bluuebunny/crossref_metadata_2025 huggingface dataset:
Optical tweezers-controlled hotspot for sensitive and reproducible surface-enhanced Raman spectroscopy characterization of native protein structures
Authors: Dai Xin , Fu Wenhao , Chi Huanyu , Mesias Vince St. Dollente , Zhu Hongni , Leung Cheuk Wai , Liu Wei , Huang Jinqing
Published: February 2021

Surface-enhanced Raman spectroscopy (SERS) has emerged as a powerful tool to detect biomolecules in aqueous environments. However, it is challenging to identify protein structures at low concentrations, especially for the proteins existing in an equilibrium mixture of various conformations. Here, we develop an in situ optical tweezers-coupled Raman spectroscopy to visualize and control the hotspot between two Ag nanoparticle-coated silica beads, generating tunable and reproducible SERS enhancements with single-molecule level sensitivity. This dynamic SERS detection window is placed in a microfluidic flow chamber to detect the passing-by proteins, which precisely characterizes the structures of three globular proteins without perturbation to their native states. Moreover, it directly identifies the structural features of the transient species of alpha-synuclein among its predominant monomers at physiological concentration of 1 μM by reducing the ensemble averaging. Hence, this SERS platform holds the promise to resolve the structural details of dynamic, heterogeneous, and complex biological systems.
Functional regeneration and repair of tendons using biomimetic scaffolds loaded with recombinant periostin
Authors: Wang Yu , Jin Shanshan , Luo Dan , He Danqing , Shi Chunyan , Zhu Lisha , Guan Bo , Li Zixin , Zhang Ting , Zhou Yanheng , Wang Cun-Yu , Liu Yan
Published: February 2021

Tendon injuries disrupt the balance between stability and mobility, causing compromised functions and disabilities. The regeneration of mature, functional tendons remains a clinical challenge. Here, we perform transcriptional profiling of tendon developmental processes to show that the extracellular matrix-associated protein periostin (Postn) contributes to the maintenance of tendon stem/progenitor cell (TSPC) functions and promotes tendon regeneration. We show that recombinant periostin (rPOSTN) promotes the proliferation and stemness of TSPCs, and maintains the tenogenic potentials of TSPCs in vitro. We also find that rPOSTN protects TSPCs against functional impairment during long-term passage in vitro. For in vivo tendon formation, we construct a biomimetic parallel-aligned collagen scaffold to facilitate TSPC tenogenesis. Using a rat full-cut Achilles tendon defect model, we demonstrate that scaffolds loaded with rPOSTN promote endogenous TSPC recruitment, tendon regeneration and repair with native-like hierarchically organized collagen fibers. Moreover, newly regenerated tendons show recovery of mechanical properties and locomotion functions.
The biosynthetic pathway of potato solanidanes diverged from that of spirosolanes due to evolution of a dioxygenase
Authors: Akiyama Ryota , Watanabe Bunta , Nakayasu Masaru , Lee Hyoung Jae , Kato Junpei , Umemoto Naoyuki , Muranaka Toshiya , Saito Kazuki , Sugimoto Yukihiro , Mizutani Masaharu
Published: February 2021

Potato (Solanum tuberosum), a worldwide major food crop, produces the toxic, bitter tasting solanidane glycoalkaloids α-solanine and α-chaconine. Controlling levels of glycoalkaloids is an important focus on potato breeding. Tomato (Solanum lycopersicum) contains a bitter spirosolane glycoalkaloid, α-tomatine. These glycoalkaloids are biosynthesized from cholesterol via a partly common pathway, although the mechanisms giving rise to the structural differences between solanidane and spirosolane remained elusive. Here we identify a 2-oxoglutarate dependent dioxygenase, designated as DPS (Dioxygenase for Potato Solanidane synthesis), that is a key enzyme for solanidane glycoalkaloid biosynthesis in potato. DPS catalyzes the ring-rearrangement from spirosolane to solanidane via C-16 hydroxylation. Evolutionary divergence of spirosolane-metabolizing dioxygenases contributes to the emergence of toxic solanidane glycoalkaloids in potato and the chemical diversity in Solanaceae.
Association between antecedent statin use and decreased mortality in hospitalized patients with COVID-19
Authors: Gupta Aakriti , Madhavan Mahesh V. , Poterucha Timothy J. , DeFilippis Ersilia M. , Hennessey Jessica A. , Redfors Bjorn , Eckhardt Christina , Bikdeli Behnood , Platt Jonathan , Nalbandian Ani , Elias Pierre , Cummings Matthew J. , Nouri Shayan N. , Lawlor Matthew , Ranard Lauren S. , Li Jianhua , Boyle Claudia , Givens Raymond , Brodie Daniel , Krumholz Harlan M. , Stone Gregg W. , Sethi Sanjum S. , Burkhoff Daniel , Uriel Nir , Schwartz Allan , Leon Martin B. , Kirtane Ajay J. , Wan Elaine Y. , Parikh Sahil A.
Published: February 2021

