bluuebunny/crossref_metadata_2025_split huggingface dataset:
Importance of interlayer H bonding structure to the stability of layered minerals
Authors: Conroy Michele , Soltis Jennifer A. , Wittman Rick S. , Smith Frances N. , Chatterjee Sayandev , Zhang Xin , Ilton Eugene S. , Buck Edgar C. 
Published: October 2017

AbstractLayered (oxy) hydroxide minerals often possess out-of-plane hydrogen atoms that form hydrogen bonding networks which stabilize the layered structure. However, less is known about how the ordering of these bonds affects the structural stability and solubility of these minerals. Here, we report a new strategy that uses the focused electron beam to probe the effect of differences in hydrogen bonding networks on mineral solubility. In this regard, the dissolution behavior of boehmite (γ-AlOOH) and gibbsite (γ-Al(OH)3) were compared and contrasted in real time via liquid cell electron microscopy. Under identical such conditions, 2D-nanosheets of boehmite (γ-AlOOH) exfoliated from the bulk and then rapidly dissolved, whereas gibbsite was stable. Further, substitution of only 1% Fe(III) for Al(III) in the structure of boehmite inhibited delamination and dissolution. Factors such as pH, radiolytic species, and knock on damage were systematically studied and eliminated as proximal causes for boehmite dissolution. Instead, the creation of electron/hole pairs was considered to be the mechanism that drove dissolution. The widely disparate behaviors of boehmite, gibbsite, and Fe-doped boehmite are discussed in the context of differences in the OH bond strengths, hydrogen bonding networks, and the presence or absence of electron/hole recombination centers.
Haplotype analysis of XRCC2 gene polymorphisms and association with increased risk of head and neck cancer
Authors: Saeed Soma , Mahjabeen Ishrat , Sarwar Romana , Bashir Kashif , Kayani Mahmood Akhtar 
Published: October 2017

AbstractWe aimed to investigate the effect of hotspot variations of XRCC2 gene on the risk of head and neck cancer (HNC) in 400 patients and 400 controls. Five polymorphisms of XRCC2 gene G4234C (rs3218384), G4088T (rs3218373), G3063A (rs2040639), R188H (rs3218536) and rs7802034 were analyzed using Allele- specific polymerase chain reaction (ARMS-PCR) followed by sequence analysis. For rs3218373, the GG genotype indicated a statistically significant 3-fold increased risk of HNC (P < 0.001) after multivariate adjustment. For rs7802034, the GG genotype suggested statistically significant 2-fold increased risk of HNC (P < 0.001). For SNP of rs3218536, the AA genotype indicated a significant 3-fold increased risk of HNC (P < 0.001). Additionally, haplotype analysis revealed that TACAG, TGGAG, TACGG and TAGGA haplotypes of XRCC2 polymorphisms are associated with HNC risk. Two SNPs in XRCC2 (rs2040639 and rs3218384) were found increased in strong linkage disequilibrium. Furthermore, joint effect model showed 20 fold (OR = 19.89; 95% CI = 2.65–149.36, P = 0.003) increased HNC risk in patients carrying four homozygous risk alleles of selected polymorphisms. These results show that allele distributions and genotypes of XRCC2 SNPs are significantly associated with increased HNC risk and could be a genetic adjuster for the said disease.
A quantitative comparison of cytosolic delivery via different protein uptake systems
Authors: Verdurmen Wouter P. R. , Mazlami Marigona , Plückthun Andreas 
Published: October 2017

AbstractOver many years, a variety of delivery systems have been investigated that have the capacity to shuttle macromolecular cargoes, especially proteins, into the cytosol. Due to the lack of an objective way to quantify cytosolic delivery, relative delivery efficiencies of the various transport systems have remained unclear. Here, we demonstrate the use of the biotin ligase assay for a quantitative comparison of protein transport to the cytosol via cell-penetrating peptides, supercharged proteins and bacterial toxins in four different cell lines. The data illustrate large differences in both the total cellular internalization, which denotes any intracellular location including endosomes, and in the cytosolic uptake of the transport systems, with little correlation between the two. Also, we found significant differences between the cell lines. In general, protein transport systems based on cell-penetrating peptides show a modest total uptake, and mostly do not deliver cargo to the cytosol. Systems based on bacterial toxins show a modest receptor-mediated internalization but an efficient delivery to the cytosol. Supercharged proteins, on the contrary, are not receptor-specific and lead to massive total internalization into endosomes, but only low amounts end up in the cytosol.
Stabilization of mouse haploid embryonic stem cells with combined kinase and signal modulation
Authors: Li Haisen , Guo Ao , Xie Zhenfei , Tu Wanzhi , Yu Jiali , Wang Huihan , Zhao Jian , Zhong Cuiqing , Kang Jiuhong , Li Jinsong , Huang Shichao , Shen Li 
Published: October 2017

