bluuebunny/crossref_metadata_2025 huggingface dataset:
Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities
Authors: Kaisers  Wolfgang , Schwender Holger , Schaal  Heiner
Published: November 2018

We apply hierarchical clustering (HC) of DNA k-mer counts on multiple Fastq files. The tree structures produced by HC may reflect experimental groups and thereby indicate experimental effects, but clustering of preparation groups indicates the presence of batch effects. Hence, HC of DNA k-mer counts may serve as a diagnostic device. In order to provide a simple applicable tool we implemented sequential analysis of Fastq reads with low memory usage in an R package (seqTools) available on Bioconductor. The approach is validated by analysis of Fastq file batches containing RNAseq data. Analysis of three Fastq batches downloaded from ArrayExpress indicated experimental effects. Analysis of RNAseq data from two cell types (dermal fibroblasts and Jurkat cells) sequenced in our facility indicate presence of batch effects. The observed batch effects were also present in reads mapped to the human genome and also in reads filtered for high quality (Phred > 30). We propose, that hierarchical clustering of DNA k-mer counts provides an unspecific diagnostic tool for RNAseq experiments. Further exploration is required once samples are identified as outliers in HC derived trees.
Gramicidin Lateral Distribution in Phospholipid Membranes: Fluorescence Phasor Plots and Statistical Mechanical Model
Authors: Sugár István P. , Bonanno Alexander P. , Chong Parkson Lee-Gau
Published: November 2018

When using small mole fraction increments to study gramicidins in phospholipid membranes, we found that the phasor dots of intrinsic fluorescence of gramicidin D and gramicidin A in dimyristoyl-sn-glycero-3-phosphocholine (DMPC) unilamellar and multilamellar vesicles exhibit a biphasic change with peptide content at 0.143 gramicidin mole fraction. To understand this phenomenon, we developed a statistical mechanical model of gramicidin/DMPC mixtures. Our model assumes a sludge-like mixture of fluid phase and aggregates of rigid clusters. In the fluid phase, gramicidin monomers are randomly distributed. A rigid cluster is formed by a gramicidin dimer and DMPC molecules that are condensed to the dimer, following particular stoichiometries (critical gramicidin mole fractions, Xcr including 0.143). Rigid clusters form aggregates in which gramicidin dimers are regularly distributed, in some cases, even to superlattices. At Xcr, the size of cluster aggregates and regular distributions reach a local maximum. Before a similar model was developed for cholesterol/DMPC mixtures (Sugar and Chong (2012) J. Am. Chem. Soc. 134, 1164–1171) and here the similarities and differences are discussed between these two models.
Imaging and Molecular Mechanisms of Alzheimer’s Disease: A Review
Authors: Femminella Grazia Daniela , Thayanandan Tony , Calsolaro Valeria , Komici Klara , Rengo Giuseppe , Corbi Graziamaria , Ferrara Nicola
Published: November 2018

Alzheimer’s disease is the most common form of dementia and is a significant burden for affected patients, carers, and health systems. Great advances have been made in understanding its pathophysiology, to a point that we are moving from a purely clinical diagnosis to a biological one based on the use of biomarkers. Among those, imaging biomarkers are invaluable in Alzheimer’s, as they provide an in vivo window to the pathological processes occurring in Alzheimer’s brain. While some imaging techniques are still under evaluation in the research setting, some have reached widespread clinical use. In this review, we provide an overview of the most commonly used imaging biomarkers in Alzheimer’s disease, from molecular PET imaging to structural MRI, emphasising the concept that multimodal imaging would likely prove to be the optimal tool in the future of Alzheimer’s research and clinical practice.
Redescriptions, Lectotype Designations, New Synonyms and New Geographic Records for the “Tiger” Species of Mycotretus Lacordaire, 1842 (Coleoptera: Erotylidae: Tritomini)
Authors: Pecci-Maddalena Italo S. C. , Lopes-Andrade Cristiano
Published: November 2018

The Neotropical Mycotretus Lacordaire, 1842 is one of the largest and most widespread genera of the Erotylidae, encompassing more than 200 described species. Among the species with a similar body coloration, there is a “group” of six valid species—called here the “tiger” Mycotretus—that possess several pronotal and elytral black spots, as follows: M. tigrinus (Olivier, 1792); M. multimaculatus Taschenberg, 1870; M. centralis Arrow, 1909; M. tigrinoides Mader, 1942; M. tigripennis Mader, 1942; and M. prioteloides Mader, 1942. Different from any other Mycotretus with spots, the spots of the “tiger” Mycotretus are numerous and are not bilaterally symmetrical in pattern. Here, new geographical records, diagnoses and redescriptions are provided for M. tigrinus, M. centralis, M. tigrinoides, M. tigripennis and M. prioteloides, including the first descriptions of their male and female terminalia. Lectotypes are designated for M. multimaculatus, M. centralis, and M. leopardus. Mycotretus multimaculatus and M. tigrinus pardalis Crotch, 1876 are proposed as new junior synonyms of M. tigrinus. Additionally, the authorship of the name M. leopardus is attributed to Crotch, 1876, because he was the first author to provide a description for that taxon, and the synonymy of M. leopardus and M. conspersus (Germar, 1824) with M. tigrinus (Olivier, 1792) is confirmed.
Effects of Compressive Stockings and Standard Stockings in Skin Temperature and Pressure Pain Threshold in Runners with Functional Ankle Equinus Condition
Authors: Rodríguez-Sanz David , Becerro-de-Bengoa-Vallejo Ricardo , Losa-Iglesias Marta Elena , Martínez-Jiménez Eva María , Muñoz-García Daniel , Pérez-Boal Eduardo , Calvo-Lobo César , López-López Daniel
Published: November 2018

