bluuebunny/crossref_metadata_2025 huggingface dataset:
Lensless Tomographic Imaging of Near Surface Structures of Frozen Hydrated Malaria-Infected Human Erythrocytes by Coherent X-Ray Diffraction Microscopy
Authors: Frank Viktoria , Chushkin Yuriy , Fröhlich Benjamin , Abuillan Wasim , Rieger Harden , Becker Alexandra S. , Yamamoto Akihisa , Rossetti Fernanda F. , Kaufmann Stefan , Lanzer Michael , Zontone Federico , Tanaka Motomu
Published: October 2017

Lensless, coherent X-ray diffraction microscopy has been drawing considerable attentions for tomographic imaging of whole human cells. In this study, we performed cryogenic coherent X-ray diffraction imaging of human erythrocytes with and without malaria infection. To shed light on structural features near the surface, “ghost cells” were prepared by the removal of cytoplasm. From two-dimensional images, we found that the surface of erythrocytes after 32 h of infection became much rougher compared to that of healthy, uninfected erythrocytes. The Gaussian roughness of an infected erythrocyte surface (69 nm) is about two times larger than that of an uninfected one (31 nm), reflecting the formation of protein knobs on infected erythrocyte surfaces. Three-dimensional tomography further enables to obtain images of the whole cells with no remarkable radiation damage, whose accuracy was estimated using phase retrieval transfer functions to be as good as 64 nm for uninfected and 80 nm for infected erythrocytes, respectively. Future improvements in phase retrieval algorithm, increase in degree of coherence, and higher flux in combination with complementary X-ray fluorescence are necessary to gain both structural and chemical details of mesoscopic architectures, such as cytoskeletons, membraneous structures, and protein complexes, in frozen hydrated human cells, especially under diseased states.
A single episode of high intensity sound inhibits long-term potentiation in the hippocampus of rats
Authors: de Deus J. L. , Cunha A. O. S. , Terzian A. L. , Resstel L. B. , Elias L. L. K. , Antunes-Rodrigues J. , Almeida S. S. , Leão R. M.
Published: October 2017

Exposure to loud sounds has become increasingly common. The most common consequences of loud sound exposure are deafness and tinnitus, but emotional and cognitive problems are also associated with loud sound exposure. Loud sounds can activate the hipothalamic-pituitary-adrenal axis resulting in the secretion of corticosterone, which affects hippocampal synaptic plasticity. Previously we have shown that long-term exposure to short episodes of high intensity sound inhibited hippocampal long-term potentiation (LTP) without affecting spatial learning and memory. Here we aimed to study the impact of short term loud sound exposure on hippocampal synaptic plasticity and function. We found that a single minute of 110 dB sound inhibits hippocampal Schaffer-CA1 LTP for 24 hours. This effect did not occur with an 80-dB sound exposure, was not correlated with corticosterone secretion and was also observed in the perforant-dentate gyrus synapse. We found that despite the deficit in the LTP these animals presented normal spatial learning and memory and fear conditioning. We conclude that a single episode of high-intensity sound impairs hippocampal LTP, without impairing memory and learning. Our results show that the hippocampus is very responsive to loud sounds which can have a potential, but not yet identified, impact on its function.
A data-driven statistical model that estimates measurement uncertainty improves interpretation of ADC reproducibility: a multi-site study of liver metastases
Authors: Pathak Ryan , Ragheb Hossein , Thacker Neil A. , Morris David M. , Amiri Houshang , Kuijer Joost , deSouza Nandita M. , Heerschap Arend , Jackson Alan
Published: October 2017

Apparent Diffusion Coefficient (ADC) is a potential quantitative imaging biomarker for tumour cell density and is widely used to detect early treatment changes in cancer therapy. We propose a strategy to improve confidence in the interpretation of measured changes in ADC using a data-driven model that describes sources of measurement error. Observed ADC is then standardised against this estimation of uncertainty for any given measurement. 20 patients were recruited prospectively and equitably across 4 sites, and scanned twice (test-retest) within 7 days. Repeatability measurements of defined regions (ROIs) of tumour and normal tissue were quantified as percentage change in mean ADC (test vs. re-test) and then standardised against an estimation of uncertainty. Multi-site reproducibility, (quantified as width of the 95% confidence bound between the lower confidence interval and higher confidence interval for all repeatability measurements), was compared before and after standardisation to the model. The 95% confidence interval width used to determine a statistically significant change reduced from 21.1 to 2.7% after standardisation. Small tumour volumes and respiratory motion were found to be important contributors to poor reproducibility. A look up chart has been provided for investigators who would like to estimate uncertainty from statistical error on individual ADC measurements.
Orbital-dependent charge dynamics in MnP revealed by optical study
Authors: Zheng P. , Xu Y. J. , Wu W. , Xu G. , Lv J. L. , Lin F. K. , Wang P. , Yang Yi-feng , Luo J. L.
Published: October 2017

