bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein and RNA dynamical fingerprinting
Authors: Niessen Katherine A. , Xu Mengyang , George Deepu K. , Chen Michael C. , Ferré-D’Amaré Adrian R. , Snell Edward H. , Cody Vivian , Pace James , Schmidt Marius , Markelz Andrea G.
Published: March 2019

Protein structural vibrations impact biology by steering the structure to functional intermediate states; enhancing tunneling events; and optimizing energy transfer. Strong water absorption and a broad continuous vibrational density of states have prevented optical identification of these vibrations. Recently spectroscopic signatures that change with functional state were measured using anisotropic terahertz microscopy. The technique however has complex sample positioning requirements and long measurement times, limiting access for the biomolecular community. Here we demonstrate that a simplified system increases spectroscopic structure to dynamically fingerprint biomacromolecules with a factor of 6 reduction in data acquisition time. Using this technique, polarization varying anisotropy terahertz microscopy, we show sensitivity to inhibitor binding and unique vibrational spectra for several proteins and an RNA G-quadruplex. The technique’s sensitivity to anisotropic absorbance and birefringence provides rapid assessment of macromolecular dynamics that impact biology.
Synthetic energy sensor AMPfret deciphers adenylate-dependent AMPK activation mechanism
Authors: Pelosse Martin , Cottet-Rousselle Cécile , Bidan Cécile M. , Dupont Aurélie , Gupta Kapil , Berger Imre , Schlattner Uwe
Published: March 2019

AMP-activated protein kinase AMPK senses and regulates cellular energy state. AMPK activation by increasing AMP and ADP concentrations involves a conformational switch within the heterotrimeric complex. This is exploited here for the construction of a synthetic sensor of cellular energetics and allosteric AMPK activation, AMPfret. Based on engineered AMPK fused to fluorescent proteins, the sensor allows direct, real-time readout of the AMPK conformational state by fluorescence resonance energy transfer (FRET). AMPfret faithfully and dynamically reports the binding of AMP and ADP to AMPK γ-CBS sites, competed by Mg2+-free ATP. FRET signals correlate with activation of AMPK by allosteric mechanisms and protection from dephosphorylation, attributed here to specific CBS sites, but does not require activation loop phosphorylation. Moreover, AMPfret detects binding of pharmacological compounds to the AMPK α/β-ADaM site enabling activator screening. Cellular assays demonstrate that AMPfret is applicable in vivo for spatiotemporal analysis of energy state and allosteric AMPK activation.
Atypical functional connectome hierarchy in autism
Authors: Hong Seok-Jun , Vos de Wael Reinder , Bethlehem Richard A. I. , Lariviere Sara , Paquola Casey , Valk Sofie L. , Milham Michael P. , Di Martino Adriana , Margulies Daniel S. , Smallwood Jonathan , Bernhardt Boris C.
Published: March 2019

One paradox of autism is the co-occurrence of deficits in sensory and higher-order socio-cognitive processing. Here, we examined whether these phenotypical patterns may relate to an overarching system-level imbalance—specifically a disruption in macroscale hierarchy affecting integration and segregation of unimodal and transmodal networks. Combining connectome gradient and stepwise connectivity analysis based on task-free functional magnetic resonance imaging (fMRI), we demonstrated atypical connectivity transitions between sensory and higher-order default mode regions in a large cohort of individuals with autism relative to typically-developing controls. Further analyses indicated that reduced differentiation related to perturbed stepwise connectivity from sensory towards transmodal areas, as well as atypical long-range rich-club connectivity. Supervised pattern learning revealed that hierarchical features predicted deficits in social cognition and low-level behavioral symptoms, but not communication-related symptoms. Our findings provide new evidence for imbalances in network hierarchy in autism, which offers a parsimonious reference frame to consolidate its diverse features.
A small secreted protein triggers a TLR2/4-dependent inflammatory response during invasive Candida albicans infection
Authors: Wang Wenjuan , Deng Zihou , Wu Hongyu , Zhao Qun , Li Tiantian , Zhu Wencheng , Wang Xiongjun , Tang Longhai , Wang Chengshu , Cui Shu-Zhong , Xiao Hui , Chen Jiangye
Published: March 2019

Candida albicans can switch from commensal to pathogenic mode, causing mucosal or disseminated candidiasis. The host relies on pattern-recognition receptors including Toll-like receptors (TLRs) and C-type lectin receptors (CLRs) to sense invading fungal pathogens and launch immune defense mechanisms. However, the complex interplay between fungus and host innate immunity remains incompletely understood. Here we report that C. albicans upregulates expression of a small secreted cysteine-rich protein Sel1 upon encountering limited nitrogen and abundant serum. Sel1 activates NF-κB and MAPK signaling pathways, leading to expression of proinflammatory cytokines and chemokines. Comprehensive genetic and biochemical analyses reveal both TLR2 and TLR4 are required for the recognition of Sel1. Further, SEL1-deficient C. albicans display an impaired immune response in vivo, causing increased morbidity and mortality in a bloodstream infection model. We identify a critical component in the Candida-host interaction that opens a new avenue to tackle Candida infection and inflammation.
Probing hydrogen bond strength in liquid water by resonant inelastic X-ray scattering
Authors: Vaz da Cruz Vinícius , Gel’mukhanov Faris , Eckert Sebastian , Iannuzzi Marcella , Ertan Emelie , Pietzsch Annette , Couto Rafael C. , Niskanen Johannes , Fondell Mattis , Dantz Marcus , Schmitt Thorsten , Lu Xingye , McNally Daniel , Jay Raphael M. , Kimberg Victor , Föhlisch Alexander , Odelius Michael
Published: March 2019

