bluuebunny/crossref_metadata_2025 huggingface dataset:
A biomaterial with a channel-like pore architecture induces endochondral healing of bone defects
Authors: Petersen A. , Princ A. , Korus G. , Ellinghaus A. , Leemhuis H. , Herrera A. , Klaumünzer A. , Schreivogel S. , Woloszyk A. , Schmidt-Bleek K. , Geissler S. , Heschel I. , Duda G. N.
Published: October 2018

Biomaterials developed to treat bone defects have classically focused on bone healing via direct, intramembranous ossification. In contrast, most bones in our body develop from a cartilage template via a second pathway called endochondral ossification. The unsolved clinical challenge to regenerate large bone defects has brought endochondral ossification into discussion as an alternative approach for bone healing. However, a biomaterial strategy for the regeneration of large bone defects via endochondral ossification is missing. Here we report on a biomaterial with a channel-like pore architecture to control cell recruitment and tissue patterning in the early phase of healing. In consequence of extracellular matrix alignment, CD146+ progenitor cell accumulation and restrained vascularization, a highly organized endochondral ossification process is induced in rats. Our findings demonstrate that a pure biomaterial approach has the potential to recapitulate a developmental bone growth process for bone healing. This might motivate future strategies for biomaterial-based tissue regeneration.
Biologically relevant laminin as chemically defined and fully human platform for human epidermal keratinocyte culture
Authors: Tjin Monica Suryana , Chua Alvin Wen Choong , Moreno-Moral Aida , Chong Li Yen , Tang Po Yin , Harmston Nathan Peter , Cai Zuhua , Petretto Enrico , Tan Bien Keem , Tryggvason Karl
Published: October 2018

The current expansion of autologous human keratinocytes to resurface severe wound defects still relies on murine feeder layer and calf serum in the cell culture system. Through our characterization efforts of the human skin basement membrane and murine feeder layer 3T3-J2, we identified two biologically relevant recombinant laminins—LN-511 and LN-421- as potential candidates to replace the murine feeder. Herein, we report a completely xeno-free and defined culture system utilizing these laminins which enables robust expansion of adult human skin keratinocytes. We demonstrate that our laminin system is comparable to the 3T3-J2 co-culture system in terms of basal markers’ profile, colony-forming efficiency and the ability to form normal stratified epidermal structure in both in vitro and in vivo models. These results show that the proposed system may not only provide safer keratinocyte use in the clinics, but also facilitate the broader use of other cultured human epithelial cells in regenerative medicine.
Improved methods for marking active neuron populations
Authors: Moeyaert Benjamien , Holt Graham , Madangopal Rajtarun , Perez-Alvarez Alberto , Fearey Brenna C. , Trojanowski Nicholas F. , Ledderose Julia , Zolnik Timothy A. , Das Aniruddha , Patel Davina , Brown Timothy A. , Sachdev Robert N. S. , Eickholt Britta J. , Larkum Matthew E. , Turrigiano Gina G. , Dana Hod , Gee Christine E. , Oertner Thomas G. , Hope Bruce T. , Schreiter Eric R.
Published: October 2018

Marking functionally distinct neuronal ensembles with high spatiotemporal resolution is a key challenge in systems neuroscience. We recently introduced CaMPARI, an engineered fluorescent protein whose green-to-red photoconversion depends on simultaneous light exposure and elevated calcium, which enabled marking active neuronal populations with single-cell and subsecond resolution. However, CaMPARI (CaMPARI1) has several drawbacks, including background photoconversion in low calcium, slow kinetics and reduced fluorescence after chemical fixation. In this work, we develop CaMPARI2, an improved sensor with brighter green and red fluorescence, faster calcium unbinding kinetics and decreased photoconversion in low calcium conditions. We demonstrate the improved performance of CaMPARI2 in mammalian neurons and in vivo in larval zebrafish brain and mouse visual cortex. Additionally, we herein develop an immunohistochemical detection method for specific labeling of the photoconverted red form of CaMPARI. The anti-CaMPARI-red antibody provides strong labeling that is selective for photoconverted CaMPARI in activated neurons in rodent brain tissue.
Author Correction: Retinal progenitor cells release extracellular vesicles containing developmental transcription factors, microRNA and membrane proteins
Authors: Zhou Jing , Benito-Martin Alberto , Mighty Jason , Chang Lynne , Ghoroghi Shima , Wu Hao , Wong Madeline , Guariglia Sara , Baranov Petr , Young Michael , Gharbaran Rajendra , Emerson Mark , Mark Milica Tesic , Molina Henrik , Canto-Soler M. Valeria , Selgas Hector Peinado , Redenti Stephen
Published: October 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Modelling Self-Organization in Complex Networks Via a Brain-Inspired Network Automata Theory Improves Link Reliability in Protein Interactomes
Authors: Cannistraci Carlo Vittorio
Published: October 2018

Protein interactomes are epitomes of incomplete and noisy networks. Methods for assessing link-reliability using exclusively topology are valuable in network biology, and their investigation facilitates the general understanding of topological mechanisms and models to draw and correct complex network connectivity. Here, I revise and extend the local-community-paradigm (LCP). Initially detected in brain-network topological self-organization and afterward generalized to any complex network, the LCP is a theory to model local-topology-dependent link-growth in complex networks using network automata. Four novel LCP-models are compared versus baseline local-topology-models. It emerges that the reliability of an interaction between two proteins is higher: (i) if their common neighbours are isolated in a complex (local-community) that has low tendency to interact with other external proteins; (ii) if they have a low propensity to link with other proteins external to the local-community. These two rules are mathematically combined in C1*: a proposed mechanistic model that, in fact, outperforms the others. This theoretical study elucidates basic topological rules behind self-organization principia of protein interactomes and offers the conceptual basis to extend this theory to any class of complex networks. The link-reliability improvement, based on the mere topology, can impact many applied domains such as systems biology and network medicine.
EzColocalization: An ImageJ plugin for visualizing and measuring colocalization in cells and organisms
Authors: Stauffer Weston , Sheng Huanjie , Lim Han N.
Published: October 2018