Unconventional superconductivity often emerges at the border of long-range magnetic orders. Understanding the low-energy charge dynamics may provide crucial information on the formation of superconductivity. Here we report the unpolarized/polarized optical conductivity study of high quality MnP single crystals at ambient pressure. Our data reveal two types of charge carriers with very different lifetimes. In combination with the first-principles calculations, we show that the short-lifetime carriers have flat Fermi sheets which become gapped in the helimagnetic phase, causing a dramatic change in the low-frequency optical spectra, while the long-lifetime carriers are anisotropic three-dimensional like which are little affected by the magnetic transitions and provide major contributions to the transport properties. This orbital-dependent charge dynamics originates from the special crystal structure of MnP and may have an influence on the unconventional superconductivity and its interplay with helimagnetism at high pressures.
Pearls in running drops on an inclined glass substrate excited by Lamb waves
Authors: Liang Wei , Tietze Sabrina
Published: October 2017

We demonstrate that pearling droplets will be released from droplets as they sliding down a partially wetting glass plate excited by Lamb waves. During the movement, we find that the transitions at generating pearling are independent of the drop size and depend only on a critical capillary number Ca. Further up, the position of the pearls must be at or around the droplet’s advancing or receding end of the initial state.
Liposome-encapsulated plasmid DNA of telomerase-specific oncolytic adenovirus with stealth effect on the immune system
Authors: Aoyama Katsuyuki , Kuroda Shinji , Morihiro Toshiaki , Kanaya Nobuhiko , Kubota Tetsushi , Kakiuchi Yoshihiko , Kikuchi Satoru , Nishizaki Masahiko , Kagawa Shunsuke , Tazawa Hiroshi , Fujiwara Toshiyoshi
Published: October 2017

Oncolytic virotherapy has the disadvantage of being unsuitable for systemic delivery due to immune elimination. Liposomal encapsulation is well-recognized to reduce immune elimination and enhance the stability of drugs in the bloodstream. In the present study, the potential of liposome-encapsulated plasmid DNA of telomerase-specific oncolytic adenovirus (TelomeScan) expressing GFP (Lipo-pTS) as an oncolytic adenoviral agent suitable for systemic delivery was investigated. Lipo-pTS, which has a diameter of 40–50 nm, showed potent antitumor effects on HCT116 colon carcinoma cells in vitro and in vivo. Tumor selectivity of Lipo-pTS was independent of coxsackie and adenovirus receptor (CAR). Importantly, Lipo-pTS reduced production of adenovirus-neutralizing antibodies (AdNAbs) after intravenous administration into immune-competent mice compared to TelomeScan, and even in the presence of AdNAbs, Lipo-pTS maintained strong cytotoxicity. In conclusion, Lipo-pTS has the potential to become an oncolytic adenoviral agent suitable for systemic delivery with the characteristics of CAR-independent antitumor activity and a stealth effect on the immune system.
Correction: Corrigendum: Epigenomic Reprogramming of Adult Cardiomyocyte-Derived Cardiac Progenitor Cells
Authors: Zhang Yiqiang , Zhong Jiang F. , Qiu Hongyu , MacLellan W. Robb , Marbán Eduardo , Wang Charles
Published: October 2017

Scientific Reports 5: Article number: 17686; published online: 14 December 2015; updated: 20 October 2017. This Article contains errors in the Material and Methods section under the subheading ‘DNA methylation analysis’. “Genomic DNA was isolated from population adult cardiomyocytes and population mCPCs using Qiagen AllPrep DNA/RNA Micro Kit.
Silylene-assisted hydride transfer to CO2 and CS2 at a [P2Si]Ru pincer-type complex
Authors: Whited Matthew T. , Zhang Jia , Ma Senjie , Nguyen Binh D. , Janzen Daron E.
Published: October 2017