Local probes of the electronic ground state are essential for understanding hydrogen bonding in aqueous environments. When tuned to the dissociative core-excited state at the O1s pre-edge of water, resonant inelastic X-ray scattering back to the electronic ground state exhibits a long vibrational progression due to ultrafast nuclear dynamics. We show how the coherent evolution of the OH bonds around the core-excited oxygen provides access to high vibrational levels in liquid water. The OH bonds stretch into the long-range part of the potential energy curve, which makes the X-ray probe more sensitive than infra-red spectroscopy to the local environment. We exploit this property to effectively probe hydrogen bond strength via the distribution of intramolecular OH potentials derived from measurements. In contrast, the dynamical splitting in the spectral feature of the lowest valence-excited state arises from the short-range part of the OH potential curve and is rather insensitive to hydrogen bonding.
The Caspase-3 homolog DrICE regulates endocytic trafficking during Drosophila tracheal morphogenesis
Authors: McSharry Saoirse S. , Beitel Greg J.
Published: March 2019

Although well known for its role in apoptosis, the executioner caspase DrICE has a non-apoptotic function that is required for elongation of the epithelial tubes of the Drosophila tracheal system. Here, we show that DrICE acts downstream of the Hippo Network to regulate endocytic trafficking of at least four cell polarity, cell junction and apical extracellular matrix proteins involved in tracheal tube size control: Crumbs, Uninflatable, Kune-Kune and Serpentine. We further show that tracheal cells are competent to undergo apoptosis, even though developmentally-regulated DrICE function rarely kills tracheal cells. Our results reveal a developmental role for caspases, a pool of DrICE that co-localizes with Clathrin, and a mechanism by which the Hippo Network controls endocytic trafficking. Given reports of in vitro regulation of endocytosis by mammalian caspases during apoptosis, we propose that caspase-mediated regulation of endocytic trafficking is an evolutionarily conserved function of caspases that can be deployed during morphogenesis.
Longitudinal tracking and quantification of individual Plasmodium falciparum clones in complex infections
Authors: Lerch Anita , Koepfli Cristian , Hofmann Natalie E. , Kattenberg Johanna H. , Rosanas-Urgell Anna , Betuela Inoni , Mueller Ivo , Felger Ingrid
Published: March 2019

Longitudinal tracking of individual Plasmodium falciparum strains in multi-clonal infections is essential for investigating infection dynamics of malaria. The traditional genotyping techniques did not permit tracking changes in individual clone density during persistent natural infections. Amplicon deep sequencing (Amp-Seq) offers a tool to address this knowledge gap. The sensitivity of Amp-Seq for relative quantification of clones was investigated using three molecular markers, ama1-D2, ama1-D3, and cpmp. Amp-Seq and length-polymorphism based genotyping were compared for their performance in following minority clones in longitudinal samples from Papua New Guinea. Amp-Seq markers were superior to length-polymorphic marker msp2 in detecting minority clones (sensitivity Amp-Seq: 95%, msp2: 85%). Multiplicity of infection (MOI) by Amp-Seq was 2.32 versus 1.73 for msp2. The higher sensitivity had no effect on estimates of force of infection because missed minority clones were detected in preceding or succeeding bleeds. Individual clone densities were tracked longitudinally by Amp-Seq despite MOI > 1, thus providing an additional parameter for investigating malaria infection dynamics. Amp-Seq based genotyping of longitudinal samples improves detection of minority clones and estimates of MOI. Amp-Seq permits tracking of clone density over time to study clone competition or the dynamics of specific, i.e. resistance-associated genotypes.
Experimental investigation on True Triaxial Deformation and Progressive Damage Behaviour of Sandstone
Authors: Li Zhaolin , Wang Lianguo , Lu Yinlong , Li Wenshuai , Wang Kai , Fan Hao
Published: March 2019

Studying the true triaxial deformation characteristics and progressive damage behavior of sandstone is of great significance for the stability control of roadways. Both the conventional triaxial test (CTT) and the true triaxial compression test (TTT) were conducted for sandstone to investigate its deformation characteristics and the variation laws of volume strain during the progressive damage process under different confining pressures. The conducted experiments showed that both the axial and lateral strains of the rock prior to failure under CTT conditions increased with increasing confining pressure. However, with increasing intermediate principal stress (σ2) under TTT conditions, both the axial strain, and the lateral strain (ε2) gradually decreased, and the lateral strain (ε3, expansion) first slow down and then accelerated. Moreover, the anisotropic characteristics first gradually weakened and then enhanced. The variation of the volume strain increment and the volume strain rate of rock combined with the acoustic emission activity and a three-dimensional rock theoretical model with microcrack defects were analyzed in detail. During the stable crack growth stage III, the volume strain increment and volume strain rate increased with increasing confining pressure under CTT conditions, while they decrease after the initial increase with increasing σ2 under TTT conditions. During the unstable crack growth stage IV, the volume strain increment increased sharply, while the volume strain rate gradually slowed down with increasing confining pressure under CTT conditions. The internal cracks of the rock were gradually suppressed and the lateral expansion was gradually constrained. The volume strain increment first increased followed by a decrease, and the volume strain rate gradually slowed down after a noticeable acceleration with increasing σ2 under TTT conditions. The internal micro-cracks gradually evolved from inhibition (in the planes parallel to plane 1–2 and plane 2–3) to accelerated expansion (the planes along the σ2 direction), and the lateral deformation first weakened and then strengthened.
Adherence to the Mediterranean diet is positively associated with sperm motility: A cross-sectional analysis
Authors: Salas-Huetos Albert , Babio Nancy , Carrell Douglas T. , Bulló Mònica , Salas-Salvadó Jordi
Published: March 2019