The coronavirus disease 2019 (COVID-19) can result in a hyperinflammatory state, leading to acute respiratory distress syndrome (ARDS), myocardial injury, and thrombotic complications, among other sequelae. Statins, which are known to have anti-inflammatory and antithrombotic properties, have been studied in the setting of other viral infections, but their benefit has not been assessed in COVID-19. This is a retrospective analysis of patients admitted with COVID-19 from February 1st through May 12th, 2020 with study period ending on June 11th, 2020. Antecedent statin use was assessed using medication information available in the electronic medical record. We constructed a multivariable logistic regression model to predict the propensity of receiving statins, adjusting for baseline sociodemographic and clinical characteristics, and outpatient medications. The primary endpoint includes in-hospital mortality within 30 days. A total of 2626 patients were admitted during the study period, of whom 951 (36.2%) were antecedent statin users. Among 1296 patients (648 statin users, 648 non-statin users) identified with 1:1 propensity-score matching, statin use is significantly associated with lower odds of the primary endpoint in the propensity-matched cohort (OR 0.47, 95% CI 0.36–0.62, p < 0.001). We conclude that antecedent statin use in patients hospitalized with COVID-19 is associated with lower inpatient mortality.
The fate of volcanic ash: premature or delayed sedimentation?
Authors: Rossi Eduardo , Bagheri Gholamhossein , Beckett Frances , Bonadonna Costanza
Published: February 2021

A large amount of volcanic ash produced during explosive volcanic eruptions has been found to sediment as aggregates of various types that typically reduce the associated residence time in the atmosphere (i.e., premature sedimentation). Nonetheless, speculations exist in the literature that aggregation has the potential to also delay particle sedimentation (rafting effect) even though it has been considered unlikely so far. Here, we present the first theoretical description of rafting that demonstrates how delayed sedimentation may not only occur but is probably more common than previously thought. The fate of volcanic ash is here quantified for all kind of observed aggregates. As an application to the case study of the 2010 eruption of Eyjafjallajökull volcano (Iceland), we also show how rafting can theoretically increase the travel distances of particles between 138–710 μm. These findings have fundamental implications for hazard assessment of volcanic ash dispersal as well as for weather modeling.
The Campylobacter jejuni CiaD effector co-opts the host cell protein IQGAP1 to promote cell entry
Authors: Negretti Nicholas M. , Gourley Christopher R. , Talukdar Prabhat K. , Clair Geremy , Klappenbach Courtney M. , Lauritsen Cody J. , Adkins Joshua N. , Konkel Michael E.
Published: February 2021

Campylobacter jejuniis a foodborne pathogen that binds to and invades the epithelial cells lining the human intestinal tract. Maximal invasion of host cells byC. jejunirequires cell binding as well as delivery of the Cia proteins (Campylobacterinvasion antigens) to the host cell cytosol via the flagellum. Here, we show that CiaD binds to the host cell protein IQGAP1 (a Ras GTPase-activating-like protein), thus displacing RacGAP1 from the IQGAP1 complex. This, in turn, leads to the unconstrained activity of the small GTPase Rac1, which is known to have roles in actin reorganization and internalization ofC. jejuni. Our results represent the identification of a host cell protein targeted by a flagellar secreted effector protein and demonstrate thatC. jejuni-stimulated Rac signaling is dependent on IQGAP1.
Orchestrating performance of healthcare networks subjected to the compound events of natural disasters and pandemic
Authors: Hassan Emad M. , Mahmoud Hussam N.
Published: February 2021

The current COVID-19 pandemic has demonstrated the vulnerability of healthcare systems worldwide. When combined with natural disasters, pandemics can further strain an already exhausted healthcare system. To date, frameworks for quantifying the collective effect of the two events on hospitals are nonexistent. Moreover, analytical methods for capturing the dynamic spatiotemporal variability in capacity and demand of the healthcare system posed by different stressors are lacking. Here, we investigate the combined impact of wildfire and pandemic on a network of hospitals. We combine wildfire data with varying courses of the spread of COVID-19 to evaluate the effectiveness of different strategies for managing patient demand. We show that losing access to medical care is a function of the relative occurrence time between the two events and is substantial in some cases. By applying viable mitigation strategies and optimizing resource allocation, patient outcomes could be substantially improved under the combined hazards.
Distinct genetic pathways define pre-malignant versus compensatory clonal hematopoiesis in Shwachman-Diamond syndrome
Authors: Kennedy Alyssa L. , Myers Kasiani C. , Bowman James , Gibson Christopher J. , Camarda Nicholas D. , Furutani Elissa , Muscato Gwen M. , Klein Robert H. , Ballotti Kaitlyn , Liu Shanshan , Harris Chad E. , Galvin Ashley , Malsch Maggie , Dale David , Gansner John M. , Nakano Taizo A. , Bertuch Alison , Vlachos Adrianna , Lipton Jeffrey M. , Castillo Paul , Connelly James , Churpek Jane , Edwards John R. , Hijiya Nobuko , Ho Richard H. , Hofmann Inga , Huang James N. , Keel Siobán , Lamble Adam , Lau Bonnie W. , Norkin Maxim , Stieglitz Elliot , Stock Wendy , Walkovich Kelly , Boettcher Steffen , Brendel Christian , Fleming Mark D. , Davies Stella M. , Weller Edie A. , Bahl Christopher , Carter Scott L. , Shimamura Akiko , Lindsley R. Coleman
Published: February 2021

To understand the mechanisms that mediate germline genetic leukemia predisposition, we studied the inherited ribosomopathy Shwachman-Diamond syndrome (SDS), a bone marrow failure disorder with high risk of myeloid malignancies at an early age. To define the mechanistic basis of clonal hematopoiesis in SDS, we investigate somatic mutations acquired by patients with SDS followed longitudinally. Here we report that multiple independent somatic hematopoietic clones arise early in life, most commonly harboring heterozygous mutations in EIF6 or TP53. We show that germline SBDS deficiency establishes a fitness constraint that drives selection of somatic clones via two distinct mechanisms with different clinical consequences. EIF6 inactivation mediates a compensatory pathway with limited leukemic potential by ameliorating the underlying SDS ribosome defect and enhancing clone fitness. TP53 mutations define a maladaptive pathway with enhanced leukemic potential by inactivating tumor suppressor checkpoints without correcting the ribosome defect. Subsequent development of leukemia was associated with acquisition of biallelic TP53 alterations. These results mechanistically link leukemia predisposition to germline genetic constraints on cellular fitness, and provide a rational framework for clinical surveillance strategies.
A family of ionic supersalts with covalent-like directionality and unconventional multiferroicity
Authors: Gao Yaxin , Wu Menghao , Jena Puru
Published: February 2021