AbstractMammalian haploid embryonic stem cells (haESCs) provide new possibilities for large-scale genetic screens because they bear only one copy of each chromosome. However, haESCs are prone to spontaneous diploidization through unknown mechanisms. Here, we report that a small molecule combination could restrain mouse haESCs from diploidization by impeding exit from naïve pluripotency and by shortening the S-G2/M phases. Combined with 2i and PD166285, our chemical cocktail could maintain haESCs in the haploid state for at least five weeks without fluorescence-activated cell sorting (FACS) enrichment of haploid cells. Taken together, we established an effective chemical approach for long-term maintenance of haESCs, and highlighted that proper cell cycle progression was critical for the maintenance of haploid state.
Morphology engineering of Streptomyces coelicolor M145 by sub-inhibitory concentrations of antibiotics
Authors: Wang Hu , Zhao Guoping , Ding Xiaoming 
Published: October 2017

AbstractGrowth ofStreptomycesin submerged culture is characterized by the formation of complex mycelial particles, known as pellets or clumps, which strongly influence antibiotic production. Also, many bioactive molecules produced byStreptomyceshave great potential to modulate soil bacteria morphological development. However, there has been no effort directed at engineering mycelial morphology using these small molecules. Here, thiostrepton was identified, using a combination of qRT-PCR, semi-preparative HPLC, and MALDI-TOF MS, as a pellet-inducing compound produced byS. laurentiiATCC31255. At sub-inhibitory concentration, thiostrepton stimulatedStreptomyces coelicolorM145 pellet formation and antibiotics production were altered, with 3-fold and 2-fold decreases in actinorhodin and undecylprodigiosin yields, respectively. It was also shown that mycelial morphology can be influenced by other antibiotic class at sub-inhibitory concentrations. For instance, in the presence of spectinomycin,S. coelicolorM145, which under typical growth conditions forms large diameter pellets with many protruding hyphae, instead formed small diameter pellets with barely visible hyphae at the edge. Importantly, this morphology produced a 4-fold increase in undecylprodigiosin production and 3-fold decrease in actinorhodin production. These results indicated that these small molecules, previously identified as antimicrobials, also have great potential for influencing mycelial morphology.
Cell-surface major vault protein promotes cancer progression through harboring mesenchymal and intermediate circulating tumor cells in hepatocellular carcinomas
Authors: Lee Hyun Min , Joh Jae Won , Seo Se-Ri , Kim Won-Tae , Kim Min Kyu , Choi Hong Seo , Kim So Young , Jang Young-Joo , Sinn Dong Hyun , Choi Gyu Seong , Kim Jong Man , Kwon Choon Hyuck David , Chang Hee Jin , Kim Dae Shick , Ryu Chun Jeih 
Published: October 2017

AbstractCirculating tumor cells (CTCs) play a major role in the metastasis and recurrence of hepatocellular carcinoma (HCC). Here, we found that major vault protein (MVP) is expressed on the surface of HCC cells and further induced under stressful environments. MVP knockdown reduces cell proliferation and induces apoptosis in HCC cells. Treatment of HCC cells with anti-MVP antibody (α-MVP) recognizing cell-surface MVP (csMVP) inhibits cell proliferation, migration, and invasion. csMVP-positive HCC cells have a higher clonogenic survival than csMVP-negative HCC cells, and treatment of HCC cells with α-MVP inhibits clonogenic survival, suggesting that csMVP contributes to HCC cell survival, migration, and invasion. The function of csMVP is mediated through mTOR, FAK, ERK and Akt signaling pathways. csMVP-positive CTCs are detected in HCC patients (89.7%) but not in healthy donors, and the number of csMVP-positive CTCs is further increased in patients with metastatic cancers. csMVP is exclusively detectable in CTCs with mesenchymal phenotype or intermediate phenotype with neither epithelial nor mesenchymal markers, suggesting that csMVP-associated survival and metastatic potential harbor CTCs with nonepithelial phenotypes. The results suggest that csMVP promotes cancer progression and serves as a surface marker for mesenchymal and intermediate CTCs in patients with HCC and metastatic cancers.
Involvement of Ubiquitin-Conjugating Enzyme (E2 Gene Family) in Ripening Process and Response to Cold and Heat Stress of Vitis vinifera
Authors: Gao Yingying , Wang Yi , Xin Haiping , Li Shaohua , Liang Zhenchang 
Published: October 2017