The aim of this cross-sectional analysis is to investigate the associations between the adherence to the Mediterranean Diet (MD) and semen quality parameters. To assess the adherence to the MD, the Trichopoulou score was used. Semen parameters were assessed as described in the 2010 WHO’s report and the results are showed across tertiles of MD adherence. A total of 106 participants were included. Compared to those in the lowest MD adherence tertile, participants in the top tertile had statistically significant higher BMI and waist circumference and consumed more energy, and also had statistically significant higher semen pH, and total sperm motility and progressive sperm motility percentages, and lower sperm immotility percentages. Moreover, percentage of total and progressive motility were significantly higher among those subjects in the higher adherence to MD in comparison with those in low-medium adherence category. The multivariable linear regression models evaluating the relationship between the sperm quality parameters and tertiles of MD adherence adjusted by age, energy and BMI showed that compared with the lowest tertile, men in the highest tertile had a higher percentage of total sperm motility [β non-standardized coefficient = 12.785]. These findings suggest that adherence to the MD was positively associated with sperm motility.
Intensive tropical land use massively shifts soil fungal communities
Authors: Brinkmann Nicole , Schneider Dominik , Sahner Josephine , Ballauff Johannes , Edy Nur , Barus Henry , Irawan Bambang , Budi Sri Wilarso , Qaim Matin , Daniel Rolf , Polle Andrea
Published: March 2019

Soil fungi are key players in nutrient cycles as decomposers, mutualists and pathogens, but the impact of tropical rain forest transformation into rubber or oil palm plantations on fungal community structures and their ecological functions are unknown. We hypothesized that increasing land use intensity and habitat loss due to the replacement of the hyperdiverse forest flora by nonendemic cash crops drives a drastic loss of diversity of soil fungal taxa and impairs the ecological soil functions. Unexpectedly, rain forest conversion was not associated with strong diversity loss but with massive shifts in soil fungal community composition. Fungal communities clustered according to land use system and loss of plant species. Network analysis revealed characteristic fungal genera significantly associated with different land use systems. Shifts in soil fungal community structure were particularly distinct among different trophic groups, with substantial decreases in symbiotrophic fungi and increases in saprotrophic and pathotrophic fungi in oil palm and rubber plantations in comparison with rain forests. In conclusion, conversion of rain forests and current land use systems restructure soil fungal communities towards enhanced pathogen pressure and, thus, threaten ecosystem health functions.
A transcriptome-wide analysis deciphers distinct roles of G1 cyclins in temporal organization of the yeast cell cycle
Authors: Teufel Lotte , Tummler Katja , Flöttmann Max , Herrmann Andreas , Barkai Naama , Klipp Edda
Published: March 2019

Oscillating gene expression is crucial for correct timing and progression through cell cycle. In Saccharomyces cerevisiae, G1 cyclins Cln1–3 are essential drivers of the cell cycle and have an important role for temporal fine-tuning. We measured time-resolved transcriptome-wide gene expression for wild type and cyclin single and double knockouts over cell cycle with and without osmotic stress. Clustering of expression profiles, peak time detection of oscillating genes, integration with transcription factor network dynamics, and assignment to cell cycle phases allowed us to quantify the effect of genetic or stress perturbations on the duration of cell cycle phases. Cln1 and Cln2 showed functional differences, especially affecting later phases. Deletion of Cln3 led to a delay of START followed by normal progression through later phases. Our data and network analysis suggest mutual effects of cyclins with the transcriptional regulators SBF and MBF.
The complete mitochondrial genomes of two sibling species of camellia weevils (Coleoptera: Curculionidae) and patterns of Curculionini speciation
Authors: Zhang Shou-ke , Shu Jin-ping , Wang Yang-dong , Liu Ya-ning , Peng Han , Zhang Wei , Wang Hao-jie
Published: March 2019

Complete mitochondrial genomes contain large and diverse datasets for species delineation. To better understand the divergence of the two morphologically indistinguishable weevil species in Curculionini, we first sequenced and compared their complete mitochondrial genomes. The complete mitochondrial genomes of Curculio chinensis and Curculio sp. were 19,713 bp with an A + T content of 76.61% and 19,216 bp with an A + T content of 76.85%, respectively. All 37 of the typical mitochondrial genes were determined in both species. The 13 protein sequences of the two species shared high homology (about 90%) except for ATP8 (73.08%). The differences in secondary structure of ATP8 were the number of possible proteins and nucleic acid binding sites. There were 22 and 15 mismatched base-pairs in the tRNA secondary structures from C. chinensis and Curculio sp., respectively. Maximum Likelihood and Bayesian analyses indicated that Curculio sp. is a novel species closely related to C. chinensis. The divergence time estimation suggests that Cryptorhynchinae and Curculionini lines diverged in the Cenozoic Period, while C. chinensis and Curculio sp. diverged at 6.7079 (95% CI 5–13) Mya. This study demonstrates the utility of using complete mitochondrial gene sets for phylogenetic analysis and enhances our understanding of the genetic basis for the evolution of the Curculionini.
Identification and genetic characterization of a novel Orthobunyavirus species by a straightforward high-throughput sequencing-based approach
Authors: Shifman Ohad , Cohen-Gihon Inbar , Beth-Din Adi , Zvi Anat , Laskar Orly , Paran Nir , Epstein Eyal , Stein Dana , Dorozko Marina , Wolf Dana , Yitzhaki Shmuel , Shapira Shmuel C. , Melamed Sharon , Israeli Ofir
Published: March 2019