Ionic crystals composed of elemental ions such as NaCl are non-polar due to directionless ionic bonding interactions. Here, we show that these can develop polarity by changing their building blocks from elemental ions to superalkali and superhalogen cluster-ions, which mimic the chemistry of alkali and halogen atoms, respectively. Due to the non-spherical geometries of these cluster ions, corresponding supersalts form anisotropic polar structures with ionic bonding, yet covalent-like directionality, akin to sp3 hybridized systems. Using density functional theory and extensive structure searches, we predict a series of stable ferroelectric/ferroelastic supersalts, PnH4MX4 (Pn = N, P; M = B, Al, Fe; X = Cl, Br) composed of superalkali PnH4 and superhalogen MX4 ions. Unlike traditional ferroelectric/ferroelastic materials, the cluster-ion based supersalts possess ultra-low switching barrier and can endure large ion displacements and reversible strain. In particular, PH4FeBr4 exhibits triferroic coupling of ferroelectricity, ferroelasticity, and antiferromagnetism with controllable spin directions via either ferroelastic or 90-degree ferroelectric switching.
Electrical switching of high-performance bioinspired nanocellulose nanocomposites
Authors: Jiao Dejin , Lossada Francisco , Guo Jiaqi , Skarsetz Oliver , Hoenders Daniel , Liu Jin , Walther Andreas
Published: February 2021

Nature fascinates with living organisms showing mechanically adaptive behavior. In contrast to gels or elastomers, it is profoundly challenging to switch mechanical properties in stiff bioinspired nanocomposites as they contain high fractions of immobile reinforcements. Here, we introduce facile electrical switching to the field of bioinspired nanocomposites, and show how the mechanical properties adapt to low direct current (DC). This is realized for renewable cellulose nanofibrils/polymer nanopapers with tailor-made interactions by deposition of thin single-walled carbon nanotube electrode layers for Joule heating. Application of DC at specific voltages translates into significant electrothermal softening via dynamization and breakage of the thermo-reversible supramolecular bonds. The altered mechanical properties are reversibly switchable in power on/power off cycles. Furthermore, we showcase electricity-adaptive patterns and reconfiguration of deformation patterns using electrode patterning techniques. The simple and generic approach opens avenues for bioinspired nanocomposites for facile application in adaptive damping and structural materials, and soft robotics.
Catalytic asymmetric reductive hydroalkylation of enamides and enecarbamates to chiral aliphatic amines
Authors: Wang Jia-Wang , Li Yan , Nie Wan , Chang Zhe , Yu Zi-An , Zhao Yi-Fan , Lu Xi , Fu Yao
Published: February 2021

To increase the reliability and success rate of drug discovery, efforts have been made to increase the C(sp3) fraction and avoid flat molecules. sp3-Rich enantiopure amines are most frequently encountered as chiral auxiliaries, synthetic intermediates for pharmaceutical agents and bioactive natural products. Streamlined construction of chiral aliphatic amines has long been regarded as a paramount challenge. Mainstream approaches, including hydrogenation of enamines and imines, C–H amination, and alkylation of imines, were applied for the synthesis of chiral amines with circumscribed skeleton structures; typically, the chiral carbon centre was adjacent to an auxiliary aryl or ester group. Herein, we report a mild and general nickel-catalysed asymmetric reductive hydroalkylation to effectively convert enamides and enecarbamates into drug-like α-branched chiral amines and derivatives. This reaction involves the regio- and stereoselective hydrometallation of an enamide or enecarbamate to generate a catalytic amount of enantioenriched alkylnickel intermediate, followed by C–C bond formation via alkyl electrophiles.
Cavity frequency-dependent theory for vibrational polariton chemistry
Authors: Li Xinyang , Mandal Arkajit , Huo Pengfei
Published: February 2021

Recent experiments demonstrate the control of chemical reactivities by coupling molecules inside an optical microcavity. In contrast, transition state theory predicts no change of the reaction barrier height during this process. Here, we present a theoretical explanation of the cavity modification of the ground state reactivity in the vibrational strong coupling (VSC) regime in polariton chemistry. Our theoretical results suggest that the VSC kinetics modification is originated from the non-Markovian dynamics of the cavity radiation mode that couples to the molecule, leading to the dynamical caging effect of the reaction coordinate and the suppression of reaction rate constant for a specific range of photon frequency close to the barrier frequency. We use a simple analytical non-Markovian rate theory to describe a single molecular system coupled to a cavity mode. We demonstrate the accuracy of the rate theory by performing direct numerical calculations of the transmission coefficients with the same model of the molecule-cavity hybrid system. Our simulations and analytical theory provide a plausible explanation of the photon frequency dependent modification of the chemical reactivities in the VSC polariton chemistry.
Maintenance of type 2 glycolytic myofibers with age by Mib1-Actn3 axis
Authors: Seo Ji-Yun , Kang Jong-Seol , Kim Ye Lynne , Jo Young-Woo , Kim Ji-Hoon , Hann Sang-Hyeon , Park Jieon , Park Inkuk , Park Hyerim , Yoo Kyusang , Rhee Joonwoo , Park Jung-Wee , Ha Yong Chan , Kong Young-Yun
Published: February 2021