Objective: To assess clinical differences in the Achilles tendons of runners with ankle equinus wearing either compressive or standard stockings. Design: Case–control study. Methods: In this study, we conducted clinical examinations of 98 sportsmen (runners) with equinus, before and after 30 min of running on a treadmill; 49 runners wore compressive stockings and 49 wore standard stockings. Clinical assessments of the runners’ Achilles tendons were based on the pressure pain threshold (PPT) and skin temperature analysis. Results: Achilles tendon evaluations identified significant differences in skin temperature modification and PPT between the compressive and standard stocking groups. Conclusions: Based on our findings, we propose that higher skin temperatures are associated with lower pressure pain thresholds in the Achilles tendons of runners with ankle equinus.
The Role of Long Noncoding RNAs in Diabetic Alzheimer’s Disease
Authors: Kim Young-Kook , Song Juhyun
Published: November 2018

Long noncoding RNAs (lncRNAs) are involved in diverse physiological and pathological processes by modulating gene expression. They have been found to be dysregulated in the brain and cerebrospinal fluid of patients with neurodegenerative diseases, and are considered promising therapeutic targets for treatment. Among the various neurodegenerative diseases, diabetic Alzheimer’s disease (AD) has been recently emerging as an important issue due to several unexpected reports suggesting that metabolic issues in the brain, such as insulin resistance and glucose dysregulation, could be important risk factors for AD. To facilitate understanding of the role of lncRNAs in this field, here we review recent studies on lncRNAs in AD and diabetes, and summarize them with different categories associated with the pathogenesis of the diseases including neurogenesis, synaptic dysfunction, amyloid beta accumulation, neuroinflammation, insulin resistance, and glucose dysregulation. It is essential to understand the role of lncRNAs in the pathogenesis of diabetic AD from various perspectives for therapeutic utilization of lncRNAs in the near future.
Blockchain-Based ICOs: Pure Hype or the Dawn of a New Era of Startup Financing?
Authors: Ante Lennart , Sandner Philipp , Fiedler Ingo
Published: November 2018

This study explores the determinants of initial coin offering (ICO) success, where success is defined as the amount of capital a project could raise. ICOs are a tool for startups in the blockchain ecosystem to raise early capital with relative ease. The market for ICOs has grown at a rapid pace since its start in 2013. We analyze a unique dataset of 278 projects that finished their ICOs by August 2017 to assess determinants of funding success that we derive from the crowdfunding and venture capital literature. Our results show that ICOs exhibit similarities to classical crowdfunding and venture capital markets. Specifically, we identify resemblances in determinants of funding success regarding human capital characteristics, business model quality, project elaboration, and social media activity.
Universe of Discourse and Existence
Authors: Usó-Doménech José Luis , Nescolarde-Selva Josué Antonio , Gash Hugh
Published: November 2018

There is a fairly widespread belief that the problem of existence is not an essential issue for logic. Logic, though formal, must deal with the problem of existence. However, logic should be limited to describing “formal existence” or “existence of a formal system”. However, the logical problem of existence and how to treat and resolve this problem differ completely from the corresponding metaphysical problem. It is possible to deduce that formal existence is nothing other than belonging to the universe of discourse, so proposing a solution to the logical problem of existence in an epistemological, rather than a metaphysical, context. In this paper, we conclude, from a formal point of view, no universe of discourse is given in advance; any universe of discourse that satisfies the necessary conditions can be used. The extended epistemological belief that there is a universe of discourse defined rigorously, which would be the true and should be “the universe of discourse of logic”, cannot be justified.
Orthosteric and/or Allosteric Binding of α-Conotoxins to Nicotinic Acetylcholine Receptors and Their Models
Authors: Kryukova Elena V. , Ivanov Igor A. , Lebedev Dmitry S. , Spirova Ekaterina N. , Egorova Natalia S. , Zouridakis Marios , Kasheverov Igor E. , Tzartos Socrates J. , Tsetlin Victor I.
Published: November 2018

α-Conotoxins from Conus snails are capable of distinguishing muscle and neuronal nicotinic acetylcholine receptors (nAChRs). α-Conotoxin RgIA and αO-conotoxin GeXIVA, blocking neuronal α9α10 nAChR, are potential analgesics. Typically, α-conotoxins bind to the orthosteric sites for agonists/competitive antagonists, but αO-conotoxin GeXIVA was proposed to attach allosterically, judging by electrophysiological experiments on α9α10 nAChR. We decided to verify this conclusion by radioligand analysis in competition with α-bungarotoxin (αBgt) on the ligand-binding domain of the nAChR α9 subunit (α9 LBD), where, from the X-ray analysis, αBgt binds at the orthosteric site. A competition with αBgt was registered for GeXIVA and RgIA, IC50 values being in the micromolar range. However, high nonspecific binding of conotoxins (detected with their radioiodinated derivatives) to His6-resin attaching α9 LBD did not allow us to accurately measure IC50s. However, IC50s were measured for binding to Aplysia californica AChBP: the RgIA globular isomer, known to be active against α9α10 nAChR, was more efficient than the ribbon one, whereas all three GeXIVA isomers had similar potencies at low µM. Thus, radioligand analysis indicated that both conotoxins can attach to the orthosteric sites in these nAChR models, which should be taken into account in the design of analgesics on the basis of these conotoxins.
Fucoidan Extracted from the New Zealand Undaria pinnatifida—Physicochemical Comparison against Five Other Fucoidans: Unique Low Molecular Weight Fraction Bioactivity in Breast Cancer Cell Lines
Authors: Lu Jun , Shi Keyu Kally , Chen Shuping , Wang Junqiao , Hassouna Amira , White Loretta Nicole , Merien Fabrice , Xie Mingyong , Kong Qingjun , Li Jinyao , Ying Tianlei , White William Lindsey , Nie Shaoping
Published: November 2018