Insight into the function and regulation of biological molecules can often be obtained by determining which cell structures and other molecules they localize with (i.e. colocalization). Here we describe an open source plugin for ImageJ called EzColocalization to visualize and measure colocalization in microscopy images. EzColocalization is designed to be easy to use and customize for researchers with minimal experience in quantitative microscopy and computer programming. Features of EzColocalization include: (i) tools to select individual cells and organisms from images; (ii) filters to select specific types of cells and organisms based on physical parameters and signal intensity; (iii) heat maps and scatterplots to visualize the localization patterns of reporters; (iv) multiple metrics to measure colocalization for two or three reporters; (v) metric matrices to systematically measure colocalization at multiple combinations of signal intensity thresholds; and (vi) data tables that provide detailed information on each cell in a sample. These features make EzColocalization well-suited for experiments with low reporter signal, complex patterns of localization, and heterogeneous populations of cells and organisms.
Microperimetry and multimodal imaging in polypoidal choroidal vasculopathy
Authors: Acton Jennifer H. , Ogino Ken , Akagi Yumiko , Wild John M. , Yoshimura Nagahisa
Published: October 2018

Polypoidal choroidal vasculopathy (PCV) is a degenerative macular disease. The study determined the topographical concordance in the areal extent of PCV, defined by indocyanine green angiography (ICGA), and the corresponding outcomes from spectral-domain optical coherence tomography (SD-OCT) and microperimetry, in 25 individuals (25 eyes) who had undergone 3 months of anti-vascular endothelial growth factor treatment. The differential light sensitivity within 10° eccentricity was evaluated by Pattern Deviation probability analysis. The concordances and proportional areal extents of the abnormality for ICGA, SD-OCT and microperimetry were compared. The concordance in the areal extent between all three modalities was 59%. The median concordance between ICGA and microperimetry was 60%; between ICGA and SD-OCT, 70%; and between SD-OCT and microperimetry, 72%. SD-OCT and microperimetry each identified a greater areal extent (>20%) compared to ICGA in 13 and 19 eyes, respectively. A greater areal extent (>20%) was present in 9 eyes for microperimetry compared to SD-OCT and in 5 eyes for SD-OCT compared to microperimetry. SD-OCT and microperimetry each identified a greater area of abnormality than ICGA which supports the clinical utility of SD-OCT. Strong concordance was present between SD-OCT and microperimetry; however, microperimetry identified additional areas of functional abnormality.
Biophotonic approach for the characterization of initial bitter-rot progression on apple specimens using optical coherence tomography assessments
Authors: Wijesinghe Ruchire Eranga , Lee Seung-Yeol , Ravichandran Naresh Kumar , Shirazi Muhammad Faizan , Kim Pilun , Jung Hee-Young , Jeon Mansik , Kim Jeehyun
Published: October 2018

The tremendous advances achieved in the biophotonics technologies have intensified the necessity for non-invasive modalities that can characterize diverse biological materials with increased sensitivity and resolution. Optical coherence tomography (OCT) is one of the techniques that has been applied for biological applications in medicine and agriculture to identify structural properties. Herein, we report the successful incorporation of OCT for the identification of morphological changes that occur as a result of the bitter rot disease, through continuous detection of structural changes. Detailed inner morphological structural changes occurring in fruit specimens were precisely analyzed as a function of the disease incubation period using OCT. The conducted histological correlation and quantitative three-dimensional evaluations provide a robust platform for further discoveries related to plant materials. The results highlight the initial identification of bitter rot progression on apple specimens owing to the non-invasive inspection capability of OCT. Therefore, we expect that the proposed method will enable immediate sensitivity improvements in the inspection of plant diseases for postharvest utility.
Coexisting crystal and liquid-like properties in a 2D long-range self-consistent model
Authors: Maciel J. M. , Amato M. A. , Firpo M. -C.
Published: October 2018

A two-dimensional class of mean-field models serving as a minimal frame to study long-range interaction in two space dimensions is considered. In the case of an anisotropic mixed attractive-repulsive interaction, an initially spatially homogeneous cold fluid is dynamically unstable and evolves towards a quasi-stationary state in which the less energetic particles get trapped into clusters forming a Bravais-like lattice, mimicking a crystalline state. Superimposed to this, one observes in symplectic numerical simulations a flux of slightly more energetic particles channeling through this crystalline background. The resultant system combines the rigidity features of a solid, as particles from a displaced core are shown to snap back into place after a transient, and the dynamical diffusive features of a liquid for the fraction of channeling and free particles. The combination of solid and liquid properties is numerically observed here within the classical context. The quantum transposition of the model may be experimentally reached using the latest ultracold atoms techniques to generate long-range interactions.
A multi-scale approach for percolation transition and its application to cement setting
Authors: Prabhu Achutha , Gimel Jean-Christophe , Ayuela Andrés , Arrese-Igor Silvia , Gaitero Juan J. , Dolado Jorge S.
Published: October 2018