The synthesis and characterization of base-stabilized and base-free pincer-type bis(phosphine)/silylene [P2Si]Ru complexes are reported. The base-free complex performs cooperative, silylene-assisted hydride transfer to CO2 and CS2.
Insight into the structural and electronic nature of chemically exfoliated molybdenum disulfide nanosheets in aqueous dispersions
Authors: Nurdiwijayanto Leanddas , Ma Renzhi , Sakai Nobuyuki , Sasaki Takayoshi
Published: October 2017

Chemically exfoliated MoS2nanosheets undergo a reoxidation process when storing the dispersion in ambient air, the chemical nature of which can be monitored from the structural evolution of the restacked nanosheets.
Three-dimensional morphometry of collagen fibrils in membranous bone
Authors: Hashimoto Mana , Nagaoka Noriyuki , Tabata Kaori , Tanaka Tomoyo , Osumi Ryuta , Odagaki Naoya , Hara Toru , Kamioka Hiroshi
Published: October 2017

The collagen network of chick embryonic calvaria in membranous bone three-dimensionally using orthogonally arranged FIB-SEM.
Tomographic magnetic particle imaging of cancer targeted nanoparticles
Authors: Arami Hamed , Teeman Eric , Troksa Alyssa , Bradshaw Haydin , Saatchi Katayoun , Tomitaka Asahi , Gambhir Sanjiv Sam , Häfeli Urs O. , Liggitt Denny , Krishnan Kannan M.
Published: October 2017

The first study of Magnetic Particle Imaging (MPI) for tomographic imaging of cancer targeted iron oxide nanoparticles.
Chip-integrated plasmonic cavity-enhanced single nitrogen-vacancy center emission
Authors: Siampour Hamidreza , Kumar Shailesh , Bozhevolnyi Sergey I.
Published: October 2017

We demonstrate a chip-integrated cavity for the selective enhancement of single photon emission from a diamond color center coupled to a plasmonic waveguide mode.
Unique hybrid Ni2P/MoO2@MoS2 nanomaterials as bifunctional non-noble-metal electro-catalysts for water splitting
Authors: Wang Yang , Williams Timothy , Gengenbach Thomas , Kong Biao , Zhao Dongyuan , Wang Huanting , Selomulya Cordelia
Published: October 2017

We successfully synthesized a novel electro-catalyst with a unique structure of Ni2P nanoparticles decorating the surface of MoO2@MoS2 sub-microwires on titanium foil (denoted as NiMoO-SP/Ti) via a temperature-programmed sulfuration-phosphorization from its NiMoO4 precursor.
Post-polymerization modification of styrene–maleic anhydride copolymer brushes
Authors: Guo Wei , Xiong Li , Reese Cassandra M. , Amato Douglas V. , Thompson Brittany J. , Logan Phillip K. , Patton Derek L.
Published: October 2017

Amine-anhydride reactions on polymer brushes provide a modular post-modification strategy to functional surfaces.
Study on the properties of Pb–Co3O4–PbO2 composite inert anodes prepared by vacuum hot pressing technique
Authors: Zhang Jingshi , Xu Ruidong , Yu Bohao , He Yunlong , Li Yiyang , Qin Ziyang
Published: October 2017

In this research, the Pb–Co3O4–PbO2 composite inert anodes were prepared by vacuum hot pressing technique, which showed good electrochemical performance.
Preparation of a graphene/silver hybrid membrane as a new nanofiltration membrane
Authors: Liu Gui-fei , Huang Lin-jun , Wang Yan-xin , Tang Jian-guo , Wang Yao , Cheng Meng-meng , Zhang Yang , Kipper Matt J. , Belfiore Laurence A. , Ranil Wickramasinghe S.
Published: October 2017

In this study, we describe the preparation, characterization, water flux and rejection performance of a composite membrane formed from reduced graphene oxide (RGO) and silver nanoparticles (AgNP) via a rapid thermal reduction method.
Regular conjugated D–A copolymer containing two benzotriazole and benzothiadiazole acceptors and dithienosilole donor units for photovoltaic application
Authors: Keshtov M. L. , Kuklin S. A. , Khokhlov A. R. , Konstantinov I. O. , Nekrasova N. V. , Xie Zhi-yuan , Sharma Ganesh D.
Published: October 2017