Age-associated muscle atrophy is a debilitating condition associated with loss of muscle mass and function with age that contributes to limitation of mobility and locomotion. However, the underlying mechanisms of how intrinsic muscle changes with age are largely unknown. Here we report that, with age, Mind bomb-1 (Mib1) plays important role in skeletal muscle maintenance via proteasomal degradation-dependent regulation of α-actinin 3 (Actn3). The disruption of Mib1 in myofibers (Mib1ΔMF) results in alteration of type 2 glycolytic myofibers, muscle atrophy, impaired muscle function, and Actn3 accumulation. After chronic exercise, Mib1ΔMF mice show muscle atrophy even at young age. However, when Actn3 level is downregulated, chronic exercise-induced muscle atrophy is ameliorated. Importantly, the Mib1 and Actn3 levels show clinical relevance in human skeletal muscles accompanied by decrease in skeletal muscle function with age. Together, these findings reveal the significance of the Mib1-Actn3 axis in skeletal muscle maintenance with age and suggest the therapeutic potential for the treatment or amelioration of age-related muscle atrophy.
A tris-spiro metalla-aromatic system featuring Craig-Möbius aromaticity
Authors: Huang Zhe , Zhang Yongliang , Zhang Wen-Xiong , Wei Junnian , Ye Shengfa , Xi Zhenfeng
Published: February 2021

As aromaticity is one of the most fundamental concepts in chemistry, the construction of aromatic systems has long been an important subject. Herein, we report the synthesis and characterization of a tris-spiroaromatic complex, hexalithio spiro vanadacycle 2. The delocalization of the four electrons within the two V 3d orbitals and the π* orbitals of the three biphenyl ligands leads to a 40π Craig-Möbius aromatic system with three metalla-aromatic rings, as revealed by both experimental measurements and theoretical analyses. For comparison, if Cr is used instead of V, a similar Craig-Möbius aromatic system can not be generated. In this case, pentalithio spiro chromacycle 3 is obtained, and the Cr center uses its two 3d orbitals to form two independent metalla-aromatic rings. This work presents a type of aromatic systems that will contribute to both aromaticity theory and organometallic chemistry.
Nanoscale redox mapping at the MoS2-liquid interface
Authors: Du He-Yun , Huang Yi-Fan , Wong Deniz , Tseng Mao-Feng , Lee Yi-Hsin , Wang Chen-Hao , Lin Cheng-Lan , Hoffmann Germar , Chen Kuei-Hsien , Chen Li-Chyong
Published: February 2021

Layered MoS2 is considered as one of the most promising two-dimensional photocatalytic materials for hydrogen evolution and water splitting; however, the electronic structure at the MoS2-liquid interface is so far insufficiently resolved. Measuring and understanding the band offset at the surfaces of MoS2 are crucial for understanding catalytic reactions and to achieve further improvements in performance. Herein, the heterogeneous charge transfer behavior of MoS2 flakes of various layer numbers and sizes is addressed with high spatial resolution in organic solutions using the ferrocene/ferrocenium (Fc/Fc+) redox pair as a probe in near-field scanning electrochemical microscopy, i.e. in close nm probe-sample proximity. Redox mapping reveals an area and layer dependent reactivity for MoS2 with a detailed insight into the local processes as band offset and confinement of the faradaic current obtained. In combination with additional characterization methods, we deduce a band alignment occurring at the liquid-solid interface.
Cell polarisation in a bulk-surface model can be driven by both classic and non-classic Turing instability
Authors: Borgqvist Johannes , Malik Adam , Lundholm Carl , Logg Anders , Gerlee Philip , Cvijovic Marija
Published: February 2021

The GTPase Cdc42 is the master regulator of eukaryotic cell polarisation. During this process, the active form of Cdc42 is accumulated at a particular site on the cell membrane called the pole. It is believed that the accumulation of the active Cdc42 resulting in a pole is driven by a combination of activation–inactivation reactions and diffusion. It has been proposed using mathematical modelling that this is the result of diffusion-driven instability, originally proposed by Alan Turing. In this study, we developed, analysed and validated a 3D bulk-surface model of the dynamics of Cdc42. We show that the model can undergo both classic and non-classic Turing instability by deriving necessary conditions for which this occurs and conclude that the non-classic case can be viewed as a limit case of the classic case of diffusion-driven instability. Using three-dimensional Spatio-temporal simulation we predicted pole size and time to polarisation, suggesting that cell polarisation is mainly driven by the reaction strength parameter and that the size of the pole is determined by the relative diffusion.
A SARS-CoV-2 cytopathicity dataset generated by high-content screening of a large drug repurposing collection
Authors: Ellinger Bernhard , Bojkova Denisa , Zaliani Andrea , Cinatl Jindrich , Claussen Carsten , Westhaus Sandra , Keminer Oliver , Reinshagen Jeanette , Kuzikov Maria , Wolf Markus , Geisslinger Gerd , Gribbon Philip , Ciesek Sandra
Published: February 2021