Shortly after mixing cement grains with water, a cementitious fluid paste is formed that immediately transforms into a solid form by a phenomenon known as setting. Setting actually corresponds to the percolation of emergent network structures consisting of dissolving cement grains glued together by nanoscale hydration products, mainly calcium-silicate-hydrates. As happens in many percolation phenomena problems, the theoretical identification of the percolation threshold (i.e. the cement setting) is still challenging, since the length scale where percolation becomes apparent (typically the length of the cement grains, microns) is many times larger than the nanoscale hydrates forming the growing spanning network. Up to now, the long-lasting gap of knowledge on the establishment of a seamless handshake between both scales has been an unsurmountable obstacle for the development of a predictive theory of setting. Herein we present a true multi-scale model which concurrently provides information at the scale of cement grains (microns) and at the scale of the nano-hydrates that emerge during cement hydration. A key feature of the model is the recognition of cement setting as an off-lattice bond percolation process between cement grains. Inasmuch as this is so, the macroscopic probability of forming bonds between cement grains can be statistically analysed in smaller local observation windows containing fewer cement grains, where the nucleation and growth of the nano-hydrates can be explicitly described using a kinetic Monte Carlo Nucleation and Growth model. The most striking result of the model is the finding that only a few links (~12%) between cement grains are needed to reach setting. This directly unveils the importance of explicitly including nano-texture on the description of setting and explains why so low amount of nano-hydrates is needed for forming a spanning network. From the simulations, it becomes evident that this low amount is least affected by processing variables like the water-to-cement ratio and the presence of large quantities of nonreactive fillers. These counter-intuitive predictions were verified by ex-professo experiments that we have carried out to check the validity of our model.
Completely stopping microwaves with extremely enhanced magnetic fields
Authors: Shen Qian , Hong Lujun , Deng Xiaohua , Shen Linfang
Published: October 2018

A microwave one-way waveguide of three-dimensional configuration is proposed and investigated theoretically. In this waveguide there exists a complete one-way propagation band, where the mode propagates only in one direction and can be immune to backscattering. By terminating the one-way waveguide with metal slab, one-way propagating waves in this waveguide system can be stopped at the terminal end without any backscattering. Meanwhile, a hotspot with extremely enhanced magnetic-field amplitude is generated in this 3D waveguide system. For an incident microwave pulse, the trapped wave packet can be compressed to deep subwavelength scale besides the magnetic field enhancement. Moreover, the magnetic field enhancement of trapped waves can be further largely increased by tapering laterally the waveguide system. The approach for trapping microwaves has promising applications in magnetic sensing and magnetic non-linearity.
Repression of Mcl-1 expression by the CDC7/CDK9 inhibitor PHA-767491 overcomes bone marrow stroma-mediated drug resistance in AML
Authors: O’ Reilly Eimear , Dhami Sukhraj Pal S. , Baev Denis V. , Ortutay Csaba , Halpin-McCormick Anna , Morrell Ruth , Santocanale Corrado , Samali Afshin , Quinn John , O’Dwyer Michael E , Szegezdi Eva
Published: October 2018

Acute myeloid leukaemia (AML) is an aggressive cancer with 50–75% of patients relapsing even after successful chemotherapy. The role of the bone marrow microenvironment (BMM) in protecting AML cells from chemotherapeutics and causing consequent relapse is increasingly recognised. However the role that the anti-apoptotic Bcl-2 proteins play as effectors of BMM-mediated drug resistance are less understood. Here we show that bone marrow mesenchymal stromal cells (BMSC) provide resistance to AML cells against BH3-mimetics, cytarabine and daunorubicin, but this is not mediated by Bcl-2 and/or Bcl-XL as previously thought. Instead, BMSCs induced Mcl-1 expression over Bcl-2 and/or Bcl-XL in AML cells and inhibition of Mcl-1 with a small-molecule inhibitor, A1210477, or repressing its expression with the CDC7/CDK9 dual-inhibitor, PHA-767491 restored sensitivity to BH3-mimetics. Furthermore, combined inhibition of Bcl-2/Bcl-XL and Mcl-1 could revert BMSC-mediated resistance against cytarabine + daunorubicin. Importantly, the CD34+/CD38− leukemic stem cell-encompassing population was equally sensitive to the combination of PHA-767491 and ABT-737. These results indicate that Bcl-2/Bcl-XL and Mcl-1 act in a redundant fashion as effectors of BMM-mediated AML drug resistance and highlight the potential of Mcl-1-repression to revert BMM-mediated drug resistance in the leukemic stem cell population, thus, prevent disease relapse and ultimately improve patient survival.
Sensorimotor stroke alters hippocampo-thalamic network activity
Authors: Baumgartner Philipp , El Amki Mohamad , Bracko Oliver , Luft Andreas R. , Wegener Susanne
Published: October 2018