Fucoidan, the complex fucose-containing sulphated polysaccharide varies considerably in structure, composition, and bioactivity, depending on the source, species, seasonality, and extraction method. In this study, we examined five fucoidans extracted from the same seaweed species Undaria pinnatifida but from different geological locations, and compared them to the laboratory-grade fucoidan from Sigma (S). The five products differed in molecular composition. The amount of over 2 kDa low molecular weight fraction (LMWF) of the New Zealand crude fucoidan (S1) was larger than that of S, and this fraction was unique, compared to the other four fucoidans. The difference of molecular compositions between S and S1 explained our previous observation that S1 exhibited different anticancer profile in some cancer cell lines, compared with S. Since we observed this unique LMWF, we compared the cytotoxic effects of a LMWF and a high molecular weight fucoidan (HMWF) in two breast cancer cell lines—MCF-7 and MDA-MB-231. Results indicated that the molecular weight is a critical factor in determining the anti-cancer potential of fucoidan, from the New Zealand U. pinnatifida, as the LMWF exhibited a dose-dependent inhibition on the proliferation of breast cancer cells, significantly better than the HMWF, in both cell lines. A time-dependent inhibition was only observed in the MCF-7. Induction of caspase-dependent apoptosis was observed in the MDA-MB-231 cells, through the intrinsic apoptosis pathway alone, or with the extrinsic pathway. LMWF stimulated a dose-dependent NOS activation in the MDA-MB-231 cells. In conclusion, the fucoidan extracted from the New Zealand U. pinnatifida contains a unique LMWF, which could effectively inhibit the growth of breast cancer cell lines. Therefore, the LMWF from New Zealand U. pinnatifida could be used as a supplement cancer treatment.
Nitrogen Removal by Sulfur-Based Carriers in a Membrane Bioreactor (MBR)
Authors: Vo Thi-Kim-Quyen , Lee Jeong-Jun , Kang Joon-Seok , Park Seogyeong , Kim Han-Seung
Published: November 2018

Sulfur-based carriers were examined to enhance the nitrogen removal efficiency in a mixed anoxic–anaerobic-membrane bioreactor system, in which sulfur from the carrier acts as an electron donor for the conversion of nitrate to nitrogen gas through the autotrophic denitrification process. A total nitrogen removal efficiency of 63% was observed in the system with carriers, which showed an increase in the removal efficiency of around 20%, compared to the system without carriers. The results also indicated that the carriers had no adverse effect on biological treatment for the organic matter and total phosphorus. The removal efficiencies for chemical oxygen demand (COD) and total phosphorus (TP) were 98% and 37% in both systems, respectively. The generation of sulfate ions was a major disadvantage of using sulfur-based carriers, and resulted in pH drop. The ratio of sulfate in the effluent to nitrate removed in the system ranged from 0.86 to 1.97 mgSO42−/mgNO3−-N, which was lower than the theoretical value and could be regarded as due to the occurrence of simultaneous heterotrophic and autotrophic denitrification.
The Effects of TIG Welding Rod Compositions on Microstructural and Mechanical Properties of Dissimilar AISI 304L and 420 Stainless Steel Welds
Authors: Başyiğit Aziz Barış , Murat Mustafa Gökhan
Published: November 2018

The usage of AISI/SAE 304L austenitic and 420 martensitic stainless steels is receiving greater interest especially in the defence and navy industries. 304L stainless steels exhibit excellent resistance to oxidizing media, while martensitic 420 alloy provides high strength values besides satisfactory corrosion properties at ambient atmospheres. In this work; 420 quality martensitic stainless steel is TIG (Tungsten Inert Gas) welded with 304L quality low carbon austenitic stainless steel plates. As filler metal dominantly determines the weld metals chemical compositions and final microstructures, 3 different TIG welding rods of ER312, ER316L ve ER2209 are used in welding operations in order to obtain 3 discrete weld metal contents under high purity argon shielding gas. Microstructural inspection, microhardness survey and Charpy V-notch impact tests are applied to all joints after welding operations. The specimen welded by ER2209 TIG welding rod executed the highest impact test results besides exhibiting the lowest micro-hardness profiles at heat affected zones and weld metals. All of the welded specimens weld region hardness profiles were determined to be lower than unwelded 420 martensitic stainless steel base metal.
A Simple and Convenient Synthesis of Unlabeled and 13C-Labeled 3-(3-Hydroxyphenyl)-3-Hydroxypropionic Acid and Its Quantification in Human Urine Samples
Authors: Khaniani Yeganeh , Lipfert Matthias , Bhattacharyya Dipanjan , Perez Pineiro Rolando , Zheng Jiamin , Wishart David S.
Published: November 2018

