bluuebunny/crossref_metadata_2025_split huggingface dataset:
Citizen science via social media revealed conditions of symbiosis between a marine gastropod and an epibiotic alga
Authors: Kagawa Osamu , Uchida Shota , Yamazaki Daishi , Osawa Yumiko , Ito Shun , Chiba Satoshi ,   The green-costumed snail’s citizen researchers, Kagawa Emiko , Tamada Akihiro , Ishida So , Yoshida Junko , Kimura Kazuki , Iijima Akiko , Suenaga Takayuki , Momoi Teruaki , Kato You , Nikaido Satoshi , Kimura Taeko , Kobayashi Shingo , Niwa Kazuo , Nishi Hirotaka , Fujita Haruto , Kakihara Hideaki , Makino Shinichi , Suzuki Hiroe , Namikawa Akane , Yamakami Ryusei , Higashi Kanae , Watanabe Kota , Yoshimura Taro , Isotomo  , Sagara Mitsunori , Aoki Yuta , Sugimoto Ryoya 
Published: November 2020

AbstractEnvironmental factors promote symbiosis, but its mechanism is not yet well understood. The algaPseudocladophora conchopheriagrows only on the shell of an intertidal gastropodLunella correensis, and these species have a close symbiotic relationship which the alga reduces heat stress of the gastropod. In collaboration with general public, we investigated how environmental conditions alter the symbiotic interaction between the alga and the gastropod. Information about the habitats of each gastropod and images of shells was obtained from the Japanese and Korean coasts via social media. We constructed the hierarchical Bayesian model using the data. The results indicated that the proportion of shell area covered byP. conchopheriaincreased as the substrate size utilized by the gastropod increased. Meanwhile, temperature did not affect the proportion ofP. conchopheriaon the shell. These suggested that the alga provides no benefits for the gastropod on small substrates because gastropod can reduce the heat stress by diving into the small sediment. Further, the gastropod’s cost incurred by growing the alga on the shell seems to be low as the algae can grow even in cooler places where no benefits of heat resistance for gastropods. Different environments can yield variable conditions in symbiosis.
Single-cell RNA sequencing confirms IgG transcription and limited diversity of VHDJH rearrangements in proximal tubular epithelial cells
Authors: Deng Zhenling , Wang Xinyao , Liu Yue , Tian Xinyu , Deng Shaohui , Sun Yingchun , Wang Song , Zheng Danxia , Cui Zhuan , Pan Yuejuan , A Lata , Yan Huige , Qiu Xiaoyan , Wang Yue 
Published: November 2020

AbstractIncreasing evidence has confirmed that immunoglobulins (Igs) can be expressed in non-B cells. Our previous work demonstrated that mesangial cells and podocytes express IgA and IgG, respectively. The aim of this work was to reveal whether proximal tubular epithelial cells (PTECs) express Igs. High-throughput single-cell RNA sequencing (scRNA-seq) detected Igs in a small number of PTECs, and then we combined nested PCR with Sanger sequencing to detect the transcripts and characterize the repertoires of Igs in PTECs. We sorted PTECs from the normal renal cortex of two patients with renal cancer by FACS and further confirmed their identify by LRP2 gene expression. Only the transcripts of the IgG heavy chain were successfully amplified in 91/111 single PTECs. We cloned and sequenced 469 VHDJH transcripts from 91 single PTECs and found that PTEC-derived IgG exhibited classic VHDJH rearrangements with nucleotide additions at the junctions and somatic hypermutations. Compared with B cell-derived IgG, PTEC-derived IgG displayed less diversity of VHDJH rearrangements, predominant VH1-24/DH2-15/JH4 sequences, biased VH1 usage, centralized VH gene segment location at the 3′ end of the genome and non-Gaussian distribution of the CDR3 length. These results demonstrate that PTECs can express a distinct IgG repertoire that may have implications for their role in the renal tubular epithelial-mesenchymal transition.
Hierarchical analysis of ontogenetic time to describe heterochrony and taxonomy of developmental stages
Authors: Lecointre Guillaume , Schnell Nalani K. , Teletchea Fabrice 
Published: November 2020