Identification and characterization of novel unknown viruses is of great importance. The introduction of high-throughput sequencing (HTS)-based methods has paved the way for genomics-based detection of pathogens without any prior assumptions about the characteristics of the organisms. However, the use of HTS for the characterization of viral pathogens from clinical samples remains limited. Here, we report the identification of a novel Orthobunyavirus species isolated from horse plasma. The identification was based on a straightforward HTS approach. Following enrichment in cell culture, RNA was extracted from the growth medium and rapid library preparation, HTS and primary bioinformatic analyses were performed in less than 12 hours. Taxonomical profiling of the sequencing reads did not reveal sequence similarities to any known virus. Subsequent application of de novo assembly tools to the sequencing reads produced contigs, of which three showed some similarity to the L, M, and S segments of viruses belonging to the Orthobunyavirus genus. Further refinement of these contigs resulted in high-quality, full-length genomic sequences of the three genomic segments (L, M and S) of a novel Orthobunyavirus. Characterization of the genomic sequence, including the prediction of open reading frames and the inspection of consensus genomic termini and phylogenetic analysis, further confirmed that the novel virus is indeed a new species, which we named Ness Ziona virus.
Long-term exercise training improves memory in middle-aged men and modulates peripheral levels of BDNF and Cathepsin B
Authors: De la Rosa Adrián , Solana Elisabeth , Corpas Rubén , Bartrés-Faz David , Pallàs Mercè , Vina Jose , Sanfeliu Coral , Gomez-Cabrera Mari Carmen
Published: March 2019

Aging is accompanied by a decline in memory and other brain functions. Physical exercise may mitigate this decline through the modulation of factors participating in the crosstalk between skeletal muscle and the brain, such as neurotrophins and oxidative stress parameters. We aimed to determine whether long term exercise training (35 ± 15 years) promotes memory maintenance in middle-aged men, and to characterize the changes in neurotrophic factors and lipid oxidation markers in peripheral blood samples in both middle-aged and young men. The neuropsychological analysis showed significant improvements in memory through the Free and Cued Immediate Recall tests, in the middle-aged trained individuals when compared to the sedentary ones. We found a significant decrease in the resting serum BDNF and plasma Cathepsin B (CTSB) levels in the trained groups at both middle and young ages. BDNF and CTSB levels were inversely correlated with weekly hours of exercise. We also found a significant decrease in plasma malondialdehyde, an index of lipid peroxidation, in middle-aged and young trained subjects. The positive impact of long-term exercise training by delaying the onset of physiological memory loss and the associated neurotrophic and redox peripheral modulation, suggests the effectiveness of exercise as preventive strategy against age-related memory loss and neurodegeneration.
A bio-coupling approach using a dextran-binding domain to immobilize an engineered streptavidin to Sephadex for easy preparation of affinity matrix
Authors: Wu Sau-Ching , Wang Chris , Chin Jonathan , Wong Sui-Lam
Published: March 2019

An engineered streptavidin, SAVSBPM18 with reversible biotin binding capability, has been successfully applied to purify biotinylated and streptavidin-binding peptide (SBP) tagged proteins. To simplify the preparation for the SAVSBPM18 affinity matrix without chemical conjugation, two bio-coupling approaches were developed based on a 14-kDa dextran-binding domain (DBD) from a Leuconostoc mesenteroides dextransucrase. The first approach offers simplicity for bio-coupling by creating a direct fusion, SAVSBPM18-Linker-DBD. Purification of the fusion from crude extract and its immobilization to Sephadex can be consolidated in one-step. The second approach aims at flexibility. A SnoopCatcher (SC) was fused to DBD to create SC-Linker-DBD. This fusion can covalently capture any recombinant proteins tagged with a SnoopTag (ST) including SAVSBPM18-Linker-ST via the formation of an isopeptide bond at the interface through the SnoopCatcher-SnoopTag interaction. Although monomeric DBD binds to dextran with nanomolar affinity, DBD tetramerized via streptavidin (SAVSBPM18-Linker-ST·SC-Linker-DBD) showed an even tighter binding to Sephadex. The majority of the fluorescently labelled DBD tetramers were retained on the Sephadex surface even after four months. Affinity columns generated using either approach effectively purified both SBP-tagged and biotinylated proteins. These columns are reusable and functional even after a year of frequent use.
Hedgehog signaling in the airway epithelium of patients with chronic obstructive pulmonary disease
Authors: Tam A. , Hughes M. , McNagny K. M. , Obeidat M. , Hackett T. L. , Leung J. M. , Shaipanich T. , Dorscheid D. R. , Singhera G. K. , Yang C. W. T. , Paré P. D. , Hogg J. C. , Nickle D. , Sin D. D.
Published: March 2019

