bluuebunny/crossref_metadata_2025 huggingface dataset:
On the structure of Dense graphs with bounded clique number
Authors: Oberkampf Heiner , Schacht Mathias
Published: June 2020

We study structural properties of graphs with bounded clique number and high minimum degree. In particular, we show that there exists a function L = L(r,ɛ) such that every Kr-free graph G on n vertices with minimum degree at least ((2r–5)/(2r–3)+ɛ)n is homomorphic to a Kr-free graph on at most L vertices. It is known that the required minimum degree condition is approximately best possible for this result.

For r = 3 this result was obtained by Łuczak (2006) and, more recently, Goddard and Lyle (2011) deduced the general case from Łuczak’s result. Łuczak’s proof was based on an application of Szemerédi’s regularity lemma and, as a consequence, it only gave rise to a tower-type bound on L(3, ɛ). The proof presented here replaces the application of the regularity lemma by a probabilistic argument, which yields a bound for L(r, ɛ) that is doubly exponential in poly(ɛ).
Numerical Modeling of Instream Wood Transport, Deposition, and Accumulation in Braided Morphologies Under Unsteady Conditions: Sensitivity and High‐Resolution Quantitative Model Validation
Authors: Ruiz‐Villanueva V. , Gamberini C. , Bladé E. , Stoffel M. , Bertoldi W.
Published: May 2020

Large wood promotes fundamental changes in river hydraulics and morphology, playing a relevant role in river ecology but also in flood hazard. Accurate predictions of large wood dynamics in terms of deposition patterns and travel distance are still lacking and only recently have numerical models been developed to this end. In this work we enhance the capabilities of the numerical model Iber‐Wood in reproducing large wood dynamics in shallow braided rivers and validate it by comparing simulations with the results of previous laboratory experiments. The flume experiments provide high‐resolution observations of wood travel distances and depositional patterns of wood. The comparison proves useful to improve the numerical simulation of (i) the interactions between wood pieces and the riverbed (e.g., when wood pieces are transported by dragging), (ii) wood pieces with roots, and (iii) the formation of wood jams (i.e., accumulations of greater than three wood pieces). A sensitivity analysis reveals the crucial role of bed topography, with limited effect played by drag and restitution coefficients. Taking advantage of a controlled environment with similar simplifying hypotheses, we combine the strengths of both physical and numerical modeling to explore the parameters that are most effective in controlling wood dynamics. We use the numerical model to explore the effect of unsteady flow conditions, with different wood supply input. The resulting wood depositional patterns, jam formation, and travel distances during floods may improve our understanding of some of the controls on biogeomorphic evolutionary trajectories of braided rivers.
Scalable nanolaminated SERS multiwell cell culture assay
Authors: Ren Xiang , Nam Wonil , Ghassemi Parham , Strobl Jeannine S. , Kim Inyoung , Zhou Wei , Agah Masoud
Published: May 2020

This paper presents a new cell culture platform enabling label-free surface-enhanced Raman spectroscopy (SERS) analysis of biological samples. The platform integrates a multilayered metal-insulator-metal nanolaminated SERS substrate and polydimethylsiloxane (PDMS) multiwells for the simultaneous analysis of cultured cells. Multiple cell lines, including breast normal and cancer cells and prostate cancer cells, were used to validate the applicability of this unique platform. The cell lines were cultured in different wells. The Raman spectra of over 100 cells from each cell line were collected and analyzed after 12 h of introducing the cells to the assay. The unique Raman spectra of each cell line yielded biomarkers for identifying cancerous and normal cells. A kernel-based machine learning algorithm was used to extract the high-dimensional variables from the Raman spectra. Specifically, the nonnegative garrote on a kernel machine classifier is a hybrid approach with a mixed nonparametric model that considers the nonlinear relationships between the higher-dimension variables. The breast cancer cell lines and normal breast epithelial cells were distinguished with an accuracy close to 90%. The prediction rate between breast cancer cells and prostate cancer cells reached 94%. Four blind test groups were used to evaluate the prediction power of the SERS spectra. The peak intensities at the selected Raman shifts of the testing groups were selected and compared with the training groups used in the machine learning algorithm. The blind testing groups were correctly predicted 100% of the time, demonstrating the applicability of the multiwell SERS array for analyzing cell populations for cancer research.
Dissecting the genome of star fruit (Averrhoa carambola L.)
Authors: Fan Yannan , Sahu Sunil Kumar , Yang Ting , Mu Weixue , Wei Jinpu , Cheng Le , Yang Jinlong , Mu Ranchang , Liu Jie , Zhao Jianming , Zhao Yuxian , Xu Xun , Liu Xin , Liu Huan
Published: May 2020

Averrhoa carambola is commonly known as star fruit because of its peculiar shape, and its fruit is a rich source of minerals and vitamins. It is also used in traditional medicines in countries such as India, China, the Philippines, and Brazil for treating various ailments, including fever, diarrhea, vomiting, and skin disease. Here, we present the first draft genome of the Oxalidaceae family, with an assembled genome size of 470.51 Mb. In total, 24,726 protein-coding genes were identified, and 16,490 genes were annotated using various well-known databases. The phylogenomic analysis confirmed the evolutionary position of the Oxalidaceae family. Based on the gene functional annotations, we also identified enzymes that may be involved in important nutritional pathways in the star fruit genome. Overall, the data from this first sequenced genome in the Oxalidaceae family provide an essential resource for nutritional, medicinal, and cultivational studies of the economically important star-fruit plant.
Molecular dynamics of pre-germinative metabolism in primed eggplant (Solanum melongena L.) seeds
Authors: Forti Chiara , Ottobrino Valentino , Bassolino Laura , Toppino Laura , Rotino Giuseppe Leonardo , Pagano Andrea , Macovei Anca , Balestrazzi Alma
Published: May 2020