AbstractEven though an accurate description of early life stages is available for some teleostean species in form of embryonic and post-embryonic developmental tables, there is poor overlap between species-specific staging vocabularies beyond the taxonomic family level. What is called “embryonic period”, “larval period”, “metamorphosis”, or “juvenile” is anatomically different across teleostean families. This problem, already pointed out 50 years ago, challenges the consistency of developmental biology, embryology, systematics, and hampers an efficient aquaculture diversification. We propose a general solution by producing a proof-of-concept hierarchical analysis of ontogenetic time using a set of four freshwater species displaying strongly divergent reproductive traits. With a parsimony analysis of a matrix where “operational taxonomic units” are species at a given ontogenetic time segment and characters are organs or structures which are coded present or absent at this time, we show that the hierarchies obtained have both very high consistency and retention index, indicating that the ontogenetic time is correctly grasped through a hierarchical graph. This allows to formally detect developmental heterochronies and might provide a baseline to name early life stages for any set of species. The present method performs a phylogenetic segmentation of ontogenetic time, which can be correctly seen as depicting ontophylogenesis.
Synthesis and molecular structure of perhalogenated rhenium-oxo corroles
Authors: Alemayehu Abraham B. , Einrem Rune F. , McCormick-McPherson Laura J. , Settineri Nicholas S. , Ghosh Abhik 
Published: November 2020

AbstractAs part of our efforts to develop rhenium-oxo corroles as photosensitizers for oxygen sensing and photodynamic therapy, we investigated the potential β-perhalogenation of five ReO meso-tris(para-X-phenyl)corroles, Re[TpXPC](O) (X = CF3, H, F, CH3, and OCH3), with elemental chlorine and bromine. With Cl2, β-octachlorinated products Re[Cl8TpXPC](O) were rapidly obtained for X = CF3, H, and CH3, but X = OCH3 resulted in overchlorination on the meso-aryl groups. Full β-octabromination proved slower relative to Cu and Ir corroles, but the desired Re[Br8TpXPC](O) products were finally obtained for X = H and F after a week at room temperature. For X = CH3 and OCH3, these conditions led to undecabrominated products Re[Br11TpXPC](O). Compared to the β-unsubstituted starting materials, the β-octahalogenated products were found to exhibit sharp 1H NMR signals at room temperature, indicating that the aryl groups are locked in place by the β-halogens, and substantially redshifted Soret and Q bands. Single-crystal X-ray structures of Re[Cl8TpCF3PC](O), Re[Cl8TpCH3PC](O), and Re[Br8TpFPC](O) revealed mild saddling for one Cl8 structure and the Br8 structure. These structural variations, however, appear too insignificant to explain the slowness of the β-octabromination protocols, which seems best attributed to the deactivating influence of the high-valent Re center.
Effects of humic acid on enhanced removal of lead ions by polystyrene-supported nano-Fe (0) nanocomposite
Authors: Wang Luyao , Wei Shiqiang , Jiang Zhenmao 
Published: November 2020

AbstractPolymer-supported nanozero-valent iron composites (D001-nZVI) were fabricated for the removal of lead ions from aqueous solutions by embedding nZVI into the porous polystyrene anion exchanger D001. Humic acid (HA) was selected as a model species because of its ubiquitous existence to gain insight into the influencing factors in the actual application process. The iron contents of the composites were approximately 11.2%, and the smallest ZVI particle size was ~ 5 nm. The experimental results showed that the effect of HA on the reduction of lead ions by D001-nZVI was a concentration-dependent process. At low HA concentrations, the surface-competitive adsorption of HA and Pb2+ dominated; therefore, the removal efficiency of Pb2+ by D001-nZVI decreased from 97.5 to 90.2% with an increasing HA concentration. When the HA concentration increased to 30 mg/L or more, the lead ions removal remained constant with the following possible cooperation mechanism: the competitive adsorption of HA and Pb2+ on the nZVI surface and the well-dispersed particles were caused by electrostatic interactions between the HA coating and the nZVI surface. In addition, the adsorption complexation between HA and Pb2+ also had a positive effect on the removal of Pb2+ at higher concentrations of HA.
Antibiofilm effects of N,O-acetals derived from 2-amino-1,4-naphthoquinone are associated with downregulation of important global virulence regulators in methicillin-resistant Staphylococcus aureus
Authors: Novais Juliana Silva , Carvalho Mariana Fernandes , Ramundo Mariana Severo , Beltrame Cristiana Ossaille , Geraldo Reinaldo Barros , Jordão Alessandro Kappel , Ferreira Vítor Francisco , Castro Helena Carla , Figueiredo Agnes Marie Sá 
Published: November 2020