Genome-wide association studies have linked gene variants of the receptor patched homolog 1 (PTCH1) with chronic obstructive pulmonary disease (COPD). However, its biological role in the disease is unclear. Our objective was to determine the expression pattern and biological role of PTCH1 in the lungs of patients with COPD. Airway epithelial-specific PTCH1 protein expression and epithelial morphology were assessed in lung tissues of control and COPD patients. PTCH1 mRNA expression was measured in bronchial epithelial cells obtained from individuals with and without COPD. The effects of PTCH1 siRNA knockdown on epithelial repair and mucous expression were evaluated using human epithelial cell lines. Ptch1+/− mice were used to assess the effect of decreased PTCH1 on mucous expression and airway epithelial phenotypes. Airway epithelial-specific PTCH1 protein expression was significantly increased in subjects with COPD compared to controls, and its expression was associated with total airway epithelial cell count and thickness. PTCH1 knockdown attenuated wound closure and mucous expression in airway epithelial cell lines. Ptch1+/− mice had reduced mucous expression compared to wildtype mice following mucous induction. PTCH1 protein is up-regulated in COPD airway epithelium and may upregulate mucous expression. PTCH1 provides a novel target to reduce chronic bronchitis in COPD patients.
Multivariate Optimization of Tenax TA-Thermal Extraction for Determining Gaseous Phase Organophosphate Esters in Air Samples
Authors: Matsiko Julius , Li Honghua , Wang Pu , Sun Huizhong , Zheng Shucheng , Wang Dou , Zhang Weiwei , Hao Yanfen , Zuo Peijie , Li Yingming , Zhang Qinghua , Zhang Jianqing , Jiang Guibin
Published: March 2019

Suitable conditions for thermal extraction of semi-volatile organic compounds have largely been arrived at by univariate optimization or based on the recommendations provided by the manufacturers of the extraction equipment. Herein, we demonstrated the multivariate optimization of Tenax TA–thermal extraction for determining organophosphate esters in the gas phase fraction of air samples. Screening and refining experiments were performed using the eighth fraction factorial and Box-Behnken designs, respectively, and satisfactory models were obtained. Subsequently, the process was optimized by Derringer’s desirability function and the global desirability was 0.7299. Following optimization, the analytes were desorbed at 290 °C for 10 minutes at a helium flow of 95 mL min−1, with the transfer line set at 290 °C. The analytes were then cryofocused at 20 °C and then cryodesorbed into the chromatographic column at 295 °C for 6 minutes. Method validation exhibited high linearity coefficients (>0.99), good precision (CV < 14%) and low detection limits (0.1–0.5 ng m−3). The method was tested by pumping 0.024 m3 of real indoor environment air through Tenax TA sorbent tubes. Furthermore, with multivariate optimization, analysis time and other resources were significantly reduced, and information about experimental factor interaction effects was investigated, as compared to the univariate optimization and other traditional methods.
Density of bulk trap states of hybrid lead halide perovskite single crystals: temperature modulated space-charge-limited-currents
Authors: Pospisil Jan , Zmeskal Oldrich , Nespurek Stanislav , Krajcovic Jozef , Weiter Martin , Kovalenko Alexander
Published: March 2019

Temperature-modulated space-charge-limited-current spectroscopy (TMSCLC) is applied to quantitatively evaluate the density of trap states in the band-gap with high energy resolution of semiconducting hybrid lead halide perovskite single crystals. Interestingly multicomponent deep trap states were observed in the pure perovskite crystals, which assumingly caused by the formation of nanodomains due to the presence of the mobile species in the perovskites.
In Vivo Flow Cytometry of Extremely Rare Circulating Cells
Authors: Tan Xuefei , Patil Roshani , Bartosik Peter , Runnels Judith M. , Lin Charles P. , Niedre Mark
Published: March 2019

Circulating tumor cells (CTCs) are of great interest in cancer research, but methods for their enumeration remain far from optimal. We developed a new small animal research tool called “Diffuse in vivo Flow Cytometry” (DiFC) for detecting extremely rare fluorescently-labeled circulating cells directly in the bloodstream. The technique exploits near-infrared diffuse photons to detect and count cells flowing in large superficial arteries and veins without drawing blood samples. DiFC uses custom-designed, dual fiber optic probes that are placed in contact with the skin surface approximately above a major vascular bundle. In combination with a novel signal processing algorithm, DiFC allows counting of individual cells moving in arterial or venous directions, as well as measurement of their speed and depth. We show that DiFC allows sampling of the entire circulating blood volume of a mouse in under 10 minutes, while maintaining a false alarm rate of 0.014 per minute. In practice, this means that DiFC allows reliable detection of circulating cells below 1 cell per mL. Hence, the unique capabilities of DiFC are highly suited to biological applications involving very rare cell types such as the study of hematogenous cancer metastasis.
Evidence for the homogeneous ferromagnetic phase in (Ga,Mn)(Bi,As) epitaxial layers from muon spin relaxation spectroscopy
Authors: Levchenko K. , Prokscha T. , Sadowski J. , Radelytskyi I. , Jakiela R. , Trzyna M. , Andrearczyk T. , Figielski T. , Wosinski T.
Published: March 2019

Ferromagnetic semiconductor thin layers of the quaternary (Ga,Mn)(Bi,As) and reference, ternary (Ga,Mn)As compounds, epitaxially grown under either compressive or tensile strain, have been characterized from a perspective of structural and magnetization homogeneity. The quality and composition of the layers have been confirmed by secondary-ion mass spectrometry (SIMS). A thorough evaluation of the magnetic properties as a function of temperature and applied magnetic field has been performed by means of SQUID magnetometry and low-energy muon spin relaxation (µSR) spectroscopy, which enables studying local (on the nanometer scale) magnetic properties of the layers. The results testify that the ferromagnetic order builds up almost homogeneously below the Curie temperature in the full volume fraction of both the (Ga,Mn)As and (Ga,Mn)(Bi,As) layers. Incorporation of a small amount of heavy Bi atoms into (Ga,Mn)As, which distinctly enhances the strength of spin-orbit coupling in the quaternary (Ga,Mn)(Bi,As) layers, does not deteriorate noticeably their magnetic properties.
The changes of microbial community and flavor compound in the fermentation process of Chinese rice wine using Fagopyrum tataricum grain as feedstock
Authors: Ren Qing , Sun Leping , Wu Huijun , Wang Yousheng , Wang Zhiwei , Zheng Fuping , Lu Xin , Xu Jialiang
Published: March 2019

