bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chi hotspot control of RecBCD helicase-nuclease by long-range intramolecular signaling
Authors: Amundsen Susan K. , Taylor Andrew F. , Smith Gerald R. 
Published: November 2020

AbstractRepair of broken DNA by homologous recombination requires coordinated enzymatic reactions to prepare it for interaction with intact DNA. The multiple activities of enterobacterial RecBCD helicase-nuclease are coordinated by Chi recombination hotspots (5′ GCTGGTGG 3′) recognized during DNA unwinding. Chi is recognized in a tunnel in RecC but activates the RecB nuclease, > 25 Ǻ away. How the Chi-dependent signal travels this long distance has been unknown. We found a Chi hotspot-deficient mutant in the RecB helicase domain located > 45 Ǻ from both the Chi-recognition site and the nuclease active site. This unexpected observation led us to find additional mutations that reduced or eliminated Chi hotspot activity in each subunit and widely scattered throughout RecBCD. Each mutation alters the intimate contact between one or another pair of subunits in crystal or cryoEM structures of RecBCD bound to DNA. Collectively, these mutations span a path about 185 Ǻ long from the Chi recognition site to the nuclease active site. We discuss these surprising results in the context of an intramolecular signal transduction accounting for many previous observations.
Amalgamation of 3D structure and sequence information for protein–protein interaction prediction
Authors: Jha Kanchan , Saha Sriparna 
Published: November 2020

AbstractProtein is the primary building block of living organisms. It interacts with other proteins and is then involved in various biological processes. Protein–protein interactions (PPIs) help in predicting and hence help in understanding the functionality of the proteins, causes and growth of diseases, and designing new drugs. However, there is a vast gap between the available protein sequences and the identification of protein–protein interactions. To bridge this gap, researchers proposed several computational methods to reveal the interactions between proteins. These methods merely depend on sequence-based information of proteins. With the advancement of technology, different types of information related to proteins are available such as 3D structure information. Nowadays, deep learning techniques are adopted successfully in various domains, including bioinformatics. So, current work focuses on the utilization of different modalities, such as 3D structures and sequence-based information of proteins, and deep learning algorithms to predict PPIs. The proposed approach is divided into several phases. We first get several illustrations of proteins using their 3D coordinates information, and three attributes, such as hydropathy index, isoelectric point, and charge of amino acids. Amino acids are the building blocks of proteins. A pre-trained ResNet50 model, a subclass of a convolutional neural network, is utilized to extract features from these representations of proteins. Autocovariance and conjoint triad are two widely used sequence-based methods to encode proteins, which are used here as another modality of protein sequences. A stacked autoencoder is utilized to get the compact form of sequence-based information. Finally, the features obtained from different modalities are concatenated in pairs and fed into the classifier to predict labels for protein pairs. We have experimented on the human PPIs dataset and Saccharomyces cerevisiae PPIs dataset and compared our results with the state-of-the-art deep-learning-based classifiers. The results achieved by the proposed method are superior to those obtained by the existing methods. Extensive experimentations on different datasets indicate that our approach to learning and combining features from two different modalities is useful in PPI prediction.
Deposits from giant floods in Gale crater and their implications for the climate of early Mars
Authors: Heydari E. , Schroeder J. F. , Calef F. J. , Van Beek J. , Rowland S. K. , Parker T. J. , Fairén A. G. 
Published: November 2020