Seed priming, a pre-sowing technique that enhances the antioxidant/DNA repair activities during the pre-germinative metabolism, still retains empirical features. We explore for the first time the molecular dynamics of pre-germinative metabolism in primed eggplant (Solanum melongena L.) seeds in order to identify hallmarks (expression patterns of antioxidant/DNA repair genes combined with free radical profiles) useful to discriminate between high- and low-quality lots. The hydropriming protocol hereby developed anticipated (or even rescued) germination, when applied to lots with variable quality. ROS (reactive oxygen species) raised during hydropriming and dropped after dry-back. Upregulation of antioxidant/DNA repair genes was observed during hydropriming and the subsequent imbibition. Upregulation of SmOGG1 (8-oxoguanine glycosylase/lyase) gene detected in primed seeds at 2 h of imbibition appeared as a promising hallmark. On the basis of these results, the investigation was restricted within the first 2 h of imbibition, to verify whether the molecular landscape was reproducible in different lots. A complex pattern of antioxidant/DNA repair gene expression emerged, reflecting the preponderance of seed lot-specific profiles. Only the low-quality eggplant seeds subjected to hydropriming showed enhanced ROS levels, both in the dry and imbibed state, and this might be a useful signature to discriminate among lots. The plasticity of eggplant pre-germinative metabolism stimulated by priming imposes a plethora of heterogeneous molecular responses that might delay the search for quality hallmarks. However, the information hereby gained could be translated to eggplant wild relatives to speed-up their use in breeding programs or other agronomical applications.
Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato
Authors: Zhang Lei , Yu Yicheng , Shi Tianye , Kou Meng , Sun Jian , Xu Tao , Li Qiang , Wu Shaoyuan , Cao Qinghe , Hou Wenqian , Li Zongyun
Published: May 2020

Dissecting the genetic regulation of gene expression is critical for understanding phenotypic variation and species evolution. However, our understanding of the transcriptional variability in sweet potato remains limited. Here, we analyzed two publicly available datasets to explore the landscape of transcriptomic variations and its genetic basis in the storage roots of sweet potato. The comprehensive analysis identified a total of 724,438 high-confidence single nucleotide polymorphisms (SNPs) and 26,026 expressed genes. Expression quantitative trait locus (eQTL) analysis revealed 4408 eQTLs regulating the expression of 3646 genes, including 2261 local eQTLs and 2147 distant eQTLs. Two distant eQTL hotspots were found with target genes significantly enriched in specific functional classifications. By combining the information from regulatory network analyses, eQTLs and association mapping, we found that IbMYB1-2 acts as a master regulator and is the major gene responsible for the activation of anthocyanin biosynthesis in the storage roots of sweet potato. Our study provides the first insight into the genetic architecture of genome-wide expression variation in sweet potato and can be used to investigate the potential effects of genetic variants on key agronomic traits in sweet potato.
Loading calcium fluorescent probes into protoplasts to detect calcium in the flesh tissue cells of Malus domestica
Authors: Qiu Lina , Wang Yongzhang , Qu Haiyong
Published: May 2020

Cytosolic Ca2+ plays a key role in signal transduction in plants. Calcium imaging is the most common approach to studying dynamic changes in the cytoplasmic Ca2+ content. Here, we used mature ‘Fuji’ apples (Malus pumila Mill.) to obtain viable protoplasts from flesh tissue cells by enzymatic hydrolysis; then, three small-molecule fluorescent probes (fluo-8/AM, fluo-4/AM, and rhod-2/AM) were loaded into the protoplasts. All three Ca2+ fluorescent probes successfully entered the cytoplasm but did not enter the vacuole. Both the Ca2+ chelator (EGTA) and Ca2+ channel blocker (La3+) reduced the fluorescence intensity in the cytoplasm. The calcium ionophore A23187 increased the fluorescence intensity in the cytoplasm at 5 µmol/L but decreased it at 50 µmol/L. Additionally, A23187 reversed the fluorescence intensity in the cytoplasm, which was decreased by La3+. Ionomycin is also a calcium ionophore that can increase the fluorescence intensity of calcium in the cytoplasm. These results suggest that small-molecule Ca2+ fluorescent probes can be used to detect changes in cytosolic calcium levels in the cells of fruit flesh tissue. In addition, the optimum concentration of fluo-8/AM was determined to be 5 µmol/L. This was the first time that protoplasts have been isolated from apple flesh tissue cells and small-molecule fluorescent probes have been used to detect calcium in the cytoplasm of flesh tissue cells. This study provides a new method to study calcium signal transduction in fruit flesh tissue.
Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’
Authors: Patel Sagar , Robben Michael , Fennell Anne , Londo Jason P. , Alahakoon Dilmini , Villegas-Diaz Roberto , Swaminathan Padmapriya
Published: May 2020