Many stroke survivors experience persisting episodic memory disturbances. Since hippocampal and para-hippocampal areas are usually spared from the infarcted area, alterations of memory processing networks remote from the ischemic brain region might be responsible for the observed clinical symptoms. To pinpoint changes in activity of hippocampal connections and their role in post-stroke cognitive impairment, we induced ischemic stroke by occlusion of the middle cerebral artery (MCAO) in adult rats and analyzed the functional and structural consequences using activity-dependent manganese (Mn2+) enhanced MRI (MEMRI) along with behavioral and histopathological analysis. MCAO caused stroke lesions of variable extent along with sensorimotor and cognitive deficits. Direct hippocampal injury occurred in some rats, but was no prerequisite for cognitive impairment. In healthy rats, injection of Mn2+ into the entorhinal cortex resulted in distribution of the tracer within the hippocampal subfields into the lateral septal nuclei. In MCAO rats, Mn2+ accumulated in the ipsilateral thalamus. Histopathological analysis revealed secondary thalamic degeneration 28 days after stroke. Our findings provide in vivo evidence that remote sensorimotor stroke modifies the activity of hippocampal-thalamic networks. In addition to potentially reversible alterations in signaling of these connections, structural damage of the thalamus likely reinforces dysfunction of hippocampal-thalamic circuitries.
Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development
Authors: Duffy Craig W. , Amambua-Ngwa Alfred , Ahouidi Ambroise D. , Diakite Mahamadou , Awandare Gordon A. , Ba Hampate , Tarr Sarah J. , Murray Lee , Stewart Lindsay B. , D’Alessandro Umberto , Otto Thomas D. , Kwiatkowski Dominic P. , Conway David J.
Published: October 2018

Parasites infect hosts in widely varying environments, encountering diverse challenges for adaptation. To identify malaria parasite genes under locally divergent selection across a large endemic region with a wide spectrum of transmission intensity, genome sequences were obtained from 284 clinical Plasmodium falciparum infections from four newly sampled locations in Senegal, The Gambia, Mali and Guinea. Combining these with previous data from seven other sites in West Africa enabled a multi-population analysis to identify discrete loci under varying local selection. A genome-wide scan showed the most exceptional geographical divergence to be at the early gametocyte gene locus gdv1 which is essential for parasite sexual development and transmission. We identified a major structural dimorphism with alternative 1.5 kb and 1.0 kb sequence deletions at different positions of the 3′-intergenic region, in tight linkage disequilibrium with the most highly differentiated single nucleotide polymorphism, one of the alleles being very frequent in Senegal and The Gambia but rare in the other locations. Long non-coding RNA transcripts were previously shown to include the entire antisense of the gdv1 coding sequence and the portion of the intergenic region with allelic deletions, suggesting adaptive regulation of parasite sexual development and transmission in response to local conditions.
Multiplexed Autoantibody Signature for Serological Detection of Canine Mammary Tumours
Authors: Hussain Shahid , Saxena Sonal , Shrivastava Sameer , Arora Richa , Singh Rajkumar James , Jena Subas Chandra , Kumar Naveen , Sharma Anil Kumar , Sahoo Monalisa , Tiwari Ashok Kumar , Mishra Bishnu Prasad , Singh Raj Kumar
Published: October 2018

Spontaneously occurring canine mammary tumours (CMTs) are the most common neoplasms of female unspayed dogs and are of potential importance as models for human breast cancer as well. Mortality rates are thrice higher in dogs as compared to humans with breast cancer, which can partly be attributed to lack of diagnostic techniques for their early detection. Human breast cancer studies reveal role of autoantibodies in early cancer diagnosis and also the usefulness of autoantibody panels in increasing the sensitivity, as well as, specificity of diagnostic assays. Therefore, in this study, we took advantage of high-throughput Luminex technique for developing a multiplex assay to detect autoantibody signatures against 5 canine mammary tumour-associated autoantigens (TAAs). These TAAs were expressed separately as fusion proteins with halo tag at the N-terminus, which allows easy and specific covalent coupling with magnetic microspheres. The multiplex assay, comprising a panel of candidate autoantigens (TPI, PGAM1, MNSOD, CMYC & MUC1) was used for screening circulating autoantibodies in 125 dog sera samples, including 75 mammary tumour sera and 50 healthy dog sera. The area under curve (AUC) of the combined panel of biomarkers is 0.931 (p < 0.0001), which validates the discriminative potential of the panel in differentiating tumour patients from healthy controls. The assay could be conducted in 3hrs using only 1ul of serum sample and could detect clinical cases of canine mammary tumour with sensitivity and specificity of 78.6% and 90%, respectively. In this study, we report for the first time a multiplexed assay for detection of autoantibodies in canine tumours, utilizing luminex technology and halo-tag coupling strategy. Further to the best of our knowledge, autoantibodies to CMYC and MUC1 have been reported for the first time in canines in this study.
Dynamics of probing a quantum-dot spin qubit with superconducting resonator photons
Authors: Zhu Xing-Yu , Tu Tao , Guo Ao-Lin , Zhou Zong-quan , Li Chuan-Feng , Guo Guang-Can
Published: October 2018

The hybrid system of electron spins and resonator photons is an attractive architecture for quantum computing owing to the long coherence times of spins and the promise of long-distance coupling between arbitrary pairs of qubits via photons. For the device to serve as a building block for a quantum processer, it is also necessary to readout the spin qubit state. Here we analyze in detail the measurement process of an electron spin singlet-triplet qubit in quantum dots using a coupled superconducting resonator. We show that the states of the spin singlet-triplet qubit lead to readily observable features in the spectrum of a microwave field through the resonator. These features provide useful information on the hybrid system. Moreover, we discuss the working points which can be implemented with high performance in the current state-of-the-art devices. These results can be used to construct the high fidelity measurement toolbox in the spin-circuit QED system.
Correlation between defect density in mechanically milled graphite and total oxygen content of graphene oxide produced from oxidizing the milled graphite
Authors: Mohanta Zinia , Atreya Hanudatta S. , Srivastava Chandan
Published: October 2018