An improved method to synthesize the highly abundant and biomedically important urinary metabolite 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA) is reported. The modified protocol is based on an indium-mediated sonochemical Reformatsky reaction. The synthesis is a simple two-step route as opposed to a complex four-step route previously reported in the literature that requires specialized equipment, flammable materials, and high-pressure reaction vessels. The described procedure also provides an expedient route to prepare a 13C isotopically labeled HPHPA that can be used as a standard for quantitative LC-MS analysis. This report also illustrates how the synthesized metabolite standard was used to detect and accurately quantify its presence in human urine samples using both NMR and LC-MS techniques.
Pseudoginsengenin DQ Exhibits Therapeutic Effects in Cisplatin-Induced Acute Kidney Injury via Sirt1/NF-κB and Caspase Signaling Pathway without Compromising Its Antitumor Activity in Mice
Authors: Qi Zeng , Li Zhuo , Li Wei , Liu Yunhe , Wang Cuizhu , Lin Hongqiang , Liu Jinping , Li Pingya
Published: November 2018

In this study, the protective effects of pseudoginsengenin DQ (PDQ) on cisplatin (CDDP)-induced nephrotoxicity were assessed, with a primary investigation into the mechanisms involved. Our results showed that pretreatment with PDQ remarkably restored levels of blood urea nitrogen (BUN) and creatinine (CRE), malondialdehyde (MDA), glutathione (GSH), superoxide dismutase (SOD), catalase (CAT), tumor necrosis factor-α (TNF-α), and interleukin-1β (IL-1β). Meanwhile, PDQ decreased the CDDP-induced overexpression of heme oxygenase 1 (HO-1), cytochrome P450 E1 (CYP2E1), TNF-α, nuclear factor-kappa B (NF-κB), cyclooxygenase-2 (COX-2), and inducible nitric oxide synthase (iNOS) in renal tissues. Hoechst 33258 and TdT-mediated dUTP nick-end labeling (TUNEL) staining showed that CDDP-induced renal tubular cell apoptosis was apparently inhibited by PDQ. Western blotting showed that PDQ reversed the CDDP-induced (1) downregulation of Sirtuin-1 (Sirt-1), nuclear-related factor 2 (Nrf2), and Bcl-2, and (2) upregulation of NF-κB, Nox-4, Bax, caspase-9, and caspase-3. In addition, PDQ enhanced the antitumor activity of cisplatin in Lewis lung cancer xenograft tumor model mice. In conclusion, we found that PDQ exerted a renal protective effect against CDDP-induced acute nephrotoxicity via Sirt1/NF-κB and the caspase signaling pathway without compromising the antitumor activity of CDDP, which provides a new potential strategy for the clinical treatment of cancer and presents a new medicinal application of PDQ.
Coptisine Suppresses Mast Cell Degranulation and Ovalbumin-Induced Allergic Rhinitis
Authors: Fu Shuilian , Ni Saihong , Wang Danni , Hong Tie
Published: November 2018

Coptisine is one of the main components of isoquinoline alkaloids in the coptidis rhizome. The effect of coptisine on allergic rhinitis has not been investigated. In this study, we report the effects and mechanisms of coptisine using monoclonal anti-2,4,6-dinitrophenyl-immunoglobulin (Ig) E/human serum albumin (DNP-IgE/HSA)-stimulated rat basophilic leukemia cells (RBL-2H3 cells) in vitro and an ovalbumin (OVA)-induced allergic rhinitis (AR) in mice. The results showed that coptisine markedly decreased the levels of β-hexosaminidase, histamine, interleukin (IL)-4, and tumor necrosis factor (TNF)-α. Coptisine also prevented morphological changes, such as restoring an elongated shape, inhibiting granule release on toluidine blue staining, and reorganizing inhibited filamentous actins (F-actin). Additionally, coptisine blocked the phosphorylation of phosphoinositide3-kinase (PI3K)/Akt (as known as protein kinase B(PKB)) in RBL-2H3 cell. Furthermore, the results showed that coptisine suppressed OVA-induced allergic rhinitis symptoms, such as nasal rubbing and OVA-specific IgE, and histamine, IL-4 and TNF-α levels in the serum of AR mice. These data suggested that coptisine should have inhibitory effects on the inflammatory responses of mast cells, and may be beneficial for the development of coptisine as a potential anti-allergic drug.
Solution Conformation of Heparin Tetrasaccharide. DFT Analysis of Structure and Spin–Spin Coupling Constants
Authors: Hricovíni Miloš , Hricovíni Michal
Published: November 2018

Density functional theory (DFT) has provided detailed information on the molecular structure and spin–spin coupling constants of heparin tetrasaccharide (GlcNS,6S-IdoA2S-GlcNS,6S-IdoA2S-OMe) representing the predominant heparin repeating-sequence. The fully optimised molecular structures of two tetrasaccharide conformations (differing from each other in the conformational form of the sulphated iduronic acid residue–one 1C4 and the other 2S0) were obtained using the B3LYP/6-311+G(d,p) level of theory and applying explicit water molecules to simulate the presence of a solvent. The theoretical data provided insight into variations of the bond lengths, bond angles and torsion angles, formations of intra- and intermolecular hydrogen bonds and ionic interactions. Optimised molecular structures indicated the formation of a complex hydrogen bond network, including interresidue and intraresidue bonds. The ionic interactions strongly influence the first hydration shell and, together with hydrogen bonds, play an important role in shaping the 3D tetrasaccharide structure. DFT-derived indirect three–bond proton–proton coupling constants (3JH-C-C-H) showed that the best agreement with experiment was obtained with a weighted average of 67:33 (1C4:2S0) of the IdoA2S forms. Detailed analysis of Fermi-contact contributions to 3JH-C-C-H showed that important contributions arise from the oxygen lone pairs of neighbouring oxygen atoms. The analysis also showed that the magnitude of diamagnetic spin–orbit contributions are sufficiently large to determine the magnitude of some proton–proton coupling constants. The data highlight the need to use appropriate quantum-chemical calculations for a detailed understanding of the solution properties of heparin oligosaccharides.
Synthesis and Biological Evaluation of Phaeosphaeride A Derivatives as Antitumor Agents
Authors: Abzianidze Victoria , Beltyukov Petr , Zakharenkova Sofya , Moiseeva Natalia , Mejia Jennifer , Holder Alvin , Trishin Yuri , Berestetskiy Alexander , Kuznetsov Victor
Published: November 2018

