Sensor-to-Segment Alignment Algorithms for Estimating 3D Hip Joint Angles
Authors: Adamowicz Lukas , Gurchiek Reed D. , Ferri Jonathan , Ursiny Anna T. , Fiorentino Niccolo , McGinnis Ryan S.
Published: November 2019

Wearable sensor-based algorithms for estimating joint angles have seen great improvements in recent years. While the knee joint has garnered most of the attention in this area, algorithms for estimating hip joint angles are less available. Herein, we propose and validate a novel algorithm for this purpose with innovations in sensor-to-sensor orientation and sensor-to-segment alignment. The proposed approach is robust to sensor placement and does not require specific calibration motions. The accuracy of the proposed approach is established relative to optical motion capture and compared to existing methods for estimating relative orientation, hip joint angles, and range of motion (ROM) during a task designed to exercise the full hip range of motion (ROM) and fast walking using root mean square error (RMSE) and regression analysis. The RMSE of the proposed approach was less than that for existing methods when estimating sensor orientation ( 12.32 ° and 11.82 ° vs. 24.61 ° and 23.76 ° ) and flexion/extension joint angles ( 7.88 ° and 8.62 ° vs. 14.14 ° and 15.64 ° ). Also, ROM estimation error was less than 2.2 ° during the walking trial using the proposed method. These results suggest the proposed approach presents an improvement to existing methods and provides a promising technique for remote monitoring of hip joint angles.
New Fast Arctangent Approximation Algorithm for Generic Real-Time Embedded Applications
Authors: Benammar Mohieddine , Alassi Abdulrahman , Gastli Adel , Ben-Brahim Lazhar , Touati Farid
Published: November 2019

Fast and accurate arctangent approximations are used in several contemporary applications, including embedded systems, signal processing, radar, and power systems. Three main approximation techniques are well-established in the literature, varying in their accuracy and resource utilization levels. Those are the iterative coordinate rotational digital computer (CORDIC), the lookup tables (LUTs)-based, and the rational formulae techniques. This paper presents a novel technique that combines the advantages of both rational formulae and LUT approximation methods. The new algorithm exploits the pseudo-linear region around the tangent function zero point to estimate a reduced input arctangent through a modified rational approximation before referring this estimate to its original value using miniature LUTs. A new 2nd order rational approximation formula is introduced for the first time in this work and benchmarked against existing alternatives as it improves the new algorithm performance. The eZDSP-F28335 platform has been used for practical implementation and results validation of the proposed technique. The contributions of this work are summarized as follows: (1) introducing a new approximation algorithm with high precision and application-based flexibility; (2) introducing a new rational approximation formula that outperforms literature alternatives with the algorithm at higher accuracy requirement; and (3) presenting a practical evaluation index for rational approximations in the literature.
Photonic Crystal Fiber Plasmonic Sensor Based on Dual Optofluidic Channel
Authors: Chen Nan , Chang Min , Lu Xinglian , Zhou Jun , Zhang Xuedian
Published: November 2019

A hexagonal photonic crystal fiber (PCF) sensor with a dual optofluidic channel based on surface plasmon resonance (SPR) effect is proposed. The sensor characteristic is numerically explored by software integrated with the finite element method (FEM). The numerical results show that, when the analyte refractive index (RI) varies from 1.32 to 1.38, high linearity between resonance wavelength and analyte RI is obtained and the value of adjusted R2 is up to 0.9993. Simultaneously, the proposed sensor has maximum wavelength sensitivity (WS) of 5500 nm/RIU and maximum amplitude sensitivity (AS) of 150 RIU−1, with an RI resolution of 1.82 × 10−5 RIU. Besides, owing to a simple structure and good tolerance of the proposed sensor, it can be easily fabricated by means of existing technology. The proposed sensor suggests promising applications in oil detection, temperature measurement, water quality monitoring, bio-sensing, and food safety.
Variation of Suspended Particles in the Bottom Layer of the East China Sea with Data from Seafloor Observatory
Authors: Shang Dinghui , Qin Rufu , Xu Huiping , Xu Changwei , Sun Kelin , Zhou Yusheng
Published: November 2019