Vitis riparia, a critically important Native American grapevine species, is used globally in rootstock and scion breeding and contributed to the recovery of the French wine industry during the mid-19th century phylloxera epidemic. This species has abiotic and biotic stress tolerance and the largest natural geographic distribution of the North American grapevine species. Here we report an Illumina short-read 369X coverage, draft de novo heterozygous genome sequence of V. riparia Michx. ‘Manitoba 37’ with the size of ~495 Mb for 69,616 scaffolds and a N50 length of 518,740 bp. Using RNAseq data, 40,019 coding sequences were predicted and annotated. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models found 96% of the complete BUSCOs in this assembly. The assembly continuity and completeness were further validated using V. riparia ESTs, BACs, and three de novo transcriptome assemblies of three different V. riparia genotypes resulting in >98% of respective sequences/transcripts mapping with this assembly. Alignment of the V. riparia assembly and predicted CDS with the latest V. vinifera ‘PN40024’ CDS and genome assembly showed 99% CDS alignment and a high degree of synteny. An analysis of plant transcription factors indicates a high degree of homology with the V. vinifera transcription factors. QTL mapping to V. riparia ‘Manitoba 37’ and V. vinifera PN40024 has identified genetic relationships to phenotypic variation between species. This assembly provides reference sequences, gene models for marker development and understanding V. riparia’s genetic contributions in grape breeding and research.
Robust dynamic community detection with applications to human brain functional networks
Authors: Martinet L.-E. , Kramer M. A. , Viles W. , Perkins L. N. , Spencer E. , Chu C. J. , Cash S. S. , Kolaczyk E. D.
Published: June 2020

While current technology permits inference of dynamic brain networks over long time periods at high temporal resolution, the detailed structure of dynamic network communities during human seizures remains poorly understood. We introduce a new methodology that addresses critical aspects unique to the analysis of dynamic functional networks inferred from noisy data. We propose a dynamic plex percolation method (DPPM) that is robust to edge noise, and yields well-defined spatiotemporal communities that span forward and backwards in time. We show in simulation that DPPM outperforms existing methods in accurately capturing certain stereotypical dynamic community behaviors in noisy situations. We then illustrate the ability of this method to track dynamic community organization during human seizures, using invasive brain voltage recordings at seizure onset. We conjecture that application of this method will yield new targets for surgical treatment of epilepsy, and more generally could provide new insights in other network neuroscience applications.
Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships
Authors: Sánchez-Valle Jon , Tejero Héctor , Fernández José María , Juan David , Urda-García Beatriz , Capella-Gutiérrez Salvador , Al-Shahrour Fátima , Tabarés-Seisdedos Rafael , Baudot Anaïs , Pancaldi Vera , Valencia Alfonso
Published: June 2020

Comorbidity is a medical condition attracting increasing attention in healthcare and biomedical research. Little is known about the involvement of potential molecular factors leading to the emergence of a specific disease in patients affected by other conditions. We present here a disease interaction network inferred from similarities between patients’ molecular profiles, which significantly recapitulates epidemiologically documented comorbidities. Furthermore, we identify disease patient-subgroups that present different molecular similarities with other diseases, some of them opposing the general tendencies observed at the disease level. Analyzing the generated patient-subgroup network, we identify genes involved in such relations, together with drugs whose effects are potentially associated with the observed comorbidities. All the obtained associations are available at the disease PERCEPTION portal (http://disease-perception.bsc.es).
Control of criticality and computation in spiking neuromorphic networks with plasticity
Authors: Cramer Benjamin , Stöckel David , Kreft Markus , Wibral Michael , Schemmel Johannes , Meier Karlheinz , Priesemann Viola
Published: June 2020

The critical state is assumed to be optimal for any computation in recurrent neural networks, because criticality maximizes a number of abstract computational properties. We challenge this assumption by evaluating the performance of a spiking recurrent neural network on a set of tasks of varying complexity at - and away from critical network dynamics. To that end, we developed a plastic spiking network on a neuromorphic chip. We show that the distance to criticality can be easily adapted by changing the input strength, and then demonstrate a clear relation between criticality, task-performance and information-theoretic fingerprint. Whereas the information-theoretic measures all show that network capacity is maximal at criticality, only the complex tasks profit from criticality, whereas simple tasks suffer. Thereby, we challenge the general assumption that criticality would be beneficial for any task, and provide instead an understanding of how the collective network state should be tuned to task requirement.
Author Correction: Weathering in a world without terrestrial life recorded in the Mesoproterozoic Velkerri Formation
Authors: Rafiei Mehrnoush , Kennedy Martin
Published: June 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Systemic lupus erythematosus favors the generation of IL-17 producing double negative T cells
Authors: Li Hao , Adamopoulos Iannis E. , Moulton Vaishali R. , Stillman Isaac E. , Herbert Zach , Moon James J. , Sharabi Amir , Krishfield Suzanne , Tsokos Maria G. , Tsokos George C.
Published: June 2020

Mature double negative (DN) T cells are a population of αβ T cells that lack CD4 and CD8 coreceptors and contribute to systemic lupus erythematosus (SLE). The splenic marginal zone macrophages (MZMs) are important for establishing immune tolerance, and loss of their number or function contributes to the progression of SLE. Here we show that loss of MZMs impairs the tolerogenic clearance of apoptotic cells and alters the serum cytokine profile, which in turn provokes the generation of DN T cells from self-reactive CD8+T cells. Increased Ki67 expression, narrowed TCR V-beta repertoire usage and diluted T-cell receptor excision circles confirm that DN T cells from lupus-prone mice and patients with SLE undergo clonal proliferation and expansion in a self-antigen dependent manner, which supports the shared mechanisms for their generation. Collectively, our results provide a link between the loss of MZMs and the expansion of DN T cells, and indicate possible strategies to prevent the development of SLE.
m5C modification of mRNA serves a DNA damage code to promote homologous recombination
Authors: Chen Hao , Yang Haibo , Zhu Xiaolan , Yadav Tribhuwan , Ouyang Jian , Truesdell Samuel S. , Tan Jun , Wang Yumin , Duan Meihan , Wei Leizhen , Zou Lee , Levine Arthur S. , Vasudevan Shobha , Lan Li
Published: June 2020