AbstractThis study reports in-situ sedimentologic evidence of giant floods in Gale crater, Mars, during the Noachian Period. Features indicative of floods are a series of symmetrical, 10 m-high gravel ridges that occur in the Hummocky Plains Unit (HPU). Their regular spacing, internal sedimentary structures, and bedload transport of fragments as large as 20 cm suggest that these ridges are antidunes: a type of sedimentary structure that forms under very strong flows. Their 150 m wavelength indicates that the north-flowing water that deposited them was at least 24 m deep and had a minimum velocity of 10 m/s. Floods waned rapidly, eroding antidune crests, and re-deposited removed sediments as patches on the up-flow limbs and trough areas between these ridges forming the Striated Unit (SU). Each patch of the SU is 50–200 m wide and long and consists of 5–10 m of south-dipping layers. The strike and dip of the SU layers mimic the attitude of the flank of the antidune on which they were deposited. The most likely mechanism that generated flood waters of this magnitude on a planet whose present-day average temperature is − 60 °C was the sudden heat produced by a large impact. The event vaporized frozen reservoirs of water and injected large amounts of CO2 and CH4 from their solid phases into the atmosphere. It temporarily interrupted a cold and dry climate and generated a warm and wet period. Torrential rainfall occurred planetwide some of which entered Gale crater and combined with water roaring down from Mt. Sharp to cause gigantic flash floods that deposited the SU and the HPU on Aeolis Palus. The warm and wet climate persisted even after the flooding ended, but its duration cannot be determined by our study.
Environmental RNA interference in two-spotted spider mite, Tetranychus urticae, reveals dsRNA processing requirements for efficient RNAi response
Authors: Bensoussan Nicolas , Dixit Sameer , Tabara Midori , Letwin David , Milojevic Maja , Antonacci Michele , Jin Pengyu , Arai Yuka , Bruinsma Kristie , Suzuki Takeshi , Fukuhara Toshiyuki , Zhurov Vladimir , Geibel Sven , Nauen Ralf , Grbic Miodrag , Grbic Vojislava 
Published: November 2020

AbstractComprehensive understanding of pleiotropic roles of RNAi machinery highlighted the conserved chromosomal functions of RNA interference. The consequences of the evolutionary variation in the core RNAi pathway genes are mostly unknown, but may lead to the species-specific functions associated with gene silencing. The two-spotted spider mite, Tetranychus urticae, is a major polyphagous chelicerate pest capable of feeding on over 1100 plant species and developing resistance to pesticides used for its control. A well annotated genome, susceptibility to RNAi and economic importance, make T. urticae an excellent candidate for development of an RNAi protocol that enables high-throughput genetic screens and RNAi-based pest control. Here, we show that the length of the exogenous dsRNA critically determines its processivity and ability to induce RNAi in vivo. A combination of the long dsRNAs and the use of dye to trace the ingestion of dsRNA enabled the identification of genes involved in membrane transport and 26S proteasome degradation as sensitive RNAi targets. Our data demonstrate that environmental RNAi can be an efficient reverse genetics and pest control tool in T. urticae. In addition, the species-specific properties together with the variation in the components of the RNAi machinery make T. urticae a potent experimental system to study the evolution of RNAi pathways.
Marigold flower like structured Cu2NiSnS4 electrode for high energy asymmetric solid state supercapacitors
Authors: Isacfranklin M. , Yuvakkumar R. , Ravi G. , Hong S. I. , Shini Foo , Thambidurai M. , Dang Cuong , Velauthapillai Dhayalan 
Published: November 2020

AbstractThe growth in energy devices and the role of supercapacitors are increasingly important in today’s world. Designing an electrode material for supercapacitors using metals that have high performance, superior structure, are eco-friendly, inexpensive and highly abundant is essentially required for commercialization. In this point of view, quaternary chalcogenide Cu2NiSnS4 with fascinating marigold flower like microstructured electrodes are synthesized using different concentrations of citric acid (0, 0.05 M, 0.1 M and 0.2 M) by employing solvothermal method. The electrode materials physicochemical characteristics are deliberated in detail using the basic characterization techniques. The electrochemical studies revealed better electrochemical performances, in particular, Cu2NiSnS4@0.1 M-CA electrode revealed high 1029 F/g specific capacitance at 0.5 A/g current density. Further, it retained 78.65% capacity over 5000 cycles. To prove the practical applicability, a full-cell asymmetric solid-state device is fabricated, and it delivered 41.25 Wh/Kg and 750 Wh/Kg energy and power density at 0.5 A/g. The optimum citric acid added Cu2NiSnS4 electrode is shown to be a promising candidate for supercapacitor applications.
Aqueous synthesis of highly adsorptive copper–gallic acid metal–organic framework
Authors: Azhar Badril , Angkawijaya Artik Elisa , Santoso Shella Permatasari , Gunarto Chintya , Ayucitra Aning , Go Alchris Woo , Tran-Nguyen Phuong Lan , Ismadji Suryadi , Ju Yi-Hsu 
Published: November 2020