AbstractDespite the existing antibiotics, antimicrobial resistance is a major challenge. Consequently, the development of new drugs remains in great demand. Quinones is part of a broad group of molecules that present antibacterial activity besides other biological properties. The main purpose of this study was to evaluate the antibiofilm activities of synthetic N,O-acetals derived from 2-amino-1,4-naphthoquinone [7a: 2-(methoxymethyl)-amino-1,4-naphthoquinone; 7b: 2-(ethoxymethyl)-amino-1,4-naphthoquinone; and 7c: 2-(propynyloxymethyl)-amino-1,4-naphthoquinone] against methicillin-resistant Staphylococcus aureus (MRSA). The derivatives 7b and 7c, specially 7b, caused strong impact on biofilm accumulation. This inhibition was linked to decreased expression of the genes fnbA, spa, hla and psmα3. More importantly, this downregulation was paralleled by the modulation of global virulence regulators. The substitution of 2-ethoxymethyl (7b) in comparison with 2-propynyloxymethyl (7c) enhanced sarA-agr inhibition, decreased fnbA transcripts (positively regulated by sarA) and strongly impaired biofilm accumulation. Indeed, 7b triggered intensive autolysis and was able to eliminate vancomycin-persistent cells. Consequently, 7b is a promising molecule displaying not only antimicrobial effects, but also antibiofilm and antipersistence activities. Therefore, 7b is a good candidate for further studies involving the development of novel and more rational antimicrobials able to act in chronic and recalcitrant infections, associated with biofilm formation.
Production of synthetic wheat lines to exploit the genetic diversity of emmer wheat and D genome containing Aegilops species in wheat breeding
Authors: Mirzaghaderi Ghader , Abdolmalaki Zinat , Ebrahimzadegan Rahman , Bahmani Farshid , Orooji Fatemeh , Majdi Mohammad , Mozafari Ali-Akbar 
Published: November 2020

AbstractDue to the accumulation of various useful traits over evolutionary time, emmer wheat (Triticum turgidumsubsp.dicoccumanddicoccoides, 2n = 4x = 28; AABB), durum wheat (T. turgidumsubsp.durum, 2n = 4x = 28; AABB),T. timopheevii(2n = 4x = 28; AAGG) and D genome containingAegilopsspecies offer excellent sources of novel variation for the improvement of bread wheat (T. aestivumL., AABBDD). Here, we made 192 different cross combinations between diverse genotypes of wheat andAegilopsspecies including emmer wheat × Ae. tauschii(2n = DD or DDDD), durum wheat × Ae. tauschii,T. timopheevii × Ae. tauschii,Ae. crassa × durum wheat,Ae. cylindrica × durum wheat andAe. ventricosa × durum wheat in the field over three successive years. We successfully recovered 56 different synthetic hexaploid and octaploid F2lines with AABBDD, AABBDDDD, AAGGDD, D1D1XcrXcrAABB, DcDcCcCcAABB and DvDvNvNvAABB genomes via in vitro rescue of F1embryos and spontaneous production of F2seeds on the Flplants. Cytogenetic analysis of F2lines showed that the produced synthetic wheat lines were generally promising stable amphiploids. Contribution of D genome bearingAegilopsand the less-investigated emmer wheat genotypes as parents in the crosses resulted in synthetic amphiploids which are a valuable resource for bread wheat breeding.
Digital holographic microscopy for real-time observation of surface-relief grating formation on azobenzene-containing films
Authors: Rekola Heikki , Berdin Alex , Fedele Chiara , Virkki Matti , Priimagi Arri 
Published: November 2020