SARS-CoV-2 is a novel coronavirus responsible for the COVID-19 pandemic, in which acute respiratory infections are associated with high socio-economic burden. We applied high-content screening to a well-defined collection of 5632 compounds including 3488 that have undergone previous clinical investigations across 600 indications. The compounds were screened by microscopy for their ability to inhibit SARS-CoV-2 cytopathicity in the human epithelial colorectal adenocarcinoma cell line, Caco-2. The primary screen identified 258 hits that inhibited cytopathicity by more than 75%, most of which were not previously known to be active against SARS-CoV-2 in vitro. These compounds were tested in an eight-point dose response screen using the same image-based cytopathicity readout. For the 67 most active molecules, cytotoxicity data were generated to confirm activity against SARS-CoV-2. We verified the ability of known inhibitors camostat, nafamostat, lopinavir, mefloquine, papaverine and cetylpyridinium to reduce the cytopathic effects of SARS-CoV-2, providing confidence in the validity of the assay. The high-content screening data are suitable for reanalysis across numerous drug classes and indications and may yield additional insights into SARS-CoV-2 mechanisms and potential therapeutic strategies.
Hospitalization and mortality associated with SARS-CoV-2 viral clades in COVID-19
Authors: Nakamichi Kenji , Shen Jolie Z. , Lee Cecilia S. , Lee Aaron , Roberts Emma A. , Simonson Paul D. , Roychoudhury Pavitra , Andriesen Jessica , Randhawa April K. , Mathias Patrick C. , Greninger Alex L. , Jerome Keith R. , Van Gelder Russell N.
Published: February 2021

The COVID-19 epidemic of 2019–20 is due to the novel coronavirus SARS-CoV-2. Following first case description in December, 2019 this virus has infected over 10 million individuals and resulted in at least 500,000 deaths world-wide. The virus is undergoing rapid mutation, with two major clades of sequence variants emerging. This study sought to determine whether SARS-CoV-2 sequence variants are associated with differing outcomes among COVID-19 patients in a single medical system. Whole genome SARS-CoV-2 RNA sequence was obtained from isolates collected from patients registered in the University of Washington Medicine health system between March 1 and April 15, 2020. Demographic and baseline clinical characteristics of patients and their outcome data including their hospitalization and death were collected. Statistical and machine learning models were applied to determine if viral genetic variants were associated with specific outcomes of hospitalization or death. Full length SARS-CoV-2 sequence was obtained 190 subjects with clinical outcome data. 35 (18.4%) were hospitalized and 14 (7.4%) died from complications of infection. A total of 289 single nucleotide variants were identified. Clustering methods demonstrated two major viral clades, which could be readily distinguished by 12 polymorphisms in 5 genes. A trend toward higher rates of hospitalization of patients with Clade 2 infections was observed (p = 0.06, Fisher’s exact). Machine learning models utilizing patient demographics and co-morbidities achieved area-under-the-curve (AUC) values of 0.93 for predicting hospitalization. Addition of viral clade or sequence information did not significantly improve models for outcome prediction. In summary, SARS-CoV-2 shows substantial sequence diversity in a community-based sample. Two dominant clades of virus are in circulation. Among patients sufficiently ill to warrant testing for virus, no significant difference in outcomes of hospitalization or death could be discerned between clades in this sample. Major risk factors for hospitalization and death for either major clade of virus include patient age and comorbid conditions.
The hyperbolic geometry of financial networks
Authors: Keller-Ressel Martin , Nargang Stephanie
Published: February 2021

Based on data from the European banking stress tests of 2014, 2016 and the transparency exercise of 2018 we construct networks of European banks and demonstrate that the latent geometry of these financial networks can be well-represented by geometry of negative curvature, i.e., by hyperbolic geometry. Using two different hyperbolic embedding methods, hydra+ and Mercator, this allows us to connect the network structure to the popularity-vs-similarity model of Papdopoulos et al., which is based on the Poincaré disc model of hyperbolic geometry. We show that the latent dimensions of ‘popularity’ and ‘similarity’ in this model are strongly associated to systemic importance and to geographic subdivisions of the banking system, independent of the embedding method that is used. In a longitudinal analysis over the time span from 2014 to 2018 we find that the systemic importance of individual banks has remained rather stable, while the peripheral community structure exhibits more (but still moderate) variability. Based on our analysis we argue that embeddings into hyperbolic geometry can be used to monitor structural change in financial networks and are able to distinguish between changes in systemic relevance and other (peripheral) structural changes.
Genome-wide identification and functional characterization of natural antisense transcripts in Salvia miltiorrhiza
Authors: Jiang Mei , Chen Haimei , Liu Jingting , Du Qing , Lu Shanfa , Liu Chang
Published: February 2021

Salvia miltiorrhiza is one of the most widely used traditional medicines. Natural antisense transcripts (NATs) are a class of long noncoding RNAs that can regulate gene expression. Here, we identified 812 NATs, including 168 cis-NATs and 644 trans-NATs from twelve root, flower, and leaf samples of S. miltiorrhiza using RNA-seq. The expression profiles for 41 of 50 NATs and their sense transcripts (STs) obtained from RNA-Seq were validated using qRT-PCR. The expression profiles of 17 NATs positively correlated with their STs. GO and KEGG pathway analyses mapped the STs for cis-NATs to pathways for biosynthesis of secondary metabolites. We characterized four NATs in detail, including NAT0001, NAT0002, NAT0004, and NAT00023. Their STs are kaurene synthase-like 1 and the homologs of UDP-glucose flavonoid 3-O-glucosyltransferase 6, UDP-glycosyltransferase 90A1, and beta-glucosidase 40, respectively. The first gene is involved in the biosynthesis of bioactive tanshinones, the next two are involved in anthocyanin biosynthesis, whereas the last is involved in phenylpropanoid biosynthesis. Besides, we found seven STs that are potential targets of miRNAs. And we found two miRNAs including miR156a and miR7208, might originate from NATs, NAT0112 and NAT0086. The results suggest that S. miltiorrhiza NATs might interact with STs, produce miRNAs, and be regulated by miRNAs. They potentially play significant regulatory roles in the biosynthesis of bioactive compounds.
Excellent mechanical properties of taenite in meteoric iron
Authors: Ueki Shohei , Mine Yoji , Takashima Kazuki
Published: February 2021