Synthesized a D–A copolymer with low bandgap of 1.53 eV, and used as donor for PSCs. The over PCE of the PSC is reached 8.91% with a low voltage loss of 0.59 eV.
Side chain length impacting thermal transitions and water uptake of acrylate–maleimide copolymers with pendent catechols
Authors: Bartucci M. A. , Napadensky E. , Lenhart J. L. , Orlicki J. A.
Published: October 2017

Significant moisture uptake was observed for a family of catechol side-chain poly(alkyl acrylate-maleimide)s (PAMs) intended to probe the effects of Tg and polarity.
Qualitative and quantitative determination of coumarin using surface-enhanced Raman spectroscopy coupled with intelligent multivariate analysis
Authors: Huang J. , Liang P. , Xu J. , Wu Y. , Shen W. , Xu B. , Zhang D. , Xia J. , Zhuang S.
Published: October 2017

Coumarin is harmful to health but still used in cosmetics, tobacco, or illegally added into food as a spice in trace amounts so that it is exceedingly difficult to be determined accurately.
An ambipolar 3,3′-dimethyl-9,9′-bianthracene derivative as a blue host material for high-performance OLEDs
Authors: Li Zhanfeng , Wang Xiangkun , Lv Xiang , Si Changfeng , Wei Bin , Wang Hua , Hao Yuying
Published: October 2017

A new ambipolar 3,3′-dimethyl-9,9′-bianthracene derivative (MBAn-(4)-tBu) was designed as a deep blue fluorophore and blue host material for high-performance OLEDs.
Colorimetric detection of epinephrine using an optimized paper-based aptasensor
Authors: Saraf Nileshi , Bosak Alexander , Willenberg Alicia , Das Soumen , Willenberg Bradley Jay , Seal Sudipta
Published: October 2017

Morphological modification of gold nanoparticles to obtain a highly efficient paper based sensor for colorimetric detection of epinephrine (LOD – Limit of Detection).
Enhanced performance of perovskite solar cells by strengthening a self-embedded solvent annealing effect in perovskite precursor films
Authors: Cao Xiaobing , Zhi Lili , Li Yahui , Cui Xian , Ci Lijie , Ding Kongxian , Wei Jinquan
Published: October 2017

Smooth perovskite films with large grains are fabricated by strengthening the self-embedded solvent annealing effect in the perovskite precursor film via pre-depositing a protective layer.
Biomimetic inorganic camouflage circumvents antibody-dependent enhancement of infection
Authors: Wang Xiaoyu , Deng Yong-Qiang , Yang Dong , Xiao Yun , Zhao Hui , Nian Qing-Gong , Xu Xurong , Li Xiao-Feng , Tang Ruikang , Qin Cheng-Feng
Published: October 2017

A biomimetic surface camouflage is applied to abrogate antibody-dependent enhancement of DENV infection, providing a flexible tactic for immune evasion.
A label-free and enzyme-free platform with a visible output for constructing versatile logic gates using caged G-quadruplex as the signal transducer
Authors: Chen Junhua , Pan Jiafeng , Chen Shu
Published: October 2017

A complete set of elementary logic gates and two multilevel circuits have been constructed on a label-free and enzyme-free biocomputing platform using caged G-quadruplex as the signal transducer.
Tailorable coaxial carbon nanocables with high storage capabilities
Authors: Guan Guozhen , Deng Jue , Ren Jing , Pan Zhiyong , Zhuang Wen , He Sisi , Wang Bingjie , Che Renchao , Peng Huisheng
Published: October 2017

A new family of coaxial carbon nanocables is designed with the ability to be tailored into desired diameters, lengths and components through a low-cost, high-efficiency slicing process. These nanocables are promising for the storage of materials and ions, and their incorporation into lithium-ion batteries demonstrates their high specific capacities.
Disrupting environmental crime at the local level: an operational perspective
Authors: Barrett Stoyan , White Rob
Published: October 2017

The multi-dimensional nature of environmental crimes requires innovative means to combat them. This paper examines the nature and dynamics of one particular collaborative law enforcement approach directed at environmental crime. While much interest in multi-agency and multi-pronged approaches has been generated in recent years, especially as this pertains to environmental crime at the international and regional levels, this paper provides a detailed description of how this can occur at the local level. Based on a case study of nefarious activities relating to illegal waste management in Durham and surrounding areas (located in the North East of England), the paper emphasises the importance of ‘disruption’ as an important operational concept, and how inter-agency cooperation under skilled leadership and with clear purpose can lead to tangible enforcement outcomes. As the article demonstrates, particular agencies on their own have limited impact and do not always address the issue of how to take away an organised criminal group’s ability to function. By contrast, multi-agency work enables authorities to work in a united front and thus to succeed in disrupting criminal activities causing environmental harm.
Pulsed magnetic flux leakage method for hairline crack detection and characterization
Authors: Okolo Chukwunonso K. , Meydan Turgut
Published: October 2017