AbstractLight-induced surface structuring of azobenzene-containing films allows for creation of complex surface relief patterns with varying heights, patterns which would be difficult to create using conventional lithography tools. In order to realize the full potential of these patternable surfaces, understanding their formation dynamics and response to different types of light fields is crucial. In the present work we introduce digital holographic microscopy (DHM) for real time, in-situ observation of surface-relief grating (SRG) formation on azobenzene-containing films. This instrument allows us to measure the surface topography of films while illuminating them with two individually controlled laser beams for creating periodically varying patterns. By utilizing the information of the grating formation dynamics, we combine multiple grating patterns to create pixels with wide gamut structural colors as well as blazed grating structures on the film surface. As long as the material behaviour is linear, any Fourier optical surface can be created utilizing this multiple patterning approach. The DHM instrument presented here has the potential for creating complex 3D surface reliefs with nanometric precision.
Structure of Nora virus at 2.7 Å resolution and implications for receptor binding, capsid stability and taxonomy
Authors: Laurinmäki Pasi , Shakeel Shabih , Ekström Jens-Ola , Mohammadi Pezhman , Hultmark Dan , Butcher Sarah J. 
Published: November 2020

AbstractNora virus, a virus of Drosophila, encapsidates one of the largest single-stranded RNA virus genomes known. Its taxonomic affinity is uncertain as it has a picornavirus-like cassette of enzymes for virus replication, but the capsid structure was at the time for genome publication unknown. By solving the structure of the virus, and through sequence comparison, we clear up this taxonomic ambiguity in the invertebrate RNA virosphere. Despite the lack of detectable similarity in the amino acid sequences, the 2.7 Å resolution cryoEM map showed Nora virus to have T = 1 symmetry with the characteristic capsid protein β-barrels found in all the viruses in the Picornavirales order. Strikingly, α-helical bundles formed from the extended C-termini of capsid protein VP4B and VP4C protrude from the capsid surface. They are similar to signalling molecule folds and implicated in virus entry. Unlike other viruses of Picornavirales, no intra-pentamer stabilizing annulus was seen, instead the intra-pentamer stability comes from the interaction of VP4C and VP4B N-termini. Finally, intertwining of the N-termini of two-fold symmetry-related VP4A capsid proteins and RNA, provides inter-pentamer stability. Based on its distinct structural elements and the genetic distance to other picorna-like viruses we propose that Nora virus, and a small group of related viruses, should have its own family within the order Picornavirales.
Asthma prevalence, lung and cardiovascular function in adolescents born preterm
Authors: Arroyas Maria , Calvo Cristina , Rueda Santiago , Esquivias Maria , Gonzalez-Menchen Cristina , Gonzalez-Carrasco Ersilia , Garcia-Garcia Maria Luz 
Published: November 2020

AbstractOur main objective was to study respiratory evolution and pulmonary and cardiac function in adolescents born preterm in the post-surfactant era. Observational cross-sectional study, comparing very preterm (< 32 weeks) and moderately-late preterm adolescents (≥ 32 weeks) (74 each group). We recorded respiratory symptoms, spirometry and functional echocardiogram. Very preterm adolescents required more respiratory admissions (45.9% vs. 28.4%) (p = 0.03, OR 2.1, CI95% 1.1–4.2) and had more current asthma (21.6% vs. 9.5%, p = 0.04, OR 2.3, CI95% 1.1–5.2). Preterm subjects with intrauterine growth restriction (IUGR) presented lower FEV1 (88.7 ± 13.9 vs. 95.9 ± 13.3, p = 0.027) and lower FVC (88.2 ± 13.6 vs. 95.5 ± 13.3, p = 0.025). When assessing right ventricle, very preterm showed a greater E/E’ ratio (p = 0.02) and longer myocardial performance index (MPI) (p = 0.001). Adolescents with IUGR showed less shortening fraction (p = 0.016), worse E/E′ ratio (p = 0.029) and longer MPI (p = 0.06). Regarding left ventricle, very preterm showed less E′ wave velocity (p = 0.03), greater E/E′ ratio (p = 0.005) and longer MPI (p < 0.001). Gestational age < 32 weeks is independently associated with current asthma in adolescence. Children 13–14 years old born very preterm required more respiratory admissions and had poorer diastolic and global function of both ventricles. IUGR is a risk factor for poorer lung function in preterm adolescents, regardless gestational age.
Efficient solution of Boolean satisfiability problems with digital memcomputing
Authors: Bearden Sean R. B. , Pei Yan Ru , Di Ventra Massimiliano 
Published: November 2020