New derivatives of phaeosphaeride A (PPA) were synthesized and characterized. Anti-tumor activity studies were carried out on the HCT-116, PC3, MCF-7, A549, К562, NCI-Н929, Jurkat, THP-1, RPMI8228 tumor cell lines, and on the HEF cell line. All of the compounds synthesized were found to have better efficacy than PPA towards the tumor cell lines mentioned. Compound 6 was potent against six cancer cell lines, HCT-116, PC-3, K562, NCI-H929, Jurkat, and RPMI8226, showing a 47, 13.5, 16, 4, 1.5, and 7-fold increase in anticancer activity comparative to those of etoposide, respectively. Compound 1 possessed selectivity toward the NCI-H929 cell line (IC50 = 1.35 ± 0.69 μM), while product 7 was selective against three cancer cell lines, HCT-116, MCF-7, and NCI-H929, each having IC50 values of 1.65 μM, 1.80 μM and 2.00 μM, respectively.
Synthesis and Properties of Novel Polyurethanes Containing Long-Segment Fluorinated Chain Extenders
Authors: Li Jia-Wun , Lee Hsun-Tsing , Tsai Hui-An , Suen Maw-Cherng , Chiu Chih-Wei
Published: November 2018

In this study, novel biodegradable long-segment fluorine-containing polyurethane (PU) was synthesized using 4,4′-diphenylmethane diisocyanate (MDI) and 1H,1H,10H,10H-perfluor-1,10-decanediol (PFD) as hard segment, and polycaprolactone diol (PCL) as a biodegradable soft segment. Nuclear magnetic resonance (NMR) was used to perform 1H NMR, 19F NMR, 19F–19F COSY, 1H–19F COSY, and HMBC analyses on the PFD/PU structures. The results, together with those from Fourier transform infrared spectroscopy (FTIR), verified that the PFD/PUs had been successfully synthesized. Additionally, the soft segment and PFD were changed, after which FTIR and XPS peak-differentiation-imitating analyses were employed to examine the relationship of the hydrogen bonding reaction between the PFD chain extender and PU. Subsequently, atomic force microscopy was used to investigate the changes in the microphase structure between the PFD chain extender and PU, after which the effects of the thermal properties between them were investigated through thermogravimetric analysis, differential scanning calorimetry, and dynamic mechanical analysis. Finally, the effects of the PFD chain extender on the mechanical properties of the PU were investigated through a tensile strength test.
Degradation of Polyacrylate in the Outdoor Agricultural Soil Measured by FTIR-PAS and LIBS
Authors: Liang Dong , Du Changwen , Ma Fei , Shen Yazhen , Wu Ke , Zhou Jianmin
Published: November 2018

Recently, polyacrylates (PA) have been applied in coated controlled-release fertilizer (CRF), but the impacts of the soil on the degradation of PA have not been evaluated. In this study, an outdoor agriculture soil buried test was carried out for 12 months to investigate the degradation of PA films. The residual degraded films were taken regularly from the soil and analyzed by SEM, Fourier transform infrared photoacoustic spectroscopy (FTIR-PAS) and laser-induced breakdown spectroscopy (LIBS). The concentration of C–H and C=O molecular groups of PA were decreased, and the element concentrations of C, O, K, Si of PA were increased under the degradation process. The surface of PA became rough and the degradation of PA occurred on the surface layer. Principal component analysis (PCA) showed that soil invaded PA. The results indicated that PA were environmentally friendly when applied to CRF. FTIR-PAS and LIBS were advanced in the in-situ surface analysis of the degradation process of the polymer.
Against Storytelling—The New Paradigm of Scientific Publishing
Authors: Weilenmann Anne-Katharina , Rajendran Lawrence
Published: November 2018

This is an interview which I conducted with Lawrence Rajendran, the founder and initiator of the platform «ScienceMatters». [...]
Grades of Openness: Open and Closed Articles in Norway
Authors: Mikki Susanne , Gjesdal Øyvind L. , Strømme Tormod E.
Published: November 2018

Based on the total scholarly article output of Norway, we investigated the coverage and degree of openness according to the following three bibliographic services: (1) Google Scholar, (2) oaDOI by Impact Story, and (3) 1findr by 1science. According to Google Scholar, we found that more than 70% of all Norwegian articles are openly available. However, the degrees of openness are profoundly lower according to oaDOI and 1findr at 31% and 52%, respectively. Varying degrees of openness are mainly caused by different interpretations of openness, with oaDOI being the most restrictive. Furthermore, open shares vary considerably by discipline, with the medicine and health sciences at the upper end and the humanities at the lower end. We also determined the citation frequencies using cited-by values in Google Scholar and applying year and subject normalization. We found a significant citation advantage for open articles. However, this was not the case for all types of openness. In fact, the category of open access journals was by far the lowest cited, indicating that young journals with a declared open access policy still lack recognition.
Reclaimed Carbon and Flax Fibre Composites: Manufacturing and Mechanical Properties
Authors: Longana Marco L. , Ondra Vaclav , Yu HaNa , Potter Kevin D. , Hamerton Ian
Published: November 2018