The in situ scattering and transmissometry laser (LISST-100X), equipped with an acoustic wave and current (AWAC) meter and conductivity, temperature, and depth (CTD) instruments over the seabed in the East China Sea, was used to monitor the variation in suspended particles in the bottom sea layer, including particle size distribution (PSD) and volume concentration. The power law approximation was tested to describe the variability in PSD based on the field data. The results show that the power law was robust in processing continuous data, accompanied with the same optimal reference particle size (~63 μm) and little change in the corresponding exponent (~3.4) in both periods. Suspended particles were divided into three types: macroflocs (>133 μm), microflocs (36–133 μm), and single grains (<36 μm). Particle sizes were coarse during the two seasons, with macroflocs representing more than 60% of all the suspended particles, especially in February, when the particle size spectra were usually open-ended. Results from the harmonic analysis method indicate that tidal-induced resuspension and advection are the major reasons for the diurnal dynamics of sediments. Due to the tidal asymmetry in the region, we only found one mode in volume concentration at the moment of maximum velocity. However, the ratios of macroflocs were bimodal, with maximum floods and ebbs in one tidal cycle in February, when the higher mode at the maximum ebbs may be contributed to by the flocculation of finer particles considering the decreasing ratios of finer particles. Due to the enhanced stratification and the clean barrier built up by the Taiwan Warm Current in the southeast corner, the significant daily variation in suspended particles observed in February weakened in September. The influence of waves was uncertain, although the correlation coefficient between significant wave height and volume concentration was about 64% in February.
Method for the Detection of Tumor Blood Vessels in Neurosurgery Using a Gripping Force Feedback System
Authors: Yokota Hiroki , Yoneyama Takeshi , Watanabe Tetsuyou , Sasagawa Yasuo , Nakada Mitsutoshi
Published: November 2019

Avoiding unnecessary bleeding during neuroendoscopic surgeries is crucial because achieving hemostasis in a narrow operating space is challenging. However, when the location of a blood vessel in a tumor cannot be visually confirmed, unintentional damage to the vessel and subsequent bleeding may occur. This study proposes a method for tumor blood vessel detection using a master–slave surgical robot system equipped with a force sensor in the slave gripper. Using this method, blood pulsation inside a tumor was detected, displayed as a gripping force wave, via the slave force sensor. The characteristics of gripping force due to blood pulsation were extracted by measuring the fluctuation of the force in real time. The presence or absence of blood vessels was determined on the basis of cross-correlation coefficients between the gripping force fluctuation waveform due to blood pulsation and model fluctuation waveform. Experimental validation using two types of simulated tumors (soft: E = 6 kPa; hard: E = 38 kPa) and a simulated blood vessel (E = 1.9 MPa, radius = 0.5 mm, thickness = 0.1 mm) revealed that the presence of blood vessels could be detected while gripping at a constant angle and during transient gripping.
A Novel Method for Identifying Crack and Shaft Misalignment Faults in Rotor Systems under Noisy Environments Based on CNN
Authors: Zhao Wang , Hua Chunrong , Dong Dawei , Ouyang Huajiang
Published: November 2019

Crack and shaft misalignment are two common types of fault in a rotor system, both of which have very similar dynamic response characteristics, and the vibration signals are vulnerable to noise contamination because of the interaction among different components of rotating machinery in the actual industrial environment, resulting in great difficulties in fault identification of a rotor system based on vibration signals. A method for identification of faults in the form of crack and shaft misalignments is proposed in this paper, which combines variational mode decomposition (VMD) and probabilistic principal component analysis (PPCA) to denoise the collected vibration signals from a test rig and then achieve signal feature extraction and fault classification with convolutional artificial neural network (CNN). The key parameters of the CNN are optimized and determined by genetic algorithm (GA) firstly, and the domain adaptability of the trained network is verified by the signals with different signal-to-noise ratio (SNR) values; then, the noisy vibration signals are decomposed into multiple band-limited intrinsic modal functions by VMD, and further data dimension reduction is performed by PPCA to realize the separation of the useful signals from noise; finally, the crack and shaft misalignment of the rotor system are identified by the optimized CNN. The results show that the proposed method can effectively remove the interference noise and extract the intrinsic features of the vibration signals, and the recognition rates of crack and shaft misalignment faults for the rotor system with different SNR values are more than 99%, which is considered to be very effective and useful.