AbstractUbiquitin-conjugating (UBC) E2 enzyme plays crucial roles in plant growth and development. Limited information can describe the function of UBC enzyme E2 in grapes. A total of 43 UBC enzyme E2 genes with conserved UBC domain were identified in grapes. These genes were divided into five groups based on phylogenetic tree with tomatoes. Sequence analyses indicated that VvUBCs in the same group possessed similar gene structures and conserved motifs. Gene distribution in chromosomes was uneven, and gene duplication existed in 36 VvUBCs. Transcriptome and qRT-PCR analysis indicated that most VvUBCs are involved in ripening and post-harvest stage, and feature functional roles in grape organs. According to the transcriptome and qRT-PCR results, seven and six VvUBCs in grape responded to cold and heat stress, respectively, whereas no remarkable VvUBCs change was noted under salt or water-deficit stress. This study provides new insights to physiological and developmental roles of these enzymes and regulation mechanism of E2 genes in grapes.
Video capillaroscopy clarifies mechanism of the photoplethysmographic waveform appearance
Authors: Volkov Mikhail V. , Margaryants Nikita B. , Potemkin Andrey V. , Volynsky Maxim A. , Gurov Igor P. , Mamontov Oleg V. , Kamshilin Alexei A. 
Published: October 2017

AbstractPhotoplethysmography (PPG) devices are widely used in clinical practice but the origin of PPG signal is still under debating. The classical theory assumes that the PPG waveform stems from variations of blood volume in pulsating arteries. In this research we analysed high-speed video recordings of capillaries in a fingernail bed. It was found that speed of erythrocytes in capillaries has pronounced modulation in time, which follows variations of instantaneous blood pressure in arteries. However, the mean speed significantly differs even for neighbour capillaries whereas change of the speed occurs in phase for the most of capillaries. Moreover, the light intensity remitted from the papillary dermis is also modulated at the heartbeat frequency displaying significant correlation with waveforms of the RBC speed. Obtained results can hardly be explained by the classical theory of PPG signal formation. Shallow penetrating visible light acquires modulation of erythrocytes density in the capillary bed without interacting with deeper situated pulsating arteries. Therefore, the capillary bed could serve as a distributed sensor for monitor the status of deep vessels. Better understanding of the photoplethysmography basis will result in a wider range of applications of this fast growing technology in both medical and research practice.
Neural Network for Nanoscience Scanning Electron Microscope Image Recognition
Authors: Modarres Mohammad Hadi , Aversa Rossella , Cozzini Stefano , Ciancio Regina , Leto Angelo , Brandino Giuseppe Piero 
Published: October 2017

AbstractIn this paper we applied transfer learning techniques for image recognition, automatic categorization, and labeling of nanoscience images obtained by scanning electron microscope (SEM). Roughly 20,000 SEM images were manually classified into 10 categories to form a labeled training set, which can be used as a reference set for future applications of deep learning enhanced algorithms in the nanoscience domain. The categories chosen spanned the range of 0-Dimensional (0D) objects such as particles, 1D nanowires and fibres, 2D films and coated surfaces, and 3D patterned surfaces such as pillars. The training set was used to retrain on the SEM dataset and to compare many convolutional neural network models (Inception-v3, Inception-v4, ResNet). We obtained compatible results by performing a feature extraction of the different models on the same dataset. We performed additional analysis of the classifier on a second test set to further investigate the results both on particular cases and from a statistical point of view. Our algorithm was able to successfully classify around 90% of a test dataset consisting of SEM images, while reduced accuracy was found in the case of images at the boundary between two categories or containing elements of multiple categories. In these cases, the image classification did not identify a predominant category with a high score. We used the statistical outcomes from testing to deploy a semi-automatic workflow able to classify and label images generated by the SEM. Finally, a separate training was performed to determine the volume fraction of coherently aligned nanowires in SEM images. The results were compared with what was obtained using the Local Gradient Orientation method. This example demonstrates the versatility and the potential of transfer learning to address specific tasks of interest in nanoscience applications.
Lure-and-Kill Yeast Interfering RNA Larvicides Targeting Neural Genes in the Human Disease Vector Mosquito Aedes aegypti
Authors: Hapairai Limb K. , Mysore Keshava , Chen Yingying , Harper Elizabeth I. , Scheel Max P. , Lesnik Alexandra M. , Sun Longhua , Severson David W. , Wei Na , Duman-Scheel Molly 
Published: October 2017