The feasibility of using the HiPerDiF (high performance discontinuous fibre) method to manufacture highly aligned discontinuous fibres intermingled hybrid composites with flax and reclaimed carbon fibres (rCF), and the potential benefits of so doing, are investigated in this paper. It is demonstrated that, despite their hydrophilic nature, flax fibres are not affected by this water-based process. Intermingled flax/rCF hybrid composites are characterised in terms of their tensile and vibrational response. It is concluded that natural/rCF fibre hybrid composites can be a viable solution for those applications where a reduction in primary mechanical properties, e.g., stiffness and strength, is an acceptable trade-off for the enhancement of secondary properties, e.g., noise, vibration, and harshness (NVH) mitigation, and the reduction of monetary costs.
Multi-Modal Sensing and Robotic Manipulation of Non-Rigid Objects: A Survey
Authors: Nadon Félix , Valencia Angel J. , Payeur Pierre
Published: November 2018

This paper aims to provide a comprehensive survey of recent advancements in modelling and autonomous manipulation of non-rigid objects. It first summarizes the recent advances in sensing and modelling of such objects with a focus on describing the methods and technologies used to measure their shape and estimate their material and physical properties. Formal representations considered to predict the deformation resulting from manipulation of non-rigid objects are then investigated. The third part provides a survey of planning and control strategies exploited to operate dexterous robotic systems while performing various tasks on objects made of different non-rigid materials.
Aboveground Tree Biomass Estimation of Sparse Subalpine Coniferous Forest with UAV Oblique Photography
Authors: Lin Jiayuan , Wang Meimei , Ma Mingguo , Lin Yi
Published: November 2018

In tree Aboveground Biomass (AGB) estimation, the traditional harvest method is accurate but unsuitable for a large-scale forest. The airborne Light Detection And Ranging (LiDAR) is superior in obtaining the point cloud data of a dense forest and extracting tree heights for AGB estimation. However, the LiDAR has limitations such as high cost, low efficiency, and complicated operations. Alternatively, the overlapping oblique photographs taken by an Unmanned Aerial Vehicle (UAV)-loaded digital camera can also generate point cloud data using the Aerial Triangulation (AT) method. However, limited by the relatively poor penetrating capacity of natural light, the photographs captured by the digital camera on a UAV are more suitable for obtaining the point cloud data of a relatively sparse forest. In this paper, an electric fixed-wing UAV loaded with a digital camera was employed to take oblique photographs of a sparse subalpine coniferous forest in the source region of the Minjiang River. Based on point cloud data obtained from the overlapping photographs, a Digital Terrain Model (DTM) was generated by filtering non-ground points along with the acquisition of a Digital Surface Model (DSM) of Minjiang fir trees by eliminating subalpine shrubs and meadows. Individual tree heights were extracted by overlaying individual tree outlines on Canopy Height Model (CHM) data computed by subtracting the Digital Elevation Model (DEM) from the rasterized DSM. The allometric equation with tree height (H) as the predictor variable was established by fitting measured tree heights with tree AGBs, which were estimated using the allometric equation on H and Diameter at Breast Height (DBH) in sample tree plots. Finally, the AGBs of all of the trees in the test site were determined by inputting extracted individual tree heights into the established allometric equation. In accuracy assessment, the coefficient of determination (R2) and Root Mean Square Error (RMSE) of extracted individual tree heights were 0.92 and 1.77 m, and the R2 and RMSE of the estimated AGBs of individual trees were 0.96 and 54.90 kg. The results demonstrated the feasibility and effectiveness of applying UAV-acquired oblique optical photographs to the tree AGB estimation of sparse subalpine coniferous forests.
Sensitivity of TDS-1 GNSS-R Reflectivity to Soil Moisture: Global and Regional Differences and Impact of Different Spatial Scales
Authors: Camps Adriano , Vall·llossera Mercedes , Park Hyuk , Portal Gerard , Rossato Luciana
Published: November 2018

The potential of Global Navigation Satellite Systems-Reflectometry (GNSS-R) techniques to estimate land surface parameters such as soil moisture (SM) is experimentally studied using 2014–2017 global data from the UK TechDemoSat-1 (TDS-1) mission. The approach is based on the analysis of the sensitivity to SM of different observables extracted from the Delay Doppler Maps (DDM) computed by the Space GNSS Receiver–Remote Sensing Instrument (SGR-ReSI) instrument using the L1 (1575.42 MHz) left-hand circularly-polarized (LHCP) reflected signals emitted by the Global Positioning System (GPS) navigation satellites. The sensitivity of different GNSS-R observables to SM and its dependence on the incidence angle is analyzed. It is found that the sensitivity of the calibrated GNSS-R reflectivity to surface soil moisture is ~0.09 dB/% up to 30° incidence angle, and it decreases with increasing incidence angles, although differences are found depending on the spatial scale used for the ground-truth, and the region. The sensitivity to subsurface soil moisture has been also analyzed using a network of subsurface probes and hydrological models, apparently showing some dependence, but so far results are not conclusive.
Quantifying Changes on Forest Succession in a Dry Tropical Forest Using Angular-Hyperspectral Remote Sensing
Authors: Garcia Millan Virginia , Sanchez-Azofeifa Arturo
Published: November 2018