Recruitment of DNA repair proteins to DNA damage sites is a critical step for DNA repair. Post-translational modifications of proteins at DNA damage sites serve as DNA damage codes to recruit specific DNA repair factors. Here, we show that mRNA is locally modified by m5C at sites of DNA damage. The RNA methyltransferase TRDMT1 is recruited to DNA damage sites to promote m5C induction. Loss of TRDMT1 compromises homologous recombination (HR) and increases cellular sensitivity to DNA double-strand breaks (DSBs). In the absence of TRDMT1, RAD51 and RAD52 fail to localize to sites of reactive oxygen species (ROS)-induced DNA damage. In vitro, RAD52 displays an increased affinity for DNA:RNA hybrids containing m5C-modified RNA. Loss of TRDMT1 in cancer cells confers sensitivity to PARP inhibitors in vitro and in vivo. These results reveal an unexpected TRDMT1-m5C axis that promotes HR, suggesting that post-transcriptional modifications of RNA can also serve as DNA damage codes to regulate DNA repair.
Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host
Authors: Gouveia Duarte , Pible Olivier , Culotta Karen , Jouffret Virginie , Geffard Olivier , Chaumot Arnaud , Degli-Esposti Davide , Armengaud Jean
Published: June 2020

Metaproteomics of gut microbiomes from animal hosts lacking a reference genome is challenging. Here we describe a strategy combining high-resolution metaproteomics and host RNA sequencing (RNA-seq) with generalist database searching to survey the digestive tract of Gammarus fossarum, a small crustacean used as a sentinel species in ecotoxicology. This approach provides a deep insight into the full range of biomasses and metabolic activities of the holobiont components, and differentiates between the intestine and hepatopancreatic caecum.
Pleomorphic adenomas and mucoepidermoid carcinomas of the breast are underpinned by fusion genes
Authors: Pareja Fresia , Da Cruz Paula Arnaud , Gularte-Mérida Rodrigo , Vahdatinia Mahsa , Li Anqi , Geyer Felipe C. , da Silva Edaise M. , Nanjangud Gouri , Wen Hannah Y. , Varga Zsuzsanna , Brogi Edi , Rakha Emad A. , Weigelt Britta , Reis-Filho Jorge S.
Published: June 2020

Primary pleomorphic adenomas (PAs) and mucoepidermoid carcinomas (MECs) of the breast are vanishingly rare. Here we sought to determine whether breast PAs and MECs would be underpinned by the fusion genes reported to occur in their salivary gland counterparts. Our study included three breast PAs and one breast MEC, which were subjected to RNA sequencing (PAs, n = 2; MEC, n = 1) or to Archer FusionPlex sequencing (PA, n = 1). Our analyses revealed the presence of the HMGA2-WIF1 fusion gene in breast PA3, the CTNNB1-PLAG1 fusion gene in breast PA2, and the CRTC1-MAML2 fusion gene in the breast MEC analyzed (1/1). No oncogenic fusion genes were detected in breast PA1, and no additional oncogenic fusion genes were detected in the cases studied. The presence of the fusion genes identified was validated by fluorescence in situ hybridization (n = 1), reverse transcription-PCR (n = 1), or by both methods (n = 1). Taken together, our findings indicate that PAs and MECs arising in the breast resemble their salivary gland counterparts not only phenotypically but also at the genetic level. Furthermore, our data suggest that the molecular analysis of breast PAs and MECs might constitute a useful tool to aid in their differential diagnosis.
Automated crystal structure analysis based on blackbox optimisation
Authors: Ozaki Yoshihiko , Suzuki Yuta , Hawai Takafumi , Saito Kotaro , Onishi Masaki , Ono Kanta
Published: June 2020

In the present study, we show that time-consuming manual tuning of parameters in the Rietveld method, one of the most frequently used crystal structure analysis methods in materials science, can be automated by considering the entire trial-and-error process as a blackbox optimisation problem. The automation is successfully achieved using Bayesian optimisation, which outperforms both a human expert and an expert-system type automation despite the absence of expertise. This approach stabilises the analysis quality by eliminating human-origin variance and bias, and can be applied to various analysis methods in other areas which also suffer from similar tiresome and unsystematic manual tuning of extrinsic parameters and human-origin variance and bias.
MutSpot: detection of non-coding mutation hotspots in cancer genomes
Authors: Guo Yu Amanda , Chang Mei Mei , Skanderup Anders Jacobsen
Published: June 2020

Recurrence and clustering of somatic mutations (hotspots) in cancer genomes may indicate positive selection and involvement in tumorigenesis. MutSpot performs genome-wide inference of mutation hotspots in non-coding and regulatory DNA of cancer genomes. MutSpot performs feature selection across hundreds of epigenetic and sequence features followed by estimation of position- and patient-specific background somatic mutation probabilities. MutSpot is user-friendly, works on a standard workstation, and scales to thousands of cancer genomes.
Energy metabolism and mitochondrial defects in X-linked Charcot-Marie-Tooth (CMTX6) iPSC-derived motor neurons with the p.R158H PDK3 mutation
Authors: Perez-Siles G. , Cutrupi A. , Ellis M. , Screnci R. , Mao D. , Uesugi M. , Yiu Eppie M. , Ryan Monique M. , Choi B. O. , Nicholson G. , Kennerson M. L.
Published: June 2020