AbstractA greener route to synthesize mesoporous copper–gallic acid metal–organic framework (CuGA MOF) than the conventional method using harmful DMF solvent was proposed in this study. Various synthesis attempts were conducted by modifying the synthesis conditions to produce CuGA MOF with comparable physical properties to a reference material (DMF-synthesized CuGA NMOF). The independent variables investigated include the molar ratio of NaOH to GA (1.1 to 4.4) and the synthesis temperature (30, 60, 90 °C). It was found that proper NaOH addition was crucial for suppressing the generation of copper oxide while maximizing the formation of CuGA MOF. On the other hand, the reaction temperature mainly affected the stability and adsorption potential of CuGA MOF. Reacting Cu, GA, and NaOH at a molar ratio of 1:1:2.2 and a temperature of 90 °C, produced mesoporous MOF (CuGA 90–2.2) with a surface area of 198.22 m2/g, a pore diameter of 8.6 nm, and a thermal stability of 219 °C. This MOF exhibited an excellent adsorption capacity for the removal of methylene blue (124.64 mg/g) and congo red (344.54 mg/g). The potential usage of CuGA 90–2.2 as a reusable adsorbent was demonstrated by its high adsorption efficiency (> 90%) after 5 adsorption–desorption cycles.
Non-classical crystallisation pathway directly observed for a pharmaceutical crystal via liquid phase electron microscopy
Authors: Cookman J. , Hamilton V. , Hall S. R. , Bangert U. 
Published: November 2020

AbstractNon-classical crystallisation (NCC) pathways are widely accepted, however there is conflicting evidence regarding the intermediate stages of crystallisation, how they manifest and further develop into crystals. Evidence from direct observations is especially lacking for small organic molecules, as distinguishing these low-electron dense entities from their similar liquid-phase surroundings presents signal-to-noise ratio and contrast challenges. Here, Liquid Phase Electron Microscopy (LPEM) captures the intermediate pre-crystalline stages of a small organic molecule, flufenamic acid (FFA), a common pharmaceutical. High temporospatial imaging of FFA in its native environment, an organic solvent, suggests that in this system a Pre-Nucleation Cluster (PNC) pathway is followed by features exhibiting two-step nucleation. This work adds to the growing body of evidence that suggests nucleation pathways are likely an amalgamation of multiple existing non-classical theories and highlights the need for the direct evidence presented by in situ techniques such as LPEM.
Establishment of a heart-on-a-chip microdevice based on human iPS cells for the evaluation of human heart tissue function
Authors: Abulaiti Mosha , Yalikun Yaxiaer , Murata Kozue , Sato Asako , Sami Mustafa M. , Sasaki Yuko , Fujiwara Yasue , Minatoya Kenji , Shiba Yuji , Tanaka Yo , Masumoto Hidetoshi 
Published: November 2020

AbstractHuman iPS cell (iPSC)-derived cardiomyocytes (CMs) hold promise for drug discovery for heart diseases and cardiac toxicity tests. To utilize human iPSC-derived CMs, the establishment of three-dimensional (3D) heart tissues from iPSC-derived CMs and other heart cells, and a sensitive bioassay system to depict physiological heart function are anticipated. We have developed a heart-on-a-chip microdevice (HMD) as a novel system consisting of dynamic culture-based 3D cardiac microtissues derived from human iPSCs and microelectromechanical system (MEMS)-based microfluidic chips. The HMDs could visualize the kinetics of cardiac microtissue pulsations by monitoring particle displacement, which enabled us to quantify the physiological parameters, including fluidic output, pressure, and force. The HMDs demonstrated a strong correlation between particle displacement and the frequency of external electrical stimulation. The transition patterns were validated by a previously reported versatile video-based system to evaluate contractile function. The patterns are also consistent with oscillations of intracellular calcium ion concentration of CMs, which is a fundamental biological component of CM contraction. The HMDs showed a pharmacological response to isoproterenol, a β-adrenoceptor agonist, that resulted in a strong correlation between beating rate and particle displacement. Thus, we have validated the basic performance of HMDs as a resource for human iPSC-based pharmacological investigations.
The antibacterial and angiogenic effect of magnesium oxide in a hydroxyapatite bone substitute
Authors: Coelho Catarina C. , Padrão Tatiana , Costa Laura , Pinto Marta T . , Costa Paulo C. , Domingues Valentina F. , Quadros Paulo A. , Monteiro Fernando J. , Sousa Susana R. 
Published: November 2020