Meteoric iron is the metal that humans first obtained and used in the earliest stage of metal culture. Advances in metallographic analysis techniques have revealed that meteoric iron largely comprises kamacite, taenite, and cohenite, which correspond to ferrite, austenite, and cementite in artificial steel, respectively. Although the mechanical properties of meteoric irons were measured previously to understand their origin and history, the genuine mechanical properties of meteoric iron remain unknown because of its complex microstructure and the pre-existing cracks in cohenite. Using micro-tensile tests to analyse the single-crystalline constituents of the Canyon Diablo meteorite, herein, we show that the taenite matrix exhibits excellent balance between yield strength and ductility superior to that of the kamacite matrix. We found that taenite is rich in nitrogen despite containing a large amount of nickel, which decreases the nitrogen solubility, suggesting that solid-solution strengthening via nitrogen is highly effective for the Fe–Ni system. Our findings not only provide insights for developing advanced high-strength steel but also help understand the mysterious relationship between nitrogen and nickel contents in steel. Like ancient peoples believed that meteoric iron was a gift from the heavens, the findings herein imply that this thought continues even now.
A novel d-xylose isomerase from the gut of the wood feeding beetle Odontotaenius disjunctus efficiently expressed in Saccharomyces cerevisiae
Authors: Silva Paulo César , Ceja-Navarro Javier A. , Azevedo Flávio , Karaoz Ulas , Brodie Eoin L. , Johansson Björn
Published: February 2021

Carbohydrate rich substrates such as lignocellulosic hydrolysates remain one of the primary sources of potentially renewable fuel and bulk chemicals. The pentose sugard-xylose is often present in significant amounts along with hexoses.Saccharomyces cerevisiaecan acquire the ability to metabolized-xylose through expression of heterologousd-xylose isomerase (XI). This enzyme is notoriously difficult to express inS. cerevisiaeand only fourteen XIs have been reported to be active so far. We cloned a newd-xylose isomerase derived from microorganisms in the gut of the wood-feeding beetleOdontotaenius disjunctus. Although somewhat homologous to the XI fromPiromycessp. E2, the new gene was identified as bacterial in origin and the host as aParabacteroidessp. Expression of the new XI inS. cerevisiaeresulted in faster aerobic growth than the XI fromPiromycesond-xylose media. Thed-xylose isomerization rate conferred by the new XI was also 72% higher, while absolute xylitol production was identical in both strains. Interestingly, increasing concentrations of xylitol (up to 8 g L−1) appeared not to inhibitd-xylose consumption. The newly described XI displayed 2.6 times higher specific activity, 37% lower KMford-xylose, and exhibited higher activity over a broader temperature range, retaining 51% of maximal activity at 30 °C compared with only 29% activity for thePiromycesXI.
Multimorbidity clusters in patients with chronic obstructive airway diseases in the EpiChron Cohort
Authors: Carmona-Pírez Jonás , Poblador-Plou Beatriz , Ioakeim-Skoufa Ignatios , González-Rubio Francisca , Gimeno-Feliú Luis Andrés , Díez-Manglano Jesús , Laguna-Berna Clara , Marin Jose M. , Gimeno-Miguel Antonio , Prados-Torres Alexandra
Published: February 2021

Chronic obstructive airway diseases such as chronic obstructive pulmonary disease (COPD), asthma, rhinitis, and obstructive sleep apnea (OSA) are amongst the most common treatable and preventable chronic conditions with high morbidity burden and mortality risk. We aimed to explore the existence of multimorbidity clusters in patients with such diseases and to estimate their prevalence and impact on mortality. We conducted an observational retrospective study in the EpiChron Cohort (Aragon, Spain), selecting all patients with a diagnosis of allergic rhinitis, asthma, COPD, and/or OSA. The study population was stratified by age (i.e., 15–44, 45–64, and ≥ 65 years) and gender. We performed cluster analysis, including all chronic conditions recorded in primary care electronic health records and hospital discharge reports. More than 75% of the patients had multimorbidity (co-existence of two or more chronic conditions). We identified associations of dermatologic diseases with musculoskeletal disorders and anxiety, cardiometabolic diseases with mental health problems, and substance use disorders with neurologic diseases and neoplasms, amongst others. The number and complexity of the multimorbidity clusters increased with age in both genders. The cluster with the highest likelihood of mortality was identified in men aged 45 to 64 years and included associations between substance use disorder, neurologic conditions, and cancer. Large-scale epidemiological studies like ours could be useful when planning healthcare interventions targeting patients with chronic obstructive airway diseases and multimorbidity.
HPV genotyping and risk factors for anal high-risk HPV infection in men who have sex with men from Toronto, Canada
Authors: Choi Yoojin , Loutfy Mona , Remis Robert S. , Liu Juan , Rebbapragada Anuradha , Huibner Sanja , Brunetta Jason , Smith Graham , Reko Tatjana , Halpenny Roberta , Kaul Rupert , Grennan Troy
Published: February 2021