AbstractNew mosquito control strategies are vitally needed to address established arthropod-borne infectious diseases such as dengue and yellow fever and emerging diseases such as Zika and chikungunya, all of which are transmitted by the disease vector mosquito Aedes aegypti. In this investigation, Saccharomyces cerevisiae (baker’s yeast) was engineered to produce short hairpin RNAs (shRNAs) corresponding to the Aedes aegypti orthologs of fasciculation and elongation protein zeta 2 (fez2) and leukocyte receptor cluster (lrc) member, two genes identified in a recent screen for A. aegypti larval lethal genes. Feeding A. aegypti with the engineered yeasts resulted in silenced target gene expression, disrupted neural development, and highly significant larval mortality. Larvicidal activities were retained following heat inactivation and drying of the yeast into tabular formulations that induced >95% mortality and were found to attract adult females to oviposit. These ready-to-use inactivated yeast interfering RNA tablets may one day facilitate the seamless integration of this new class of lure-and-kill species-specific biorational mosquito larvicides into integrated mosquito control programs.
Extensive gain and loss of photosystem I subunits in chromerid algae, photosynthetic relatives of apicomplexans
Authors: Sobotka Roman , Esson Heather J. , Koník Peter , Trsková Eliška , Moravcová Lenka , Horák Aleš , Dufková Petra , Oborník Miroslav 
Published: October 2017

AbstractIn oxygenic photosynthesis the initial photochemical processes are carried out by photosystem I (PSI) and II (PSII). Although subunit composition varies between cyanobacterial and plastid photosystems, the core structures of PSI and PSII are conserved throughout photosynthetic eukaryotes. So far, the photosynthetic complexes have been characterised in only a small number of organisms. We performed in silico and biochemical studies to explore the organization and evolution of the photosynthetic apparatus in the chromerids Chromera velia and Vitrella brassicaformis, autotrophic relatives of apicomplexans. We catalogued the presence and location of genes coding for conserved subunits of the photosystems as well as cytochrome b6f and ATP synthase in chromerids and other phototrophs and performed a phylogenetic analysis. We then characterised the photosynthetic complexes of Chromera and Vitrella using 2D gels combined with mass-spectrometry and further analysed the purified Chromera PSI. Our data suggest that the photosynthetic apparatus of chromerids underwent unique structural changes. Both photosystems (as well as cytochrome b6f and ATP synthase) lost several canonical subunits, while PSI gained one superoxide dismutase (Vitrella) or two superoxide dismutases and several unknown proteins (Chromera) as new regular subunits. We discuss these results in light of the extraordinarily efficient photosynthetic processes described in Chromera.
Quantitative microglia analyses reveal diverse morphologic responses in the rat cortex after diffuse brain injury
Authors: Morrison Helena , Young Kimberly , Qureshi Mahir , Rowe Rachel K. , Lifshitz Jonathan 
Published: October 2017

AbstractDetermining regions of altered brain physiology after diffuse brain injury is challenging. Microglia, brain immune cells with ramified and dynamically moving processes, constantly surveil the parenchyma for dysfunction which, when present, results in a changed morphology. Our purpose was to define the spatiotemporal changes in microglia morphology over 28 days following rat midline fluid percussion injury (mFPI) as a first step in exploiting microglia morphology to reflect altered brain physiology. Microglia morphology was quantified from histological sections using Image J skeleton and fractal analysis procedures at three time points and in three regions post-mFPI: impact site, primary somatosensory cortex barrel field (S1BF), and a remote region. Microglia ramification (process length/cell and endpoints/cell) decreased in the impact and S1BF but not the remote region (p < 0.05). Microglia complexity was decreased in the S1BF (p = 0.003) and increased in the remote region (p < 0.02). Rod-shaped microglia were present in the S1BF and had a 1.8:1.0 length:width ratio. An in-depth quantitative morphologic analysis revealed diverse and widespread changes to microglia morphology in the cortex post-mFPI. Due to their close link to neuronal function, changes in microglia morphology, summarized in this study, likely reflect altered physiology with diverse and widespread impact on neuronal and circuit function.
Conversion of FeCo from soft to hard magnetic material by lattice engineering and nanopatterning
Authors: Hasegawa Takashi , Kanatani Shunsuke , Kazaana Miyu , Takahashi Kairi , Kumagai Kohei , Hirao Maiko , Ishio Shunji 
Published: October 2017