AbstractBone graft infections are serious complications in orthopaedics and the growing resistance to antibiotics is increasing the need for antibacterial strategies. The use of magnesium oxide (MgO) is an interesting alternative since it possesses broad-spectrum antibacterial activity. Additionally, magnesium ions also play a role in bone regeneration, which makes MgO more appealing than other metal oxides. Therefore, a bone substitute composed of hydroxyapatite and MgO (HAp/MgO) spherical granules was developed using different sintering heat-treatment cycles to optimize its features. Depending on the sintering temperature, HAp/MgO spherical granules exhibited distinct surface topographies, mechanical strength and degradation profiles, that influenced the in vitro antibacterial activity and cytocompatibility. A proper balance between antibacterial activity and cytocompatibility was achieved with HAp/MgO spherical granules sintered at 1100 ºC. The presence of MgO in these granules was able to significantly reduce bacterial proliferation and simultaneously provide a suitable environment for osteoblasts growth. The angiogenic and inflammation potentials were also assessed using the in vivo chicken embryo chorioallantoic membrane (CAM) model and the spherical granules containing MgO stimulated angiogenesis without increasing inflammation. The outcomes of this study evidence a dual effect of MgO for bone regenerative applications making this material a promising antibacterial bone substitute.
Klein paradox for bosons, wave packets and negative tunnelling times
Authors: Gutiérrez de la Cal X. , Alkhateeb M. , Pons M. , Matzkin A. , Sokolovski D. 
Published: November 2020

AbstractWe analyse a little known aspect of the Klein paradox. A Klein–Gordon boson appears to be able to cross a supercritical rectangular barrier without being reflected, while spending there a negative amount of time. The transmission mechanism is demonstrably acausal, yet an attempt to construct the corresponding causal solution of the Klein–Gordon equation fails. We relate the causal solution to a divergent multiple-reflections series, and show that the problem is remedied for a smooth barrier, where pair production at the energy equal to a half of the barrier’s height is enhanced yet remains finite.
Genome skimming and NMR chemical fingerprinting provide quality assurance biotechnology to validate Sarsaparilla identity and purity
Authors: Kesanakurti Prasad , Thirugnanasambandam Arunachalam , Ragupathy Subramanyam , Newmaster Steven G. 
Published: November 2020

AbstractSarsaparilla is a popular natural health product (NHP) that has been reported to be one of the most adulterated botanicals in the marketplace. Several plausible explanations are documented including economically motivated product substitution, unintentional errors due to ambiguous trade name associated with several different taxa, and wild harvesting of incorrect non-commercial plants. Unfortunately, this includes the case of an adulterant speciesDecalepis hamiltonii,a Red listed medicinal plant species by the International Union for Conservation of Nature (IUCN) and declared as a species with high conservation concern by the National Biodiversity Authority of India (NBA). This study provides validated genomic (genome skimming & DNA probes) and metabolomic (NMR chemical fingerprints) biotechnology solutions to prevent adulteration on both raw materials and finished products. This is also the first use of Oxford Nanopore on herbal products enabling the use of genome skimming as a tool for quality assurance within the supply chain of botanical ingredients. The validation of both genomics and metabolomics approach provided quality assurance perspective for both product identity and purity. This research enables manufactures and retailers to verify their supply chain is authentic and that consumers can enjoy safe, healthy products.
Mediated amperometry as a prospective method for the investigation of electroporation
Authors: Simonis Povilas , Garjonyte Rasa , Stirke Arunas 
Published: November 2020

AbstractPulsed electric field effects induced in a membrane, as well as intracellular structures, depend on cell type, field and media parameters. To achieve desired outcomes, membranes should be permeabilized in a controlled manner, and thus efficiency of electroporation should be investigated in advance. Here, we present a framework for using mediated amperometry as a prospective method for the investigation of electroporation and its effects on cellular machinery. Whole-cell sensors with single mediator systems comprised of hydrophilic or lipophilic mediators were successfully employed to investigate membrane permeability as well as cellular responses. Exposure of yeast cells to single electric field pulse (τ = 300 µs, E = 16 kV/cm) resulted in up to tenfold increase of current strength mediated with hydrophilic mediators. Exposure to PEF resulted in decrease of menadione mediated current strength (from 138 ± 15 to 32 ± 15 nA), which could be completely compensated by supplementing electrolyte with NADH.
Chemical composition and biological effects of kratom (Mitragyna speciosa): In vitro studies with implications for efficacy and drug interactions
Authors: Todd D. A. , Kellogg J. J. , Wallace E. D. , Khin M. , Flores-Bocanegra L. , Tanna R. S. , McIntosh S. , Raja H. A. , Graf T. N. , Hemby S. E. , Paine M. F. , Oberlies N. H. , Cech N. B. 
Published: November 2020