The Magnetic Flux leakage (MFL) method is a well-established branch of electromagnetic Non-Destructive Testing (NDT), extensively used for evaluating defects both on the surface and far-surface of pipeline structures. However the conventional techniques are not capable of estimating their approximate size, location and orientation, hence an additional transducer is required to provide the extra information needed. This research is aimed at solving the inevitable problem of granular bond separation which occurs during manufacturing, leaving pipeline structures with miniature cracks. It reports on a quantitative approach based on the Pulsed Magnetic Flux Leakage (PMFL) method, for the detection and characterization of the signals produced by tangentially oriented rectangular surface and far-surface hairline cracks. This was achieved through visualization and 3D imaging of the leakage field. The investigation compared finite element numerical simulation with experimental data. Experiments were carried out using a 10mm thick low carbon steel plate containing artificial hairline cracks with various depth sizes, and different features were extracted from the transient signal. The influence of sensor lift-off and pulse width variation on the magnetic field distribution which affects the detection capability of various hairline cracks located at different depths in the specimen is explored. The findings show that the proposed technique can be used to classify both surface and far-surface hairline cracks and can form the basis for an enhanced hairline crack detection and characterization for pipeline health monitoring.
Experimental study on charge/discharge characteristics of zinc-nickel single-flow battery
Authors: Xiao Min , Liao Peng , Yao Shouguang , Cheng Jie , Cai Wenwen
Published: October 2017

The terminal voltage, coulombic efficiency, voltage efficiency, and energy efficiency of a zinc-nickel single-flow battery (ZNB) during charging/discharging were studied. The effect of the charge/discharge current on these parameters and the effect of the ambient temperature on the battery performance were investigated. The experimental results show that increasing the charge/discharge current reduces the charge/discharge time, self-discharge, and occurrence of side reactions, thus increasing the coulombic efficiency of the battery; however, this also reduces the voltage efficiency and energy efficiency of the battery. With the temperature decreasing from 30 °C to −15 °C, the charge/discharge capacity and energy and the energy efficiency of ZNB decrease, while the coulombic efficiency gradually increases with decreasing temperature below 0 °C.
Retro-reflective metasurfaces for backscattering enhancement under oblique incidence
Authors: Jia Yuxiang , Wang Jiafu , Li Yongfeng , Pang Yongqiang , Yang Jie , Fan Ya , Qu Shaobo
Published: October 2017

In this letter, we propose the design of retro-reflective metasurfaces for enhancing backscattering under oblique incidence. Through reflective phase profile design along the surface, an equivalent wave-vector can be generated, with double magnitude but opposite direction to the parallel component k|| of the wave-vector k0 of incident waves. Due to this artificial parallel wave-vector, the main lobe of reflective waves can be reoriented backwards. As an example, we demonstrate an X-band retro-reflective metasurface that can operate effectively under oblique incidence θ=20°. A modified metallic square loop structure is used to achieve the required phase profile under oblique incidence. Through the phase gradient design, the metasurface can reflect incident waves backwards at 9.8GHz under transverse electric (TE) polarizations. A prototype was fabricated and measured. Both the simulation and experiment results verify the good retro-reflection performance of the metasurface.
Macro-level modeling of solid oxide fuel cells, approaches, and assumptions revisited
Authors: Zabihian Farshid , Fung Alan S.
Published: October 2017