AbstractThe development of magnetic materials with large uniaxial magnetic anisotropy (Ku) and high saturation magnetization has attracted much attention in various areas such as high-density magnetic storage, spintronic devices, and permanent magnets. Although FeCo alloys with the body-centred cubic structure exhibit the highest Ms among all transition metal alloys, their low Ku and coercivity (Hc) make them unsuitable for these applications. However, recent first-principles calculations have predicted large Ku for the FeCo films with the body-centred tetragonal structure. In this work, we experimentally investigated the hard magnetic properties and magnetic domain structures of nanopatterned FeCo alloy thin films. As a result, a relatively large value of the perpendicular uniaxial magnetic anisotropy Ku = 2.1 × 106 J·m−3 was obtained, while the Hc of the nanopatterned FeCo layers increased with decreasing dot pattern size. The maximum Hc measured in this study was 4.8 × 105 A·m−1, and the corresponding value of μ0Hc was 0.60 T, where μ0 represented the vacuum permeability.
Prediction of high-pressure phases of Weyl semimetal NbAs and NbP
Authors: Zhang Jingyun , Yang Cuihong , Rao Weifeng , Hao Jian , Li Yinwei 
Published: October 2017

AbstractAs the first known Weyl semimetals, binary compounds including TaP, TaAs, NbAs, and NbP have received worldwide interest. This work explored the phase behaviours of NbAs and NbP under high pressure up to 200 GPa via first-principles calculations combined with intelligent particle swarm optimization. Upon compression, a new phase of NbAs with P-6m2 symmetry appeared above 23 GPa and remained stable until 38 GPa, whereupon a monoclinic structure with space group P21/c became more energetically favourable. This lasted until 73 GPa, when a Pm-3m phase followed. Surprisingly, NbP underwent a single phase transition around 63.5 GPa to a new phase with Cmcm symmetry that was completely distinct from the structures shown by TaAs-class compounds such as NbAs and TaAs. All these newly pressure-stabilized structures were dynamically stable at both high and ambient pressure. Electronic band structure calculations revealed a transition from semimetal to metal under high pressure. This work is meaningful and fundamental for future studies and applications of TaAs-class Weyl semimetals under compression or extreme conditions.
Hybrid Printing Metal-mesh Transparent Conductive Films with Lower Energy Photonically Sintered Copper/tin Ink
Authors: Chen Xiaolian , Wu Xinzhou , Shao Shuangshuang , Zhuang Jinyong , Xie Liming , Nie Shuhong , Su Wenming , Chen Zheng , Cui Zheng 
Published: October 2017

AbstractWith the help of photonic sintering using intensive pulse light (IPL), copper has started to replace silver as a printable conductive material for printing electrodes in electronic circuits. However, to sinter copper ink, high energy IPL has to be used, which often causes electrode destruction, due to unreleased stress concentration and massive heat generated. In this study, a Cu/Sn hybrid ink has been developed by mixing Cu and Sn particles. The hybrid ink requires lower sintering energy than normal copper ink and has been successfully employed in a hybrid printing process to make metal-mesh transparent conductive films (TCFs). The sintering energy of Cu/Sn hybrid films with the mass ratio of 2:1 and 1:1 (Cu:Sn) were decreased by 21% compared to sintering pure Cu film, which is attributed to the lower melting point of Sn for hybrid ink. Detailed study showed that the Sn particles were effectively fused among Cu particles and formed conducting path between them. The hybrid printed Cu/Sn metal-mesh TCF with line width of 3.5 μm, high transmittance of 84% and low sheet resistance of 14 Ω/□ have been achieved with less defects and better quality than printed pure copper metal-mesh TCFs.