Charcot-Marie-Tooth (CMT) is a group of inherited diseases clinically and genetically heterogenous, characterised by length dependent degeneration of axons of the peripheral nervous system. A missense mutation (p.R158H) in the pyruvate dehydrogenase kinase 3 gene (PDK3) has been identified as the genetic cause for an X-linked form of CMT (CMTX6) in two unrelated families. PDK3 is one of four PDK isoenzymes that regulate the activity of the pyruvate dehydrogenase complex (PDC). The balance between kinases (PDKs) and phosphatases (PDPs) determines the extend of oxidative decarboxylation of pyruvate to generate acetyl CoA, critically linking glycolysis and the energy producing Krebs cycle. We had shown the p.R158H mutation causes hyperactivity of PDK3 and CMTX6 fibroblasts show hyperphosphorylation of PDC, leading to reduced PDC activity and ATP production. In this manuscript we have generated induced pluripotent stem cells (iPSCs) by re-programming CMTX6 fibroblasts (iPSCCMTX6). We also have engineered an isogenic control (iPSCisogenic) and demonstrated that genetic correction of the p.R158H mutation reverses the CMTX6 phenotype. Patient-derived motor neurons (MNCMTX6) show increased phosphorylation of the PDC, energy metabolism defects and mitochondrial abnormalities, including reduced velocity of trafficking mitochondria in the affected axons. Treatment of the MNCMTX6 with a PDK inhibitor reverses PDC hyperphosphorylation and the associated functional deficits founds in the patient motor neurons, demonstrating that the MNCMTX6 and MNisogenic motor neurons provide an excellent neuronal system for compound screening approaches to identify drugs for the treatment of CMTX6.
A flexible rGO electrode: a new platform for the direct voltammetric detection of salicylic acid
Authors: Yu Qinghua , Zhao Ying , Huang Lihui , Sun Jiawei , Jin Dangqin , Shu Yun , Xu Qin , Hu Xiao-Ya
Published: June 2020

Herein, a flexible electrode based on reduced graphene oxide (rGO) was developedviaa simple extruded process which showed good sensitivity and selectivity for salicylic acid detection.
Facile synthesis of a nickel(0) phosphine complex at ambient temperature
Authors: Hanf Schirin , Grell Toni , Waters Jessica E. , García-Rodríguez Raúl , Hey-Hawkins Evamarie , Wright Dominic S.
Published: June 2020

The reaction of the bis(methoxy)-2-pyridyl-phosphine (MeO)2P(2-py) with [Ni(MeCN)6](BF4)2 leads to the unexpected, single-step reduction of NiII and the formation of a tetrahedral nickel(0) complex.
Interplays between copper and Mycobacterium tuberculosis GroEL1
Authors: Yang Dong , Klebl David P , Zeng Sheng , Sobott Frank , Prévost Martine , Soumillion Patrice , Vandenbussche Guy , Fontaine Véronique
Published: June 2020

The recalcitrance of pathogenic Mycobacterium tuberculosis, the agent of tuberculosis, to eradication is due to various factors allowing bacteria to escape from stress situations. The mycobacterial chaperone GroEL1, overproduced after macrophage entry and under oxidative stress, could be one of these key players. We previously reported that GroEL1 is necessary for the biosynthesis of phthiocerol dimycocerosate, a virulence-associated lipid and for reducing antibiotic susceptibility. In the present study, we showed that GroEL1, bearing a unique C-terminal histidine-rich region, is required for copper tolerance during Mycobacterium bovis BCG biofilm growth. Mass spectrometry analysis demonstrated that GroEL1 displays high affinity for copper ions, especially at its C-terminal histidine-rich region. Furthermore, the binding of copper protects GroEL1 from destabilization and increases GroEL1 ATPase activity. Altogether, these findings suggest that GroEL1 could counteract copper toxicity, notably in the macrophage phagosome, and further emphasizes that M. tuberculosis GroEL1 could be an interesting antitubercular target.
Video-rate upconversion display from optimized lanthanide ion doped upconversion nanoparticles
Authors: Gao Laixu , Shan Xuchen , Xu Xiaoxue , Liu Yongtao , Liu Baolei , Li Songquan , Wen Shihui , Ma Chenshuo , Jin Dayong , Wang Fan
Published: June 2020

A method for video-rate display with optimized single UCNP brightness by integrating the full emission intensity over excitation time and lifetime.
Palladium-catalyzed C8–H alkoxycarbonylation of 1-naphthylamines with alkyl chloroformates
Authors: Shi Yaqi , Yang Fan , Wu Yangjie
Published: June 2020

A simple and efficient protocol for palladium-catalyzed C8–H alkoxycarbonylation of 1-naphthylamine derivatives with alkyl chloroformates has been developed.
(Co)polymerization of (−)-menthide and β-butyrolactone with yttrium-bis(phenolates): tuning material properties of sustainable polyesters
Authors: Adams Friederike , Pehl Thomas M. , Kränzlein Moritz , Kernbichl Sebastian A. , Kang Jia-Jhen , Papadakis Christine M. , Rieger Bernhard
Published: June 2020

Sustainable thermoplastic elastomers derived from block copolymers of syndiotactic poly(3-hydroxybutyrate) and poly((−)-menthide) were synthesized via yttrium-mediated ring-opening polymerization.
Dimensional reduction of the small-bandgap double perovskite Cs2AgTlBr6
Authors: Connor Bridget A. , Biega Raisa-Ioana , Leppert Linn , Karunadasa Hemamala I.
Published: June 2020