It has been reported that defect density in ball-milled graphite lattice increases with the milling time. Guided by this, we hypothesized that the oxygen content of graphene oxide can be substantially enhanced by oxidizing ball-milled graphite and also, the oxygen content would monotonically increase with the milling time as the defect sites would be preferred sites for oxidation. Interestingly, we observed that this correlation was not directly proportional for all milling hours. Even though, the defect density of graphite monotonically increased with milling time, the oxygen content of graphene oxide initially increased and then decreased. This was due to milling time dependent change in the size of the graphite plates and consequent relative abundance of the different oxygen containing functional groups on graphene oxide (GO) produced from the milled graphite.
Microtubule plus-end tracking Adenopolyposis Coli negatively regulates proplatelet formation
Authors: Strassel C. , Moog S. , Mallo L. , Eckly A. , Freund M. , Gachet C. , Lanza F.
Published: October 2018

Platelets are produced upon profound reorganization of mature megakaryocytes (MK) leading to proplatelet elongation and release into the blood stream, a process termed thrombopoiesis. This highly dynamic process requires microtubules (MT) reorganization by mechanisms that are still incompletely understood. Adenomatous polyposis coli (APC) is a microtubule plus-end tracking protein involved in the regulation of MT in a number of cell systems and its inactivation has been reported to alter hematopoiesis. The aim of our study was to investigate the role of APC in megakaryopoiesis and the final steps of platelet formation. Down-regulation of APC in cultured human MK by RNA interference increased endomitosis and the proportion of cells able to extend proplatelets (68.8% (shAPC1) and 52.5% (shAPC2) vs 28.1% in the control). Similarly an increased ploidy and amplification of the proplatelet network were observed in MK differentiated from Lin- cells of mice with APC-deficiency in the MK lineage. In accordance, these mice exhibited increased platelet counts when compared to wild type mice (1,323 ± 111 vs 919 ± 52 platelets/µL; n = 12 p 0.0033**). Their platelets had a normal size, ultrastructure and number of microtubules coils and their main functions were also preserved. Loss of APC resulted in lower levels of acetylated tubulin and decreased activation of the Wnt signaling pathway. Thus, APC appears as an important regulator of proplatelet formation and overall thrombopoiesis.
A network analysis of female sexual function: comparing symptom networks in women with decreased, increased, and stable sexual desire
Authors: Gunst Annika , Werner Marlene , Waldorp Lourens J. , Laan Ellen T. M. , Källström Marianne , Jern Patrick
Published: October 2018

Problems related to low sexual desire in women are common clinical complaints, and the aetiology is poorly understood. We investigated predictors of change in levels of sexual desire using a novel network approach, which assumes that mental disorders arise from direct interactions between symptoms. Using population-based data from 1,449 Finnish women, we compared between-subject networks of women whose sexual desire decreased, increased, or remained stable over time. Networks were estimated and analyzed at T1 (2006) and replicated at T2 (2013) using R. Domains included were, among others, sexual functions, sexual distress, anxiety, depression, body dissatisfaction, and relationship status. Overall, networks were fairly similar across groups. Sexual arousal, satisfaction, and relationship status were the most central variables, implying that they might play prominent roles in female sexual function; sexual distress mediated between general distress and sexual function; and sexual desire and arousal showed different patterns of relationships, suggesting that they represent unique sexual function aspects. Potential group-differences suggested that sex-related pain and body dissatisfaction might play roles in precipitating decreases of sexual desire. The general network structure and similarities between groups replicated well; however, the potential group-differences did not replicate. Our study sets the stage for future clinical and longitudinal network modelling of female sexual function.
The biological role of N-acyl-homoserine lactone-based quorum sensing (QS) in EPS production and microbial community assembly during anaerobic granulation process
Authors: Ma Haijun , Ma Sijia , Hu Haidong , Ding Lili , Ren Hongqiang
Published: October 2018

Although N-acyl-L-homoserine lactone (AHL) based quorum sensing (QS) phenomenon has been observed in mature anaerobic granules, the biological role of AHL-based QS system in anaerobic granulation process remains unexplored. For the first time, a long-term anaerobic bioreactor was operated for 168 days to investigate the biological role of AHL in the granulation process which was divided into three phases (phase I: floccular, phase II: granulation, phase III: maturation). Two different AHLs including C8-HSL and C10-HSL were characterized at nanogram levels. The AHL level was elevated over 20-fold and strongly positively correlated with extracellular polymeric substances (EPS) production and sludge particle size during phase I-II. Exogenous addition of AHL to the floccular sludge also resulted in significantly increased EPS production. Metadata analysis suggested that the granulation process was accompanied by an increase in the abundance of QS-relevant microorganisms. The strong relationships (R > 0.9233, p < 0.01) among AHL concentrations, EPS (except loosely bound EPS), granulation and community variation indicated that AHL-mediated QS played an important role in coordinating community level behaviors associated with granulation, potentially through the regulation of EPS production and composition. This study gives a deep insight into the underlying QS-relevant mechanism of anaerobic granulation process.
Hyperhomocysteinemia Causes Chorioretinal Angiogenesis with Placental Growth Factor Upregulation
Authors: Lee Yih-Jing , Ke Chia-Ying , Tien Ni , Lin Po-Kang
Published: October 2018