Chinese rice wine (CRW), a unique wine species, has a long history in China. Fagopyrum tataricum grain is a kind of high-quality grain with function in health care. The production of CRW wine with F. tataricum grain is beneficial to the development of new rice wine products. The flavor compounds and microorganisms in F. tataricum grain rice wine were studied. One hundred and seven volatile compounds (including 11 kinds of pyrazines that were rarely detected in wine) were detected and eight organic acids were measured. The microecological diversity in the fermentation process of F. tataricum rice wine was studied. It was found that Bacillus was the main bacterial genus, and the unclassfied_O_Saccharomycetales was the main fungi. Correlation analysis between microorganism and flavor compound shown there are 838 correlations. A total of 108 microbial genera maybe participate in the formation of flavor compounds. In addition, fourteen genera included unclassified_O_Saccharomycetales, Lactococcus, Pediococcus, Aspergillus, Cladosporium, Cochliobolus, Sporidiobolus, Pichia and Saccharomycopsis et al. were screened as functional significant microbiota and built correlation with flavor compounds. This work provides a perspective for bridging the gap between flavor compound and microbial community, and advances our understanding of mechanisms in F. tataricum rice wine fermentation.
Secondary (Agostic Si–H/Electrostatic C–F) Interactions in Alkaline Earth-based Catalysts
Authors: Sarazin Yann , Carpentier Jean-Francois
Published: March 2019

The design and implementation of a selection of homogeneous alkaline earth (Ae) catalysts and precatalysts for hydroamination and hydrophosphination of olefins and for ring-opening polymerization of cyclic esters are surveyed. Emphasis is placed on the three large elements calcium, strontium and barium. The role of Ae⋯H–Si and Ae⋯F–C noncovalent interactions in the stabilization of (pre)catalysts is highlighted.
Soft Forces in Organic Synthesis by C–N Coupling Reactions
Authors: Bose Anima , Maiti Saikat , Mal Prasenjit
Published: March 2019

Chemical reactions controlled by the systems involved are essential to elucidate the complex functions of living systems and create new functional molecules. This chapter proposes the utilization of simultaneous cooperative multiple weak interactions or soft forces in the synthesis of C–N bonds. In general, metal-mediated synthetic methods for the syntheses of C–N bonds are associated with drawbacks, e.g. (a) requirements for prefunctionalized starting materials, for example aryl halides, prior to the amination (making overall transformation multi-step in nature), and (b) production of stoichiometric amounts of metal halides as waste after the amination. In contrast, by performing C–N coupling reactions via direct C–H activation or functionalization (without using any prefunctionalized systems), many amination reactions can be successfully achieved. This chapter mainly covers selective C–N bond formation reactions under mild conditions with the intention that the reactivity of those systems could be controlled through soft forces or cooperative noncovalent interactions.
Noncovalent Interactions in the Nitroaldol (Henry) Reaction
Authors: Hazra Susanta , Pombeiro Armando J. L.
Published: March 2019

The Henry (nitroaldol) reaction provides a useful method for C–C bond formation between a nitroalkane and an aldehyde or a ketone to form a β-nitro alcohol. Noncovalent interactions can play important roles in this reaction, namely by orienting the reactant molecules, lowering the reaction barriers or even building suitable supramolecular catalysts. This chapter considers the influence of noncovalent interactions (mainly H-bonding) in the Henry reaction (excluding the aza-Henry reaction) and the product selectivity including diastereoselectivity (anti or syn) and enantioselectivity.
Noncovalent Interactions in Asymmetric Reactions Catalysed by Chiral Phosphoric Acids
Authors: Phillips Ana Maria Faisca
Published: March 2019

Noncovalent interactions play an important role in enzyme catalysis, helping to stabilize transition states. Favourable interactions, including hydrogen bonding, π-stacking, CH⋯π and lone pair⋯π interactions, amongst others, may also be responsible for the regioselectivity and high degrees of stereoselectivity that can be achieved with some small-molecule catalysts. Noncovalent interactions often compete with steric effects and identifying and understanding them is not always straightforward. Nevertheless, this can provide a basis for the rational design of new catalysts, to be applied in the synthesis of single enantiomers needed for various applications ranging from pharmaceuticals to advanced materials. This chapter provides an overview of recent findings in the area of chiral phosphoric acid-catalysed reactions. It considers the types of reactions and the modes of activation possible, the models used to predict stereoselectivity and the types of interactions involved. A few case studies selected from the recent literature illustrate the state-of-the-art in this important branch of catalysis.
Noncovalent Interaction-assisted Redox Catalysis in Reductive Dehalogenation
Authors: Kurek Stefan S. , Romańczyk Piotr P.
Published: March 2019

This chapter demonstrates how common are noncovalent interactions assisting catalytic reductive dehalogenation, including enzymatic reactions in reductive dehalogenases. Examples are given of halogen bonding, specific to the reactants in this process, facilitating it, but also hydrogen bonding, which may make the carbon–halogen bond more prone to cleavage or even provide a path for the electron transfer. Various types of noncovalent interactions locate the enzyme substrate in a position ideal for dehalogenation to proceed. Such systems are described, and also model systems, in which proximity effects have been shown to operate. The importance of quantum-chemical calculations in the discovery of noncovalent effects and revealing their significance for the efficiency and selectivity of reductive dehalogenation is also stressed.
Ionic Liquid Effect in Catalysed Multicomponent Reactions
Authors: Neto Brenno A. D. , Alvim Haline G. O. , Lapis Alexandre A. M.
Published: March 2019