The tropical dry forest (TDF) is one the most threatened ecosystems in South America, existing on a landscape with different levels of ecological succession. Among satellites dedicated to Earth observation and monitoring ecosystem succession, CHRIS/PROBA is the only satellite that presents quasi-simultaneous multi-angular pointing and hyperspectral imaging. These two characteristics permit the study of structural and compositional differences of TDFs with different levels of succession. In this paper, we use 2008 and 2014 CHRIS/PROBA images from a TDF in Minas Gerais, Brazil to study ecosystem succession after abandonment. Using a −55° angle of observation; several classifiers including spectral angle mapper (SAM), support vector machine (SVM), and decision trees (DT) were used to test how well they discriminate between different successional stages. Our findings suggest that the SAM is the most appropriate method to classify TDFs as a function of succession (accuracies ~80 for % for late stage, ~85% for the intermediate stage, ~70% for early stage, and ~50% for other classes). Although CHRIS/PROBA cannot be used for large-scale/long-term monitoring of tropical forests because of its experimental nature; our results support the potential of using multi-angle hyperspectral data to characterize the structure and composition of TDFs in the near future.
Exploring the Potential of High Resolution WorldView-3 Imagery for Estimating Yield of Mango
Authors: Rahman Muhammad Moshiur , Robson Andrew , Bristow Mila
Published: November 2018

Pre-harvest yield estimation of mango fruit is important for the optimization of inputs and other resources on the farm. Current industry practice of visual counting the fruit on a small number of trees for yield forecasting can be highly inaccurate due to the spatial variability, especially if the trees selected do not represent the entire crop. Therefore, this study evaluated the potential of high resolution WorldView-3 (WV3) satellite imagery to estimate yield of mango by integrating both geometric (tree crown area) and optical (spectral vegetation indices) data using artificial neural network (ANN) model. WV3 images were acquired in 2016–2017 and 2017–2018 growing seasons at the early fruit stage from three orchards in Acacia Hills region, Northern Territory, Australia. Stratified sampling technique (SST) was applied to select 18 trees from each orchard and subsequently ground truthed for yield (kg·tree−1) and fruit number per tree. For each sampled tree, spectral reflectance data and tree crown area (TCA) was extracted from WV3 imagery. The TCA was identified as the most important predictor of both fruit yield (kg·tree−1) and fruit number, followed by NDVI red-edge band when all trees from three orchards in two growing seasons were combined. The results of all sampled trees from three orchards in two growing seasons using ANN model produced a strong correlation (R2 = 0.70 and 0.68 for total fruit yield (kg·tree−1) and fruit number respectively), which suggest that the model can be obtained to predict yield on a regional level. On orchard level also the ANN model produced a high correlation when both growing seasons were combined. However, the model developed in one season could not be applied in another season due to the influence of seasonal variation and canopy condition. Using the relationship derived from the measured yield parameters against combined VIs and TCA data, the total fruit yield (t·ha−1) and fruit number were estimated for each orchard, produced 7% under estimation to less than 1% over estimation. The accuracy of the findings showed the potential of WV3 imagery to better predict the yield parameters than the current practice across the mango industry as well as to quantify lost yield as a result of delayed harvest.
A Novel Microfluidic Point-of-Care Biosensor System on Printed Circuit Board for Cytokine Detection
Authors: Evans Daniel , Papadimitriou Konstantinos , Vasilakis Nikolaos , Pantelidis Panagiotis , Kelleher Peter , Morgan Hywel , Prodromakis Themistoklis
Published: November 2018

Point of Care (PoC) diagnostics have been the subject of considerable research over the last few decades driven by the pressure to detect diseases quickly and effectively and reduce healthcare costs. Herein, we demonstrate a novel, fully integrated, microfluidic amperometric enzyme-linked immunosorbent assay (ELISA) prototype using a commercial interferon gamma release assay (IGRA) as a model antibody binding system. Microfluidic assay chemistry was engineered to take place on Au-plated electrodes within an assay cell on a printed circuit board (PCB)-based biosensor system. The assay cell is linked to an electrochemical reporter cell comprising microfluidic architecture, Au working and counter electrodes and a Ag/AgCl reference electrode, all manufactured exclusively via standard commercial PCB fabrication processes. Assay chemistry has been optimised for microfluidic diffusion kinetics to function under continual flow. We characterised the electrode integrity of the developed platforms with reference to biological sampling and buffer composition and subsequently we demonstrated concentration-dependent measurements of H2O2 depletion as resolved by existing FDA-validated ELISA kits. Finally, we validated the assay technology in both buffer and serum and demonstrate limits of detection comparable to high-end commercial systems with the addition of full microfluidic assay architecture capable of returning diagnostic analyses in approximately eight minutes.
Extended Joint Sparsity Reconstruction for Spatial and Temporal ERT Imaging
Authors: Chen Bo , Abascal Juan , Soleimani Manuchehr
Published: November 2018