Hyperhomocysteinemia is a risk factor for atherosclerosis, which may also be associated with retinal vascular disease, diabetic retinopathy, retinal vein occlusion, and glaucoma. For this study, we established a hyperhomocysteinemia animal model to explore homocysteine (hcy)-related choroidal angiogenesis and possible related factors. We injected Sprague Dawley (SD) rats with different concentrations of hcy and performed color fundus imaging, fluorescein angiography, image-guided optical coherence tomography, and retinal histology to observe the retinal and choroidal changes. Subsequently, we observed prominent choroidal vasculature with congested and tortuous retinal and choroidal vessels in fundus angiographies of the hyperhomocysteinemia animal model. In the histological study, the choroidal capillaries proliferated in the hcy-treated eyes, mimicking choroidal neovascularization. Disrupted retinal pigment epithelium (RPE), abnormal branching vascular network (BVN), and polyp-like structures were also observed in the hcy-treated eyes. Furthermore, we found that placental growth factor (PlGF), but not vascular epithelial growth factor (VEGF), was the key mediating factor of this phenomenon. Our findings suggest that hyperhomocysteinemia might cause choroidal angiogenesis.
Nanoscale enhancement of photoconductivity by localized charge traps in the grain structures of monolayer MoS2
Authors: Yang Myungjae , Kim Tae-Young , Lee Takhee , Hong Seunghun
Published: October 2018

We report a method for mapping the nanoscale anomalous enhancement of photoconductivity by localized charge traps in the grain structures of a molybdenum disulfide (MoS2) monolayer. In this work, a monolayer MoS2film was laterally scanned by a nanoscale conducting probe that was used to make direct contact with the MoS2surface. Electrical currents and noise maps were measured through the probe. By analyzing the data, we obtained maps for the sheet resistance and charge trap density for the MoS2grain structures. The maps clearly show grains for which sheet resistance and charge trap density were lower than those of the grain boundaries. Interestingly, we found an unusual inverse proportionality between the sheet resistance and charge trap density in the grains, which originated from the unique role of sulfur vacancies acting as both charge hopping sites and traps in monolayer MoS2. In addition, under light illumination, the larger the trap density of a region was, the larger the photocurrent of the region was, indicating anomalous enhancement of the photocurrent by traps. Since our method provides valuable insights to understand the nanoscale effects of traps on photoconductive charge transport, it can be a powerful tool for noise studies and the practical application of two-dimensional materials.
Efficient cosubstrate enzyme pairs for sequence-specific methyltransferase-directed photolabile caging of DNA
Authors: Heimes Michael , Kolmar Leonie , Brieke Clara
Published: October 2018

Efficient and selective methyltransferase-catalyzed transfer of photolabile groups onto DNA enables photoregulation of gene expression and can be performed even in the presence of AdoMet.
Compartmentalized host spaces accommodating guest aromatic molecules in a chiral way in a helix-peptide-aromatic framework
Authors: Uji Hirotaka , Ogawa Junya , Itabashi Kenji , Imai Tomoya , Kimura Shunsaku
Published: October 2018

Nanosheets with void host spaces that can accommodate aromatic groups in a right-handed helical way with long distance channels were prepared.
Inverse mean field theories
Authors: Schmitteckert Peter
Published: October 2018

In this work we discuss the extraction of mean field single particle Hamiltonians from many body wave functions of fermionic systems.
Interfacially synthesized Fe-soc-MOF nanoparticles combined with ICG for photothermal/photodynamic therapy
Authors: Cai Xuechao , Liu Bei , Pang Maolin , Lin Jun
Published: October 2018

Fe-soc-MOF@PEG-NH2-ICG was constructed as a multifunctional theranostic platform for photothermal/photodynamic therapy for the first time.
Enhancement of anion recognition exhibited by a zinc-imidazole-based ion-pair receptor composed of C–H hydrogen- and halogen-bond donor groups
Authors: Sabater Paula , Zapata Fabiola , López Bernardo , Fernández Israel , Caballero Antonio , Molina Pedro
Published: October 2018

A 2-haloimidazole derivative behaves as an anion-pair receptor in which the anion is recognised by a combination of nonconventional interactions.
Solvent-dependent transition from concerted electron–proton to proton transfer in photoinduced reactions between phenols and polypyridine Ru complexes with proton-accepting sites
Authors: Lymar Sergei V. , Ertem Mehmed Z. , Polyansky Dmitry E.
Published: October 2018

Transition from photo-induced concerted electron–proton transfer to a proton transfer is enhanced in more polar solvent.
Synthesis, growth and characterization of a new acentric 4-[4-(4-dimethylamino-phenyl)buta-1,3-dienyl]-1-methyl pyridinium p-chlorobenzenesulfonate dihydrate crystal for nonlinear optical applications
Authors: Sundaram S. John , Ramaclus Jerald V. , Antony Priya , Jaccob M. , Sagayaraj P.
Published: October 2018

A new organic crystal with a noncentrosymmetric structure is developed, and its structural, thermal, linear and nonlinear optical properties are reported.
Acetylcholinesterase biosensor modified with ATO/OMC for detecting organophosphorus pesticides
Authors: Hou Wenjie , Zhang Qianqian , Dong Haowei , Li Falan , Zhang Yanyan , Guo Yemin , Sun Xia
Published: October 2018

This work demonstrates the sensitive amperometric determination of organophosphorus pesticides (OPs) on screen-printed electrodes (SPEs) modified with antimony tin oxide-chitosan (ATO-CS) and ordered mesoporous carbon-chitosan (OMC-CS) composite nanomaterials.
Porosity- and content-controlled metal/metal oxide/metal carbide@carbon (M/MO/MC@C) composites derived from MOFs: mechanism study and application for lithium-ion batteries
Authors: Kang Min Seok , Lee Dae-Hyuk , Lee Kyung-Jae , Kim Hee Soo , Ahn Jihoon , Sung Yung-Eun , Yoo Won Cheol
Published: October 2018