In this book chapter the effects produced in using ionic liquids over multicomponent reactions are presented and discussed. Ionic liquids may be used as reaction media (solvents) or as catalysts for several multicomponent reactions. It is observed that many multicomponent reactions characteristically proceed through charged intermediates, thereby rendering them as desirable features to interact with cations and/or anions of ionic liquids. These interactions are mostly ruled by Coulombic attraction/stabilisation between the charged intermediates and the ionic liquid ions. These Coulombic interactions give rise to new ion pairs and larger supramolecular aggregates (higher ion clusters). Additional interactions such as hydrogen bonds and van der Waals forces also play a role in the formation, directionality (entropic drivers) and stabilisation of these ion pairs (and larger supramolecular clusters) between the charged intermediates and the ionic liquid ions; an effect typically noted for imidazolium derivatives. Understanding the multicomponent reaction mechanism in this context is essential in aiming at predicting a positive ionic liquid effect. Many multicomponent reactions have proven to be capable of undergoing two or more competitive reaction mechanisms, but usually the final multicomponent reaction adduct is the same regardless of the reaction pathway. Ionic liquids may also contribute to tune the reaction through one specific mechanism. As we intend to show herein, the combination of multicomponent reactions and ionic liquids typically returns excellent results and produces many achievements, although both are a huge challenge to understand and to predict their effects over multicomponent reactions.
Cavity Effects in Metal–Organic Frameworks
Authors: Rechac Víctor L. , Sanchis Encarnación Peris , Llabrés i Xamena Francesc X.
Published: March 2019

Metal–organic frameworks (MOFs) have attracted enormous interest in recent years owing to their potential use as heterogeneous catalysts. MOF catalysts can be designed with active sites at the metallic units or at the organic ligands or trapped inside their regular pore system. This chapter illustrates how cavity effects (i.e. the chemical environment in which the active sites are located) can have a large influence on their final catalytic properties through specific host–guest interactions, thereby introducing additional tools to modulate chemical specificity.
Application of Metal–Organic Frameworks in CO2 Capture and Conversion
Authors: Zhang Li , Liu Jiewei , Su Cheng-Yong
Published: March 2019

Metal–organic frameworks (MOFs) are promising candidates for CO2 capture and conversion as they possess remarkable properties, including large surface area, open channels and permanent porosity. Through the judicious selection of metal clusters and organic linkers, a framework with a desired topology can be realized. Furthermore, the study of the noncovalent interactions in MOFs provides significant insights into the relationship between the catalytic performance and the framework structure, which will also further promote the development of MOFs as heterogeneous catalysts for CO2 capture and conversion. This chapter is divided into four sections. The first section gives a brief introduction to the structures and chemical features of MOFs. The second section concentrates on MOFs as heterogeneous catalysts for the chemical fixation of CO2 with organic compounds. The third section presents MOFs as photocatalysts for CO2 reduction. The last section covers the application of MOFs in the electrocatalytic reduction of CO2. Particular challenges in the rational design and application of MOF catalysts and research opportunities for further development are highlighted. It is hoped that this chapter will not only serve as a starting point to gain insights into this challenging field but will also stimulate more intensive research on the development of creative MOFs as heterogeneous catalysts towards CO2 capture and conversion.
Hybrids of Metal–Organic Frameworks as Organized Supramolecular Nano-reactors
Authors: Kustov Leonid M. , Isaeva Vera I.
Published: March 2019

The concept of using hybrids of metal–organic frameworks (MOFs) with encapsulated structures, such as calixarenes, crown ethers, phthalocyanines and porphyrins, as nano-reactors or nano-containers for specific catalytic reactions is considered from the point of view of noncovalent interactions and molecular confinement in the porous architecture of MOFs of different structural types. Materials of this kind can be called “Russian matryoshka-type metal organic frameworks.” Controlling such interactions provides a key to enhancement of the efficiency of the catalysts and performance of adsorbents. The design of “green” and robust MOFs is of prime importance.
Role of Ion Pairing in the Mechanisms of Au(i)-catalysed Reactions: Theory and Experiment
Authors: Zuccaccia Daniele , Belanzoni Paola , Belpassi Leonardo , Ciancaleoni Gianluca , Del Zotto Alessandro
Published: March 2019

In this chapter, the role of ion pairing in the mechanism of the reactions promoted by gold(i) catalysts L–Au–X is elucidated by means of both experimental findings and theoretical calculations. The synergy of the approach allowed the full elucidation of the role of the counterion X−. The catalytic performance in the alkoxylation and hydration of alkynes promoted by gold(i) is influenced by the coordinating ability and basicity (proton affinity) of the counterion, the anion/cation relative orientation and the appropriate matching of X− and L. Finally, how the nature of the anion plays a fundamental role in solvent-, silver- and acid-free gold(i)-catalysed hydration of alkynes is highlighted.
Quantitative structure–activity relationship (QSAR) study of carcinogenicity of polycyclic aromatic hydrocarbons (PAHs) in atmospheric particulate matter by random forest (RF)
Authors: Li Nan , Qi Juan , Wang Ping , Zhang Xin , Zhang Tianlong , Li Hua
Published: March 2019

Prediction of the carcinogenicity of PAHs in atmospheric particulate matter using the quantitative structure–activity relationship (QSAR) combined with the random forest (RF) method.
Ultrafine ternary metal oxide particles with carbon nanotubes: a metal–organic-framework-based approach and superior lithium-storage performance
Authors: Tang Xuxu , Liang Ming , Zhang Yanfeng , Sun Weiwei , Wang Yong
Published: March 2019