Men who have sex with men (MSM) are disproportionately affected by anal cancer, predominantly caused by high-risk (HR) human papillomavirus (HPV) infection. Currently, the nonavalent HPV vaccine provides coverage against nine HPV genotypes, including seven HR-HPV genotypes. Here, we characterize anal HR-HPV genotype distribution and associated risk factors in MSM from Toronto, Canada recruited between September 2010 and June 2012. Wilcoxon–Mann–Whitney test was used for continuous variables, Chi-square test was performed for categorical variables, and a multivariable model using logistic regression was created to assess for correlates of anal HR-HPV infection. A total of 442 MSM were recruited, with a median age of 45 (IQR 38–50) and an overall HPV prevalence of 82%. The prevalence of any HR-HPV infection was 65.3% and 50.7% in the HIV-positive and HIV-negative MSM, respectively. No participant tested positive for all genotypes covered by the nonavalent vaccine. HIV status (aOR 1.806; 95% CI 1.159–2.816), smoking (aOR 2.176; 95% CI 1.285–3.685) and the number of lifetime sexual partners (aOR 2.466; 95% CI 1.092–5.567) were independent risk factors for anal HR-HPV infection. Our findings will be useful to inform HPV vaccine rollout and HPV prevention strategies in Canadian MSM.
Biogenic selenium nanoparticles (SeNPs) from citrus fruit have anti-bacterial activities
Authors: Alvi Ghalia Batool , Iqbal Muhammad Shahid , Ghaith Mazen Mohammed Saeed , Haseeb Abdul , Ahmed Bilal , Qadir Muhammad Imran
Published: February 2021

Nanotechnology deals with the synthesis of materials and particles at nanoscale with dimensions of 1–100 nm. Biological synthesis of nanoparticles, using microbes and plants, is the most proficient method in terms of ease of handling and reliability. Core objectives of this study were to synthesize metallic nanoparticles using selenium metal salt from citrus fruit extracts, their characterization and evaluation for antimicrobial activities against pathogenic microbes. In methodology, simple green method was implicated using sodium selenite salt solution and citrus fruit extracts of Grapefruit and Lemon as precursors for synthesizing nanoparticles. Brick red color of the solution indicated towards the synthesis of selenium nanoparticles (SeNPs). Nanoparticle’s initial characterization was done by UV–Vis Spectrophotometry and later FTIR analysis and DLS graphs via Zetasizer were obtained for the confirmation of different physical and chemical parameters of the nanoparticles. Different concentrations of SeNPs were used for antimicrobial testing against E. coli, M. luteus, B. subtilis and K. pneumoniae comparative with the standard antibiotic Ciprofloxacin. SeNPs possessed significant antimicrobial activities against all the bacterial pathogens used. Conclusively, SeNPs made from citrus fruits can act as potent antibacterial candidates.
Phosphorescent Ir(III) complexes conjugated with oligoarginine peptides serve as optical probes for in vivo microvascular imaging
Authors: Yasukagawa Mami , Shimada Aya , Shiozaki Shuichi , Tobita Seiji , Yoshihara Toshitada
Published: February 2021

Imaging the vascular structures of organ and tumor tissues is extremely important for assessing various pathological conditions. Herein we present the new vascular imaging probe BTQ-Rn (n = 8, 12, 16), a phosphorescent Ir(III) complex containing an oligoarginine peptide as a ligand. This microvasculature staining probe can be chemically synthesized, unlike the commonly used tomato lectins labeled with a fluorophore such as fluorescein isothiocyanate (FITC). Intravenous administration of BTQ-R12 to mice and subsequent confocal luminescence microscope measurements enabled in vivo vascular imaging of tumors and various organs, including kidney, liver and pancreas. Dual color imaging of hepatic tissues of living mice fed a high-fat diet using BTQ-R12 and the lipid droplet-specific probe PC6S revealed small and large lipid droplets in the hepatocytes, causing distortion of the sinusoidal structure. BTQ-R12 selectively stains vascular endothelium and thus allows longer-term vascular network imaging compared to fluorescent dextran with a molecular weight of 70 kDa that circulate in the bloodstream. Furthermore, time-gated measurements using this phosphorescent vascular probe enabled imaging of blood vessel structures without interference from autofluorescence.
Mayetiola destructor (Diptera: Cecidomyiidae) host preference and survival on small grains with respect to leaf reflectance and phytohormone concentrations
Authors: Sadeghi Rohollah , Odubiyi Steven , Nikoukar Atoosa , Schroeder Kurtis L. , Rashed Arash
Published: February 2021

The Hessian fly Mayetiola destructor (Diptera: Cecidomyiidae) is a major pest of wheat, globally. We conducted a series of laboratory choice and no-choice assays to quantify Hessian fly host preference for barley (cv. Champion), oat (cv. Cayuse), susceptible (cv. Alturas), and resistant (cv. Hollis) wheat. In addition, larval survivorship and adult emergence were compared among the evaluated host plants. We then examined whether insect preference for a host can be explained by differences in plant spectral reflectance. Further, larval survivorship and adult emergence were compared among host plants in relation to phytohormone concentrations. Hessian flies laid more eggs on wheat compared to either oat or barley. Spectral reflectance measurements of leaves were similar between susceptible and resistant wheat cultivars but different from those of barley and oat. Our results suggested that higher reflectance in the near-infrared range and lower reflectance in the visible range may be used by females for host selection. Hessian fly larvae were unable to develop into the pupal stage on resistant wheat and oat. No significant difference in larval survivorship was detected between the susceptible wheat and barley. However, adult emergence was significantly higher on barley than the susceptible wheat. Phytohormonal evaluations revealed that salicylic acid (SA) may be an important contributor to plant defense response to larval feeding as relatively higher concentrations of SA were present in oat and resistant wheat. While resistance in the resistant wheat is achieved only through antibiosis, both antibiosis and antixenosis were in effect rendering oat as a non-host for Hessian flies.
A three-dimensional discrete element model of triaxial tests based on a new flexible membrane boundary
Authors: Qin Yan , Liu Chun , Zhang Xiaoyu , Wang Xingang , Shi Bin , Wang Yue , Deng Shang
Published: February 2021