Facile method for morphology-preserved transformation of MOFs to porosity and content-controlled M/MO/MC@C composites is presented.
Fabrication of sub-20 nm patterns using dopamine chemistry in self-aligned double patterning
Authors: Li Yinyong , Choi Jaewon , Sun Zhiwei , Russell Thomas P. , Carter Kenneth R.
Published: October 2018

A self-aligned double patterning approach using a dopamine chemistry-inspired coating technique has been developed for the fabrication of sub-20 nm patterns.
AFM assessing of nanomechanical fingerprints for cancer early diagnosis and classification: from single cell to tissue level
Authors: Stylianou Andreas , Lekka Malgorzata , Stylianopoulos Triantafyllos
Published: October 2018

AFM measurements could be employed to complement standard biopsy procedures, offering an objective, novel and quantitative diagnostic approach with the properties of a blind assay, allowing unbiased evaluation of the sample.
Retracted Article: Size-selected silver nanoparticles for MALDI-TOF mass spectrometry of amyloid-beta peptides
Authors: Ding Feng , Qian Yuna , Deng Zaian , Zhang Jitai , Zhou Yongchao , Yang Lan , Wang Fangyan , Wang Juping , Zhou Zhihua , Shen Jianliang
Published: October 2018

Size-selected (2–45 nm) Ag NPs for matrix assisted desorption and ionization of Aβ peptides in MALDI-TOF MS.
Sulfinates and thiocyanates triggered 6-endocyclization ofo-alkynylisocyanobenzenes
Authors: Khaikate Onnicha , Meesin Jatuporn , Pohmakotr Manat , Reutrakul Vichai , Leowanawat Pawaret , Soorukram Darunee , Kuhakarn Chutima
Published: October 2018

An efficient synthesis of 2-sulfonyl- and 2-thiocyanato-3-substituted quinolines through sequential nucleophilic addition/cyclization ofo-alkynylisocyanobenzenes is described.
Reactive cycloalkane plasticizers covalently linked to energetic polyurethane bindersviafacile control of anin situCu-free azide–alkyne 1,3-dipolar cycloaddition reaction
Authors: Ma Mingyang , Kwon Younghwan
Published: October 2018

The kinetic performance of a spacer-controlled Huisgen azide–alkyne cycloaddition reaction for alkyne-bearing reactive cycloalkane plasticizers is explored in combination with the computational protocol.
Efficient synthesis of N-butadiene substituted oxindole derivatives
Authors: Li Chao , Li Wei-Huan , Dong Lin
Published: October 2018

A novel rhodium(iii)-catalyzed amide carbonyl group directed alkenylation reaction between oxindoles and alkenes has been reported, which provides an efficient method for the synthesis of valuable and versatile functionalized N-(2E,4Z)-butadiene substituted oxindole derivatives.
Comparative thermodynamic analysis in solution of a next generation antibody mimetic to VEGF
Authors: Khalili Hanieh , Brocchini Steve , Khaw Peng Tee , Filippov Sergey K.
Published: October 2018

ITC illustrated similar binding thermodynamics for anti-VEGF IgG and FpFs. Bivalent FpFrani displayed larger enthalpy and entropy than monovalent ranibizumab.
Concentration dependence of As2S3 chalcogenide glass cluster size in amine solution
Authors: Dutta Nikita S. , Arnold Craig B.
Published: October 2018

A mechanism for cluster size determination in solution-processed chalcogenide glasses is proposed, enabling improved property control in optoelectronic device fabrication.
Pt-grown carbon nanofibers for enzymatic glutamate biosensors and assessment of their biocompatibility
Authors: Isoaho Noora , Peltola Emilia , Sainio Sami , Koskinen Jari , Laurila Tomi
Published: October 2018

Pt-grown carbon nanofibers were utilized for the fabrication of glutamate biosensors and in addition their biocompatibility was assessed.
A new approach to the synthesis of legionaminic acid analogues
Authors: Carter James R. , Kiefel Milton J.
Published: October 2018

We report the synthesis of the bacterial nonulosonic acid legionaminic acid, together with its C-7 epimer, from a common precursor derived from N-acetylneuraminic acid.
Reversibility and reactivity in an acid catalyzed cyclocondensation to give furanochromanes – a reaction at the ‘oxonium-Prins’ vs. ‘ortho-quinone methide cycloaddition’ mechanistic nexus
Authors: Nielsen Christian D.-T. , Mooij Wouter J. , Sale David , Rzepa Henry S. , Burés Jordi , Spivey Alan C.
Published: October 2018

Herein we report a combined experimental and computational investigation of the acid catalyzed cyclocondensation reaction between styrenyl homoallylic alcohols and salicylaldehyde to form furanochromanes.
Clustering of microswimmers: interplay of shape and hydrodynamics
Authors: Theers Mario , Westphal Elmar , Qi Kai , Winkler Roland G. , Gompper Gerhard
Published: October 2018

Motility-induced phase separation in systems of active self-propelled particles (puller, pusher, neutral) is strongly affected by hydrodynamic interactions—suppressed for spherical, enhanced for prolate ellipsoidal particles.
The laterally acquired GH5 ZgEngAGH5_4 from the marine bacterium Zobellia galactanivorans is dedicated to hemicellulose hydrolysis
Authors: Dorival Jonathan , Ruppert Sophie , Gunnoo Melissa , Orłowski Adam , Chapelais-Baron Maylis , Dabin Jérôme , Labourel Aurore , Thompson Damien , Michel Gurvan , Czjzek Mirjam , Genicot Sabine
Published: October 2018