The Ag–Tl perovskites provide the first clear evidence that quantum confinement can significantly alter the optical properties of 2D halide double perovskites.
Approximation‐free design for distributed consensus tracking of networked uncertain non‐linear multi‐agent systems with heterogenous high powers
Authors: Yoo Sung Jin
Published: June 2020

This study investigates a distributed approximation‐free design problem for guaranteed consensus tracking quality of networked uncertain heterogenous power‐chained multi‐agent systems with completely unknown non‐linearities. Compared with the existing studies in the presence of power‐chained state variables, the main contribution of this study is to provide a distributed low‐complexity consensus tracker design strategy using only the relative output information among agents, without the use of adaptive neural or fuzzy function approximators for estimating unknown non‐linear functions. A novel recursive design strategy independent of the feedback domination technique is established to deal with power‐chained state variables under directed networks. Using the Lyapunov stability theorem, it is shown that the preselected performance of the consensus tracking error is ensured.
Suboptimal closed‐form feedback control of input‐affine non‐linear systems
Authors: Nanavati Rohit V. , Kumar Shashi Ranjan , Maity Arnab
Published: June 2020

A closed‐form feedback solution to finite‐time optimal control problems for input‐affine non‐linear systems is presented here. Based on the state‐dependent Riccati equation (SDRE) framework, this suboptimal solution, called balanced‐cost SDRE (BCSDRE), is proposed to minimise the overall control effort required for driving the system from an arbitrary initial condition to an acceptable neighbourhood around origin, within a pre‐specified final time. The state error is dynamically penalised to balance the overall state error and the control cost, resulting in a modified SDRE. Unlike the existing finite‐horizon SDRE methods, the proposed technique does not require to solve algebraic Riccati and Lyapunov equations at every time step, which makes this approach computationally efficient. Based on the Lyapunov theory, the origin of the BCSDRE controlled system is shown to be locally exponentially stable. Furthermore, the state profile is also shown to be locally predefined time ultimately bounded, under appropriate tuning of the proposed controller. The proposed technique is implemented to design a controller for the Van der Pol oscillator and impact angle guidance design problem, and its performance is compared with the existing finite‐horizon SDRE‐based techniques.
Robust fault detection filter design for a class of discrete‐time conic‐type non‐linear Markov jump systems with jump fault signals
Authors: Dong Xuefei , He Shuping , Stojanovic Vladimir
Published: June 2020

This study investigates the robust fault detection filter design problem for a class of discrete‐time conic‐type non‐linear Markov jump systems with jump fault signals. The conic‐type non‐linearities satisfy a restrictive condition that lies in an n ‐dimensional hyper‐sphere with an uncertain centre. A crucial idea is to formulate the robust fault detection filter design problem of non‐linear Markov jump systems as filtering problem. The authors aim to design a fault detection filter such that the augmented Markov jump systems with conic‐type non‐linearities are stochastically stable and satisfy the given performance against the external disturbances. By means of the appropriate mode‐dependent Lyapunov functional method, sufficient conditions for the existence of the designed fault detection filter are presented in terms of linear matrix inequalities. Finally, a practical circuit model example is employed to demonstrate the availability of the main results.
Distributed fusion estimation for non‐linear networked systems with random access protocol and cyber attacks
Authors: Lu Jiyong , Wang Weizhen , Li Li , Guo Yanping
Published: June 2020

This study investigates the distributed fusion estimation problem for multi‐sensor non‐linear networked systems with random access protocol (RAP) and cyber attacks. For each sensor, the RAP is applied to determine which channel can enter the communication networks at each transmission instant. The process of transmitting measurements to a corresponding local estimator (LE) via the wireless network may be attacked by a vicious attacker. Hence, a detector based on cross‐correlation of the causal sequence is proposed in the LE. Moreover, a distributed fusion estimation algorithm based on a sequential covariance intersection fusion technique is designed utilising local estimations calculated by modified unscented Kalman filter. A sufficient condition is obtained to guarantee the boundedness of fusion estimation error. Finally, a numerical simulation is given to demonstrate the effectiveness of the theoretical results.
Occlusion‐handling tracker based on discriminative correlation filters
Authors: Xie Yue , Zhang Hanling , Li Lijun
Published: June 2020

Visual object tracking (VOT) based on discriminative correlation filters (DCF) has received great attention due to its higher computational efficiency and better robustness. However, DCF‐based methods suffer from the problem of model contamination. The tracker will drift into the background due to the uncertainties brought by shifting among peaks, which will further lead to the issues of model degradation. To deal with occlusions, a novel Occlusion‐Handling Tracker Based on Discriminative Correlation Filters (OHDCF) framework is proposed for online visual object tracking, where an occlusion‐handling strategy is integrated into the spatial–temporal regularized correlation filters (STRCF). The occlusion‐handling tracker follows a hybrid approach to handle partial occlusion and complete occlusion. Specifically, we first present a function to determine whether occlusion occurs. Then, the proposed filter uses block‐based and feature‐matching methods to determine whether an object is partially occluded or completely occluded. Following this, we use different methods to track the target. Extensive experiments have performed on OTB‐100, Temple‐Color‐128, VOT‐2016 and VOT‐2018 datasets, the results show that OHDCF achieves promising performance compared to other state‐of‐the‐art trackers. On VOT‐2018, OHDCF significantly outperforms STRCF from the challenge with a relative gain of 4.8 in EAO and a gain of 4.6 in Accuracy.
3D Modelling and simulation analysis of electric field under HV overhead line using improved optimisation method
Authors: Djekidel Rabah , Bessedik Sid Ahmed , Akef Samar
Published: June 2020