Electrical resistance tomography (ERT) is an imaging technique to recover the conductivity distribution with boundary measurements via attached electrodes. There are a wide range of applications using ERT for image reconstruction or parameter calculation due to high speed data collection, low cost, and the advantages of being non-invasive and portable. Although ERT is considered a high temporal resolution method, a temporally regularized method can greatly enhance such a temporal resolution compared to frame-by-frame reconstruction. In some of the cases, especially in the industrial applications, dynamic movement of an object is critical. In practice, it is desirable for monitoring and controlling the dynamic process. ERT can determine the spatial conductivity distribution based on previous work, and ERT potentially shows good performance in exploiting temporal information as well. Many ERT algorithms reconstruct images frame by frame, which is not optimal and would assume that the target is static during collection of each data frame, which is inconsistent with the real case. Although spatiotemporal-based algorithms can account for the temporal effect of dynamic movement and can generate better results, there is not that much work aimed at analyzing the performance in the time domain. In this paper, we discuss the performance of a novel spatiotemporal total variation (STTV) algorithm in both the spatial and temporal domain, and Temporal One-Step Tikhonov-based algorithms were also employed for comparison. The experimental results show that the STTV has a faster response time for temporal variation of the moving object. This robust time response can contribute to a much better control process which is the main aim of the new generation of process tomography systems.
A CMOS SPAD Imager with Collision Detection and 128 Dynamically Reallocating TDCs for Single-Photon Counting and 3D Time-of-Flight Imaging
Authors: Zhang Chao , Lindner Scott , Antolovic Ivan , Wolf Martin , Charbon Edoardo
Published: November 2018

Per-pixel time-to-digital converter (TDC) architectures have been exploited by single-photon avalanche diode (SPAD) sensors to achieve high photon throughput, but at the expense of fill factor, pixel pitch and readout efficiency. In contrast, TDC sharing architecture usually features high fill factor at small pixel pitch and energy efficient event-driven readout. While the photon throughput is not necessarily lower than that of per-pixel TDC architectures, since the throughput is not only decided by the TDC number but also the readout bandwidth. In this paper, a SPAD sensor with 32 × 32 pixels fabricated with a 180 nm CMOS image sensor technology is presented, where dynamically reallocating TDCs were implemented to achieve the same photon throughput as that of per-pixel TDCs. Each 4 TDCs are shared by 32 pixels via a collision detection bus, which enables a fill factor of 28% with a pixel pitch of 28.5 μm. The TDCs were characterized, obtaining the peak-to-peak differential and integral non-linearity of −0.07/+0.08 LSB and −0.38/+0.75 LSB, respectively. The sensor was demonstrated in a scanning light-detection-and-ranging (LiDAR) system equipped with an ultra-low power laser, achieving depth imaging up to 10 m at 6 frames/s with a resolution of 64 × 64 with 50 lux background light.
Dynamic Cipher Puzzle for Efficient Broadcast Authentication in Wireless Sensor Networks
Authors: Afianti Farah , Wirawan  , Suryani Titiek
Published: November 2018

The use of signature-based broadcast authentication for code and data dissemination in wireless sensor networks (WSNs) cannot be avoided. It increases security but requires high computation. Adversaries can exploit the latter condition as an opportunity to send many false signatures. Filtering methods can overcome this vulnerability. Cipher Puzzle is a filtering method that has low storage overhead along with high security, especially against denial of service (DoS) attacks. However, its number of hash iterations cannot be bounded, which causes sender-side delay. This paper proposes a Dynamic Cipher Puzzle (DCP), which uses a threshold function to limit the number of hash iterations. Hence, time at the sender-side can be used more efficiently. Besides, its dynamic puzzle-strength increases the obscurity of the transmitted packet. Simulation and experimental results were analyzed with Arduino 2560. The theoretical results show that the quadratic function outperformed the compared methods. The scheme decreased sender-side delay by 94.6% with a guarantee of zero solution probability in 1.728 × 10 − 13 . The experimental results show that the consumption of resources at the sensor node increases with an acceptable value. Moreover, DCP increases the complexity for the attacker to implement probability and signature-based DoS attacks.
Gas-Sensor Drift Counteraction with Adaptive Active Learning for an Electronic Nose
Authors: Liu Tao , Li Dongqi , Chen Jianjun , Chen Yanbing , Yang Tao , Cao Jianhua
Published: November 2018

Gas sensors are the key components of an electronic nose (E-nose) in violated odour analysis. Gas-sensor drift is a kind of physical change on a sensor surface once an E-nose works. The perturbation of gas-sensor responses caused by drift would deteriorate the performance of the E-nose system over time. In this study, we intend to explore a suitable approach to deal with the drift effect in an online situation. Considering that the conventional drift calibration is difficult to implement online, we use active learning (AL) to provide reliable labels for online instances. Common AL learning methods tend to select and label instances with low confidence or massive information. Although this action clarifies the ambiguity near the classification boundary, it is inadequate under the influence of gas-sensor drift. We still need the samples away from the classification plane to represent drift variations comprehensively in the entire data space. Thus, a novel drift counteraction method named AL on adaptive confidence rule (AL-ACR) is proposed to deal with online drift data dynamically. By contrast with conventional AL methods selecting instances near the classification boundary of a certain category, AL-ACR collects instances distributed evenly in different categories. This action implements on an adjustable rule according to the outputs of classifiers. Compared with other reference methods, we adopt two drift databases of E-noses to evaluate the performance of the proposed method. The experimental results indicate that the AL-ACR reaches higher accuracy than references on two E-nose databases, respectively. Furthermore, the impact of the labelling number is discussed to show the trend of performance for the AL-type methods. Additionally, we define the labelling efficiency index (LEI) to assess the contribution of certain labelling numerically. According to the results of LEI, we believe AL-ACR can achieve the best effect with the lowest cost among the AL-type methods in this work.