Cell walls of marine macroalgae are composed of diverse polysaccharides that provide abundant carbon sources for marine heterotrophic bacteria. Among them, Zobellia galactanivorans is considered as a model for studying algae–bacteria interactions. The degradation of typical algal polysaccharides, such as agars or alginate, has been intensively studied in this model bacterium, but the catabolism of plant-like polysaccharides is essentially uncharacterized. Here, we identify a polysaccharide utilization locus in the genome of Z. galactanivorans, induced by laminarin (β-1,3-glucans), and containing a putative GH5 subfamily 4 (GH5_4) enzyme, currently annotated as a endoglucanase (ZgEngAGH5_4). A phylogenetic analysis indicates that ZgEngAGH5_4 was laterally acquired from an ancestral Actinobacteria. We performed the biochemical and structural characterization of ZgEngAGH5_4 and demonstrated that this GH5 is, in fact, an endo-β-glucanase, most active on mixed-linked glucan (MLG). Although ZgEngAGH5_4 and GH16 lichenases both hydrolyze MLG, these two types of enzymes release different series of oligosaccharides. Structural analyses of ZgEngAGH5_4 reveal that all the amino acid residues involved in the catalytic triad and in the negative glucose-binding subsites are conserved, when compared with the closest relative, the cellulase EngD from Clostridium cellulovorans, and some other GH5s. In contrast, the positive glucose-binding subsites of ZgEngAGH5_4 are different and this could explain the preference for MLG, with respect to cellulose or laminarin. Molecular dynamics computer simulations using different hexaoses reveal that the specificity for MLG occurs through the +1 and +2 subsites of the binding pocket that display the most important differences when compared with the structures of other GH5_4 enzymes.
Comparison of efficiency and safety of rivaroxaban, apixaban and enoxaparin for thromboprophylaxis after arthroplastic surgery: a meta-analysis
Authors: Yu Zhi , Shan Ping , Yang Xiaoxia , Lou Xin-jiang
Published: October 2018

Objective: To compare the efficacy and safety of rivaroxaban, apixaban and enoxaparin for thromboprophylaxis after arthroplastic surgery. Methods: We conducted a meta-analysis containing a wide range of randomized controlled trials about efficiency and safety of rivaroxaban, apixaban and enoxaparin for thromboprophylaxis after arthroplastic surgery in the recent decade from January 2006 to June 2018. The present study separately analyzed the following key components: the different efficiency and safety for rivaroxaban and enoxaparin; apixaban and enoxaparin; and enoxaparin and other new developed anticoagulants. Results: Sixteen studies containing 58885 patients were included. In results of efficacy outcomes, total events occurred in 4.89% patients of rivaroxaban group and 9.55% patients of the control group; however, no significant difference was observed in apixaban groups of their efficacy outcomes. Primary events didn’t show significant difference when comparing apixaban with the control or comparing enoxaparin with the control. In analysis of safety outcomes, bleeding events occurred in 3.41% patients of rivaroxaban group compared with 2.84% patients of the control groups; bleeding events in apixaban groups were 4.09% compared with the control groups 4.64%. Bleeding events occurred in 3.51% patients of enoxaparin group, slightly lower than 5.82% of the control group. Conclusion: Direct oral anticoagulant, rivaroxaban might have better efficacy outcomes in thromboprophylaxis after arthroplastic surgery; however, apixaban showed no significantly different efficacy outcomes compared with enoxaparin, and enoxaparin may have equal or even better safety outcomes compared with direct oral anticoagulants.
Association between CTSS gene polymorphism and the risk of acute atherosclerotic cerebral infarction in Chinese population: a case–control study
Authors: Luo Lian , Zhu Mingli , Zhou Jiajun
Published: October 2018

Objective: To investigate the association between the gene polymorphisms of rs774320676, rs768437857, rs928508030, and rs2275235 loci of Cathepsin S (CTSS) and risk of acute atherosclerotic cerebral infarction. Methods: A total of 315 patients with acute atherosclerotic cerebral infarction (study group) and 220 healthy subjects (control group) were enrolled in the present study. The genetic polymorphism of rs774320676, rs768437857, rs928508030, and rs2275235 loci of CTSS of subjects was analyzed by PCR-Sanger sequencing. Results: The proportion of carriers with mutant T allele at rs774320676 locus and mutant G allele at rs928508030 locus of CTSS in study group was significantly higher than the proportion in control group (P=0.000, adjusted odds ratio (OR) = 1.332, 95% confidence interval (CI) = 1.200–1.460; P<0.001, adjusted OR = 1.185, 95% CI = 1.055–1.314; P=0.002). The T allele at rs774320676 locus and the G allele at rs928508030 locus of CTSS were independent risk factors for acute atherosclerotic cerebral infarction (OR = 2.534, 95% CI = 1.020–4.652, P=0.006; OR = 2.016, 95% CI = 1.031–4.385, P=0.031). Conclusion: The single nucleotide polymorphisms (SNPs) of rs774320676 and rs928508030 of CTSS gene were related with risk for acute atherosclerotic cerebral infarction. The T allele at rs774320676 locus and G allele at rs928508030 locus of CTSS were genetic susceptibility genes of acute atherosclerotic cerebral infarction.