Based on a new elastic clump model, a flexible membrane is proposed for the discrete element numerical simulations of triaxial tests. Conversional triaxial tests of sandstone under the confining pressures of 2 MPa and 8 MPa were carried out, in order to validate the effectiveness of the proposed numerical simulation method. The numerical model is validated by comparing the numerical results with the test results. The deformation and failure process of numerical model is analyzed by stress–strain curves, micro fractures, displacement fields, stress fields and energy fields. The model shows an X-shape shear failure zone, of which the angle is very close to that of the test; the dip angle of most shear fractures is close to the angle of the internal friction; and there is a large amount of slipping frictional heat generated on the failure surface. During the loading process, the stress chain and stress concentration appear in the middle of the model, which lead to displacement zoning in the model. The failure of the model is associated with the growth of the micro tensile- and shear fractures. This study provides an effective tool for the macro–micro investigation of rock failure processes.
Molecular characteristics of Neisseria meningitidis in Qatar
Authors: Hamed Manal Mahmoud , Mir Fayaz Ahmad , Elmagboul Emad Bashier Ibrahim , Al-Khal Abdullatif , Maslamani Muna A. Rahman S. Al. , Deshmukh Anand Sarwottam , Al-Romaihi Hamad Eid , Janahi Mohd. Ahmed M. Sharif , Abid Fatma Ben , Kashaf Adila Shaukat Ali , Sher Gulab , Gupta Vinod Kumar , Wilson Godwin J. , Kadalayi Junais , Doiphode Sanjay H.
Published: February 2021

The aim of the current study is to review the molecular characteristics of Neisseria meningitidis (N. meningitidis) in Hamad Medical Corporation, which is the provider of secondary and tertiary care in the state of Qatar. A total of 39 isolates of N. meningitidis from the period of 2013 to 2018 were revived and identified by Vitek, and susceptibility on the basis of the E test was retrieved from the patient’s files. The revived isolates were subjected to multilocus sequence typing. The most common serogroup (19) of N. meningitidis was W135, of which 12 were isolated from blood and CSF. ST-11 was the most predominant ST clonal complex causing N. meningitidis cases (61.53%). Clonal complex ST-41/44 was the second most observed complex (3, 2 of which were related to serogroup B). The most frequent sequence type was 9596 (8 isolates). Determining the molecular pattern of N. meningitidis in Qatar is helpful for understanding the strains circulating in Qatar, and the study of the resistance trend of such strains may be very helpful for empirical treatment of future patients.
Point of care airway ultrasound to select tracheal tube and determine insertion depth in cleft repair surgery
Authors: Ahn Jung Hwan , Park Jae Hyun , Kim Min Soo , Kang Hyun Cheol , Kim Il Seok
Published: February 2021

We aimed to evaluate the efficacy of using airway ultrasonography to select the correct tracheal tube size and insertion depth in pediatric patients who underwent cleft repair surgery as a way to decrease airway complications and adverse events during perioperative periods. Fifty-one patients (age < 28 months) were consecutively divided into conventional (n = 28) and ultrasound (n = 23) groups. Tracheal tube size and insertion depth were determined using the age-based formula and auscultation in the conventional group, whereas using ultrasonographic measurement of subglottic diameter with auscultation and lung ultrasonography in the ultrasound group. We evaluated the initially selected tube size, insertion depth, ventilatory indices, and the incidence of airway complications and adverse events. Tube insertion depth (median [interquartile range]) was significantly greater in the ultrasound group than in the conventional group (13.5 cm [12.5–14.0] vs 13.0 cm [11.8–13.0], P = 0.045). The number of complications and adverse events was significantly higher in the conventional group than in the ultrasound group (32.1% vs 4.3%, P = 0.013). Airway ultrasound application could reduce airway-related complications and adverse events by determining the appropriate tracheal tube size and insertion depth.
Photochemically induced cyclic morphological dynamics via degradation of autonomously produced, self-assembled polymer vesicles
Authors: Lin Chenyu , Katla Sai Krishna , Pérez-Mercader Juan
Published: February 2021

Autonomous and out-of-equilibrium vesicles synthesised from small molecules in a homogeneous aqueous medium are an emerging class of dynamically self-assembled systems with considerable potential for engineering natural life mimics. Here we report on the physico-chemical mechanism behind a dynamic morphological evolution process through which self-assembled polymeric structures autonomously booted from a homogeneous mixture, evolve from micelles to giant vesicles accompanied by periodic growth and implosion cycles when exposed to oxygen under light irradiation. The system however formed nano-objects or gelation under poor oxygen conditions or when heated. We determined the cause to be photoinduced chemical degradation within hydrated polymer cores inducing osmotic water influx and the subsequent morphological dynamics. The process also led to an increase in the population of polymeric objects through system self-replication. This study offers a new path toward the design of chemically self-assembled systems and their potential application in autonomous material artificial simulation of living systems.
Computational analysis of the effect of [Tea][Ms] and [Tea][H2PO4] ionic liquids on the structure and stability of Aβ(17–42) amyloid fibrils
Authors: Gobbo D. , Cavalli A. , Ballone P. , Benedetto A.
Published: February 2021

Tight coordination of peptides by organic anions driven by hydrogen bonding affects the fibrillation kinetics of Aβ peptides in ionic liquid/water solutions.
Pre-carbonized nitrogen-rich polytriazines for the controlled growth of silver nanoparticles: catalysts for enhanced CO2 chemical conversion at atmospheric pressure
Authors: Liu Jian , Zhang Xiaoyi , Wen Bingyan , Li Yipei , Wu Jingjing , Wang Zhipeng , Wu Ting , Zhao Rusong , Yang Shenghong
Published: February 2021

Mono-dispersed Ag NPs were generated controllably in pre-carbonized covalent triazine frameworks for CO2 conversion at mild conditions with excellent catalytic activity.