A metal–organic-framework template approach was used to fabricate ultrafine ternary metal oxide nanoparticles embedded in CNTs, which exhibit larger-than-theoretical reversible capacities for lithium-ion batteries.
Insights into operational stability and processing of halide perovskite active layers
Authors: Schelhas Laura T. , Li Zhen , Christians Jeffrey A. , Goyal Anuj , Kairys Paul , Harvey Steven P. , Kim Dong Hoe , Stone Kevin H. , Luther Joseph M. , Zhu Kai , Stevanovic Vladan , Berry Joseph J.
Published: March 2019

The structural stability of mixed A-site perovskite solar cells during operation is observed by in situ XRD and the de-mixing behavior is described by calculating the Gibbs free energy of mixing.
Vivid-colored silicon solar panels with high efficiency and non-iridescent appearance
Authors: Ji Chengang , Zhang Zhong , Masuda Taizo , Kudo Yuki , Guo L. Jay
Published: March 2019

A novel approach was proposed for fabricating bright-colored solar cells with high power conversion efficiency and excellent angular insensitivity.
Free-standing flexible film as a binder-free electrode for an efficient hybrid deionization system
Authors: Sriramulu Deepa , Yang Hui Ying
Published: March 2019

Capacitive deionization (CDI) is an energy efficient and cost-effective technology for the desalination of brackish water.
Gate-tuned conductance of graphene-ribbon junctions with nanoscale width variations
Authors: Yu Young-Jun , Choe Jong-Ho , Kim Jong Yun , Gwon Oh Hun , Choi Hong Kyw , Choi Jin Sik , Kim Jin Hong , Kim Jin-Soo , Kim Jin Tae , Shin Jun-Hwan , Choi Young Kyu
Published: March 2019

On applying partial gate voltages, we were able to perceive precise and minute conductance variations for the entire graphene electrode, arising mainly from different sub-micrometer scale widths of the graphene ribbons (GRs), which could not be distinguished using conventional global gating methods.
Borax promotes the facile formation of hollow structure in Cu single crystalline nanoparticles for multifunctional electrocatalysis
Authors: Jia Baorui , Zhao Yongzhi , Zhang Zili , Liu Luan , Qin Mingli , Wu Haoyang , Liu Ye , Qu Xuanhui , Qi Genggeng
Published: March 2019

Hollow Cu2O and Cu are efficiently prepared using borax as structure-directing agent for electrocatalysis of glucose oxidation and H2O2 reduction.
Characterization of contact resistances in ceramic-coated vertically aligned carbon nanotube arrays
Authors: Li Meng , Yang Ning , Wood Vanessa , Park Hyung Gyu
Published: March 2019

End- and side-contact resistances between carbon nanotubes and contacts are easily probed in vertically aligned arrays.
Ochrasperfloroid, an ochratoxin–ergosteroid heterodimer with inhibition of IL-6 and NO production from Aspergillus flocculosus 16D-1
Authors: Gu Bin-Bin , Jiao Fu-Rong , Wu Wei , Liu Lei , Jiao Wei-Hua , Sun Fan , Wang Shu-Ping , Yang Fan , Lin Hou-Wen
Published: March 2019

A novel ochratoxin–ergosteroid heterodimer, ochrasperfloroid (1), together with a known mycotoxin, ochratoxin A (2), were isolated from the sponge-derived fungus Aspergillus flocculosus 16D-1.
Proline bulky substituents consecutively act as steric hindrances and directing groups in a Michael/Conia-ene cascade reaction under synergistic catalysis
Authors: Putatunda Salil , Alegre-Requena Juan V. , Meazza Marta , Franc Michael , Rohal'ová Dominika , Vemuri Pooja , Císařová Ivana , Herrera Raquel P. , Rios Ramon , Veselý Jan
Published: March 2019

In this study, we report a highly stereoselective and versatile synthesis of spiro pyrazolones, promising motifs that are being employed as pharmacophores.
Design of Pd-based pseudo-binary alloy catalysts for highly active and selective NO reduction
Authors: Jeon Jaewan , Kon Ken-ichi , Toyao Takashi , Shimizu Ken-ichi , Furukawa Shinya
Published: March 2019

Drastic tuning of NO reduction activity and N2 selectivity based on the catalyst design with pseudo-binary alloy structures.
Copper-free dual labeling of DNA by triazines and cyclopropenes as minimal orthogonal and bioorthogonal functions
Authors: Reisacher Ulrike , Ploschik Damian , Rönicke Franziska , Cserép Gergely B. , Kele Péter , Wagenknecht Hans-Achim
Published: March 2019

Two different and small functions for inverse electron demand Diels–Alder reactions were applied for dual labeling of DNA: the 1,2,4-triazine was attached to the 5-position of 2′-deoxyuridine, and the 1-methylcyclopropene to the 7-position of 7-deaza-2′-deoxyadenosine.
Cu nanoparticles constrain segmental dynamics of cross-linked polyethers: a trade-off between non-fouling and antibacterial properties
Authors: Nikitin Daniil , Madkour Sherif , Pleskunov Pavel , Tafiichuk Renata , Shelemin Artem , Hanuš Jan , Gordeev Ivan , Sysolyatina Elena , Lavrikova Alexandra , Ermolaeva Svetlana , Titov Valerii , Schönhals Andreas , Choukourov Andrei
Published: March 2019

Copper nanoparticles induce constraints to segmental dynamics of poly(ethylene oxide) macromolecules which influence non-fouling/antibacterial properties of Cu/PEO nanocomposite films.