AbstractThe safety and efficacy of kratom (Mitragyna speciosa) for treatment of pain is highly controversial. Kratom produces more than 40 structurally related alkaloids, but most studies have focused on just two of these, mitragynine and 7-hydroxymitragynine. Here, we profiled 53 commercial kratom products using untargeted LC–MS metabolomics, revealing two distinct chemotypes that contain different levels of the alkaloid speciofoline. Both chemotypes were confirmed with DNA barcoding to be M. speciosa. To evaluate the biological relevance of variable speciofoline levels in kratom, we compared the opioid receptor binding activity of speciofoline, mitragynine, and 7-hydroxymitragynine. Mitragynine and 7-hydroxymitragynine function as partial agonists of the human µ-opioid receptor, while speciofoline does not exhibit measurable binding affinity at the µ-, δ- or ƙ-opioid receptors. Importantly, mitragynine and 7-hydroxymitragynine demonstrate functional selectivity for G-protein signaling, with no measurable recruitment of β-arrestin. Overall, the study demonstrates the unique binding and functional profiles of the kratom alkaloids, suggesting potential utility for managing pain, but further studies are needed to follow up on these in vitro findings. All three kratom alkaloids tested inhibited select cytochrome P450 enzymes, suggesting a potential risk for adverse interactions when kratom is co-consumed with drugs metabolized by these enzymes.
Rapid mono and biexponential 3D-T1ρ mapping of knee cartilage using variational networks
Authors: Zibetti Marcelo V. W. , Johnson Patricia M. , Sharafi Azadeh , Hammernik Kerstin , Knoll Florian , Regatte Ravinder R. 
Published: November 2020

AbstractIn this study we use undersampled MRI acquisition methods to obtain accelerated 3D mono and biexponential spin–lattice relaxation time in the rotating frame (T1ρ) mapping of knee cartilage, reducing the usual long scan time. We compare the accelerated T1ρmaps obtained by deep learning-based variational network (VN) and compressed sensing (CS). Both methods were compared with spatial (S) and spatio-temporal (ST) filters. Complex-valued fitting was used for T1ρparameters estimation. We tested with seven in vivo and six synthetic datasets, with acceleration factors (AF) from 2 to 10. Median normalized absolute deviation (MNAD), analysis of variance (ANOVA), and coefficient of variation (CV) were used for analysis. The methods CS-ST, VN-S, and VN-ST performed well for accelerating monoexponential T1ρmapping, with MNAD around 5% for AF = 2, which increases almost linearly with the AF to an MNAD of 13% for AF = 8, with all methods. For biexponential mapping, the VN-ST was the best method starting with MNAD of 7.4% for AF = 2 and reaching MNAD of 13.1% for AF = 8. The VN was able to produce 3D-T1ρmapping of knee cartilage with lower error than CS. The best results were obtained by VN-ST, improving CS-ST method by nearly 7.5%.
Infant expectations of instant or delayed gratification
Authors: Luo Yuyan , Pattanakul Duangporn 
Published: November 2020

AbstractChoices between immediate gratification and long-term (but larger) gains are prevalent in human life, which is why the decision-making processes to delay gratification have been studied extensively throughout different developmental ages. Children’s delay-of-gratification behaviors have been examined in the well-known “marshmallow test,” in which 3- to 5-year-olds are given a marshmallow and told by an experimenter that they can eat it immediately or wait for an unspecified duration of time (which can be capped at 15 min) until the experimenter returns so that they can receive another marshmallow. Children's wait time has been viewed as a good indicator of their later development. Here we show that a group of 22-month-old infants (N = 32) already held expectations about others’ choices in a violation-of-expectation looking-time task modeled after the marshmallow test. The infants expected an agent to defer gratification based on a speaker’s promise of the second marshmallow available in the future, but to eat the currently attainable marshmallow when the speaker made no such promise. Our findings indicate an early-emerging understanding of others’ choices of delayed or instant gratification and shed new light on the development of delay-of-gratification behaviors.