AbstractBoolean satisfiability is a propositional logic problem of interest in multiple fields, e.g., physics, mathematics, and computer science. Beyond a field of research, instances of the SAT problem, as it is known, require efficient solution methods in a variety of applications. It is the decision problem of determining whether a Boolean formula has a satisfying assignment, believed to require exponentially growing time for an algorithm to solve for the worst-case instances. Yet, the efficient solution of many classes of Boolean formulae eludes even the most successful algorithms, not only for the worst-case scenarios, but also for typical-case instances. Here, we introduce a memory-assisted physical system (a digital memcomputing machine) that, when its non-linear ordinary differential equations are integrated numerically, shows evidence for polynomially-bounded scalability while solving “hard” planted-solution instances of SAT, known to require exponential time to solve in the typical case for both complete and incomplete algorithms. Furthermore, we analytically demonstrate that the physical system can efficiently solve the SAT problem in continuous time, without the need to introduce chaos or an exponentially growing energy. The efficiency of the simulations is related to the collective dynamical properties of the original physical system that persist in the numerical integration to robustly guide the solution search even in the presence of numerical errors. We anticipate our results to broaden research directions in physics-inspired computing paradigms ranging from theory to application, from simulation to hardware implementation.
Neurotrophic effects of dental pulp stem cells on trigeminal neuronal cells
Authors: Sultan Nessma , Amin Laila E. , Zaher Ahmed R. , Grawish Mohammed E. , Scheven Ben A. 
Published: November 2020

AbstractEvidence indicates that dental pulp stem cells (DPSC) secrete neurotrophic factors which play an important role in neurogenesis, neural maintenance and repair. In this study we investigated the trophic potential of DPSC-derived conditioned medium (CM) to protect and regenerate isolated primary trigeminal ganglion neuronal cells (TGNC). DPSC and TGNC were harvested by enzymatic digestion from Wister-Hann rats. CM was collected from 72 h serum-free DPSC cultures and neurotrophic factors; nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), neurotrophin-3 (NT-3), and glial cell line-derived neurotrophic factor (GDNF) were analysed by specific enzyme-linked immunosorbent assays (ELISAs). Primary co-cultures of DPSC and TGNC were established to evaluate the paracrine effects of DPSC. In comparison, NGF was used to evaluate its neurotrophic and neuritogenic effect on TGNC. Immunocytochemistry was performed to detect the neuronal-markers; neuronal nuclei (NeuN), microtubule-associated protein-2 (MAP-2) and βIII-tubulin. Quantitative real time polymerase chain reaction (qRT-PCR) was used to analyse neuronal-associated gene expression of NeuN, MAP-2, βIII-tubulin in addition to growth-associated protein-43 (GAP-43), Synapsin-I and thermo-sensitive transient receptor potential vanilloid channel-1 (TRPV1). DPSC-CM contained significant levels of NGF, BDNF, NT-3 and GDNF. DPSC and DPSC-CM significantly enhanced TGNC survival with extensive neurite outgrowth and branching as evaluated by immunocytochemistry of neuronal markers. DPSC-CM was more effective in stimulating TGNC survival than co-cultures or NGF treated culture. In comparison to controls, DPSC-CM significantly upregulated gene expression of several neuronal markers as well as TRPV1. This study demonstrated that DPSC-derived factors promoted survival and regeneration of isolated TGNC and may be considered as cell-free therapy for TG nerve repair.
Withaferin A activates TRIM16 for its anti-cancer activity in melanoma
Authors: Nagy Zsuzsanna , Cheung Belamy B. , Tsang Wing , Tan Owen , Herath Mika , Ciampa Olivia C. , Shadma Fatima , Carter Daniel R. , Marshall Glenn M. 
Published: November 2020

AbstractAlthough selective BRAF inhibitors and novel immunotherapies have improved short-term treatment responses in metastatic melanoma patients, acquired resistance to these therapeutics still represent a major challenge in clinical practice. In this study, we evaluated the efficacy of Withaferin A (WFA), derived from the medicinal plant Withania Somnifera, as a novel therapeutic agent for the treatment of melanoma. WFA showed selective toxicity to melanoma cells compared to non-malignant cells. WFA induced apoptosis, significantly reduced cell proliferation and inhibited migration of melanoma cells. We identified that repression of the tumour suppressor TRIM16 diminished WFA cytotoxicity, suggesting that TRIM16 was in part responsible for the cytotoxic effects of WFA in melanoma cells. Together our data indicates that WFA has potent cytopathic effects on melanoma cells through TRIM16, suggesting a potential therapeutic application of WFA in the disease.