This study proposes a three‐dimensional (3D) quasi‐static modelling of the electric field produced by high voltage (HV) overhead power lines using charge simulation method combined with intelligent optimisation algorithms, such as particle swarm optimisation, genetic algorithm and grey Wolf optimiser (GWO), to find the optimal values of parameters for an accurate calculation. Results show that the GWO works better than other algorithms. Several parameters affecting the electric field have been studied; it is observed that taking into account the effect of the exact catenary curve of the power line conductors is much more interesting particularly at the mid‐span level where the electric field becomes very significant. According to these values, the limits set by the International Commission on Non‐Ionising Radiation Protection guidelines for electric field strength are met for occupational and public exposure. The simulation results are compared with those obtained by the 3D Integration method, a fairly good agreement is found. To confirm the performance and effectiveness of the proposed method, the results obtained are also verified with measurement values available in the literature, a good similarity is achieved.
The Use of Fungal Endophyte Penicillium citrinum on Tree Seedling: Applicability and Limitation
Authors: Surya Hakim Safinah , Yuwati Tri W.
Published: June 2020

Penicillium citrinum is an endophyte fungus isolated from plant tissues that live in tropical peatland. Various study reveals that endophytic fungi give advantages to plant health. Since 2015, series of experiments were conducted to investigate the capability of P. citrinum P3.10 as biofertilizer of plant tree in nursery stage which are: pathogenicity test, in vitro assay, direct application to seeds, dosage test, and fertilizer formulation. This paper presents a review from our research of P. citrinum isolate P3.10 from the isolation stage to the biofertilizer product formulation. Resear ch results showed that the application of endophytic fungi to seedlings gave positive responses. However, during the research process there were also obstacles in the application of endophytic fungi to plants, which are: (a) difficulties in application due to the varied response, (b) formulation, (c) storage, (d) isolate viability, and (d) fungal isolate maintenance. Risk management was needed during biofertilizer production. Hence, the utilization of biofertilizer made from endophyte fungi is applicable and can be used not only on an experimental scale but also on a larger scale.
Cytotoxic, Anti-bacterial, and Wound-healing Activity of Prenylated Phenols from the Kurdish Traditional Medicinal Plant Onobrychis Carduchorum (Fabaceae)
Authors: Clericuzio Marco , Hussain Faiq H. S. , Amin Hawraz Ibrahim M. , Bona Elisa , Gamalero Elisa , Giorgia Novello , Lappano Rosamaria , Talia Marianna , Maggiolini Marcello , Bazzicalupo Miriam , Cornara Laura
Published: June 2020

Onobrychis carduchorum (Fabaceae) is a plant widely employed in Kurdish traditional medicine to cure wounds, inflammations, and other skin diseases. We could isolate ten different polyphenols from the acetone extract of this plant: 1–4 are isoflavones, having a genistein skeleton; 5–7 are flavanones, having a naringenin skeleton; and 8–10 are prenylated dihydro-stilbenes. In particular, 8–10 have been isolated, so far, only from Glycyrrhiza glabra (liquorice). Many of the above prenylated phenols showed significant toxicity on some human breast cancer cell lines, and a relevant growth inhibition of Staphylococcus aureus strains. In addition, 9 and 10 had marked wound healing activity. It is suggested that these bioactivities are responsible, at least partly, for the plant’s traditional use.
Artificial intelligence-based diagnostic system classifying gastric cancers and ulcers: comparison between the original and newly developed systems
Authors: Namikawa Ken , Hirasawa Toshiaki , Nakano Kaoru , Ikenoyama Yohei , Ishioka Mitsuaki , Shiroma Sho , Tokai Yoshitaka , Yoshimizu Shoichi , Horiuchi Yusuke , Ishiyama Akiyoshi , Yoshio Toshiyuki , Tsuchida Tomohiro , Fujisaki Junko , Tada Tomohiro
Published: June 2020

Background We previously reported for the first time the usefulness of artificial intelligence (AI) systems in detecting gastric cancers. However, the “original convolutional neural network (O-CNN)” employed in the previous study had a relatively low positive predictive value (PPV). Therefore, we aimed to develop an advanced AI-based diagnostic system and evaluate its applicability for the classification of gastric cancers and gastric ulcers.

Methods We constructed an “advanced CNN” (A-CNN) by adding a new training dataset (4453 gastric ulcer images from 1172 lesions) to the O-CNN, which had been trained using 13 584 gastric cancer and 373 gastric ulcer images. The diagnostic performance of the A-CNN in terms of classifying gastric cancers and ulcers was retrospectively evaluated using an independent validation dataset (739 images from 100 early gastric cancers and 720 images from 120 gastric ulcers) and compared with that of the O-CNN by estimating the overall classification accuracy.

Results The sensitivity, specificity, and PPV of the A-CNN in classifying gastric cancer at the lesion level were 99.0 % (95 % confidence interval [CI] 94.6 %−100 %), 93.3 % (95 %CI 87.3 %−97.1 %), and 92.5 % (95 %CI 85.8 %−96.7 %), respectively, and for classifying gastric ulcers were 93.3 % (95 %CI 87.3 %−97.1 %), 99.0 % (95 %CI 94.6 %−100 %), and 99.1 % (95 %CI 95.2 %−100 %), respectively. At the lesion level, the overall accuracies of the O- and A-CNN for classifying gastric cancers and gastric ulcers were 45.9 % (gastric cancers 100 %, gastric ulcers 0.8 %) and 95.9 % (gastric cancers 99.0 %, gastric ulcers 93.3 %), respectively.

Conclusion The newly developed AI-based diagnostic system can effectively classify gastric cancers and gastric ulcers.
Spherical and cylindrical shocks in a non-ideal dusty gas with magnetic field under the action of heat conduction and radiation heat flux
Authors: Sahu P. K.
Published: June 2020

In this article, the propagation of spherical or cylindrical shock waves in a mixture of small solid particles of microsize and a non-ideal gas with conductive as well as radiative heat fluxes are studied under the influence of an azimuthal or axial magnetic field. The solid particles are uniformly distributed in the mixture, and the shock wave is assumed to be driven by a piston. It is assumed that the equilibrium flow conditions are maintained and the moving piston continuously supplies the variable energy input. The density of the undisturbed medium is assumed to be constant in order to obtain the self-similar solutions. Heat conduction is expressed in terms of Fourier’s law, and the radiation is considered to be of diffusion type for an optically thick gray gas model. The thermal conductivity and the absorption coefficient are assumed to vary with temperature and density. Numerical calculations have been performed to obtain the flow profiles of variables. The effects of different values of the non-idealness parameter, the strength of the magnetic field, the mass concentration, the ratio of the density of solid particles to the initial density of the gas, the piston velocity index, and the adiabatic index are shown in detail. It is interesting to note that in the presence of an azimuthal magnetic field, the pressure and density vanish at the piston, and hence, a vacuum is formed at the center of symmetry, which is in excellent agreement with the laboratory condition to produce the shock wave.

The author of the article agrees to the retraction of the article effective AUGUST 20, 2021.
Investigating the effect of reagent parameters on the efficiency of cell lysis within droplets
Authors: Shamloo Amir , Hassani-Gangaraj Mojtaba
Published: June 2020

Cell lysis is an essential primary step in cell assays. In the process of cell lysis, the cell membrane is destroyed and the substances inside the cell are extracted. By utilizing a droplet-based microfluidic platform for cell lysis, the mixer unit that is required for mixing lysis reagents with the cells can be excluded, and thus, the complexity of the fabrication process is reduced. In addition, lysing the cells within the droplets will prevent the cells from exposure to the channel walls, and as a result, cleanliness of the samples and the device is maintained. In this study, cell lysis within the droplets and the parameters affecting the efficiency of this process are investigated using a computational fluid dynamics model. Both the cell solution and the lysis reagents are encapsulated within a droplet and the lysis procedure is simulated inside the droplet. It is known that the secondary flows generated inside the droplet facilitate the mixing process. In this study, we used this effect to improve the efficiency of cell lysis in droplet and the improvement is shown to be attributed to activating an advection mechanism besides the diffusion mechanism inside the droplet. It is also shown that increasing the concentration of the lysis reagents does not have a significant effect on the efficiency of the cell lysis. The effect of the volume fraction of the lysis reagents is also studied, which is shown to be an effective factor in controlling the efficiency of the cell lysis. The lysis procedure is simulated with lysis reagent volume fractions of 50%, 66%, 80%, 90%, and 97%. The lysis efficiency is found to be 38.45%, 45.3%, 57.6%, 82.4%, and 100%, respectively, while the droplet travels through a 2 mm-long microchannel within 0.25 s. This study shows that the droplet microfluidic platform is a powerful tool for performing fast and reliable cell lysis.
Field-induced shaping of sessile paramagnetic drops
Authors: Dodoo Jennifer , Stokes Adam A.
Published: June 2020

We use the electromagnetic stress tensor to describe the elongation of paramagnetic drops in uniform magnetic fields. This approach implies a linear relationship between the shape of the drops and the square of the applied field, which we confirm experimentally. We show that this effect scales with the volume and susceptibility of the drops. By using this unified electromagnetic approach, we highlight the potential applications of combining electric and magnetic techniques for controlled shaping of drops in liquid displays, liquid lenses, and chemical mixing of drops in microfluidics.
Genetic variation and phylogeography of the Australian and New Zealand fern Asplenium flabellifolium (Aspleniaceae)
Authors: Ohlsen Daniel J. , Shepherd Lara D. , Perrie Leon R. , Brownsey Patrick J. , Bayly Michael J.
Published: May 2020

Asplenium flabellifolium Cav. is a cytologically variable Australian and New Zealand fern. Here, we sequence chloroplast trnL-trnF and rps4-trnS from samples throughout its range to provide the first phylogeographic investigation of a fern common in both countries. Twenty-three haplotypes were detected, which formed six haplogroups in a network. Australian specimens were placed in all haplogroups. The placement of New Zealand haplotypes in five of the haplogroups suggests that this species has dispersed across the Tasman Sea at least five times. Sexually reproducing plants of lower ploidy, detected only in south-eastern Australia, contained haplotypes from the two haplogroups that are successive sisters to the remaining diversity in the phylogeny. This likely suggests that A. flabellifolium was originally a sexually reproducing species in south-eastern Australia and spread to the rest of its distribution where apomictic plants dominate. More than one haplogroup was detected in several areas across its distribution, suggesting that these areas were colonised several times. Other areas harboured several haplotypes from a single haplogroup or haplogroups not recovered elsewhere, indicating possible long-term persistence in these areas. Haplotypes and morphological features were not found to be exclusive to either breeding system or ploidy and no taxonomic revision is proposed.