Fuel cells are considered as major components of the future energy infrastructure in many applications due to their high efficiency, simplicity of operation, scalability, and low pollution. The inherent complexity of the internal operation of fuel cells and limitations in the experimental studies on fuel cells make the numerical simulation a vital tool for the fuel cell research and development. This field has experienced remarkable advancements in the past three decades. A wide variety of modeling approaches have been introduced in the literature. Many mathematical formulations have been employed for the macro-level modeling of solid oxide fuel cells (SOFCs). In this paper, the common fundamental bases behind different modeling approaches are identified and presented. Similarly, many assumptions have been used to simplify the modeling process. Some of the most common assumptions for modeling SOFCs are identified, and their appropriateness is reevaluated in the light of recent advancements in the experimental and numerical findings. It was found that while 0-D models cannot predict the internal dynamics of SOFCs, they are very useful for applications where the objective is to study the interaction among system components, such as SOFC hybrid plants. While several types of fuel reformers have been proposed, the identification of the most efficient technology at the operating conditions of SOFCs, particularly small-size applications, requires more research. Similarly, more research is needed to determine if the direct electrochemical reaction of carbon monoxide can be ignored in SOFC models. On the other hand, it has been experimentally proven that internal fuel reformers are thermally self-sufficient. While the assumption that the steam reforming reaction reaches chemical equilibrium has been supported by several experimental studies, the similar assumption for the water-gas shift reaction is not proven, rather there are some strong evidences against its validity. It is also proven that the methane reforming reaction reaches equilibrium when all the inlet methane moles are consumed. The presented assumptions, mathematical formulations, model constants, system operating parameters, and model validation can assist researchers in making informed decisions on their choices for future SOFC models. Also, it identifies the areas where more research, particularly experimental research, is needed to verify the validity of the assumptions.
Polarity tuning of spin-orbit-induced spin splitting in two-dimensional transition metal dichalcogenides
Authors: Absor Moh. Adhib Ulil , Santoso Iman , Harsojo  , Abraha Kamsul , Kotaka Hiroki , Ishii Fumiyuki , Saito Mineo
Published: October 2017

The established spin splitting in a monolayer (ML) of transition metal dichalcogenides (TMDs) induced by inversion symmetry breaking is dictated by mirror symmetry operations to exhibit the fully out-of-plane direction of spin polarization. Through first-principles density functional theory calculations, we show that polarity inducing mirror symmetry breaking leads to sizable spin splitting having in-plane spin polarization. These splittings are effectively controlled by tuning the polarity using biaxial strain. Furthermore, admixtures between the out-of-plane and in-plane spin-polarized states in the strained polar systems are identified, which are expected to influence the spin relaxation through the Dyakonov–Perel mechanism. Our study clarified that polarity plays an important role in controlling the spin splitting and spin relaxation in the TMD ML, which is useful for designing future spintronic devices.
From manipulation to social interaction
Authors: Ponsford Dan
Published: October 2017

This paper is about constructional change that is brought about through change in non-linguistic practice. The English construction of interest is one that speakers use to initiate bets with their addressees. Its verb islay, its subject is the speaker, and its direct object is the stake the speaker proposes to risk. It is argued that the motivation for the use oflaycomes partly from the practice of laying down stakes when making bets. However, it is shown that over the seventeenth to the nineteenth centuries this practice declines, weakening the basis for a physical interpretation and leading hearers to attend instead to the speaker-addressee relation. Concurrently, this relation is increasingly expressed through the use of a dative argument. This development is discussed in relation toAriel et al.’s (2015)account of added datives.
Head-Driven Phrase Structure Grammar, Sign-Based Construction Grammar, and Fluid Construction Grammar
Authors: Müller Stefan
Published: October 2017

Van Trijp (2013,2014) claims that Sign-Based Construction Grammar (SBCG) and Head-Driven Phrase Structure Grammar (HPSG) are fundamentally different from Fluid Construction Grammar (FCG). He claims that the former approaches are generative ones while the latter is a cognitive-functional one. I argue that it is not legitimate to draw these distinctions on the basis of what is done in FCG. Van Trijp claims that there are differences in the scientific model, the linguistic approach, formalization, the way constructions are seen, and in terms of processing. This paper discusses all these alleged differences. Van Trijp also claims that his cognitive-functional approach is superior in terms of completeness, explanatory adequacy, and theoretical parsimony. In order to facilitate a discussion and comparison, I introduce the reader to basic assumptions made in FCG and the analyses suggested by Van Trijp: I first deal with the representations that are used in FCG, talk about argument structure constructions, the combination operations fusion and merging that are used in FCG, I than discuss the analysis of nonlocal dependencies and show that the suggested FCG analysis is not explanatorily adequate since it is not descriptively adequate and that a full formalization of approaches with discontinuous constituents is not more parsimonious than existing HPSG analyses either. After the discussion of specific analyses, I then provide a detailed comparison of FCG and SBCG/HPSG and discuss questions like the competence/performance distinction, mathematical formalization vs. computer implementation, fuzziness and fluidity in grammars, and permissiveness of theories. I conclude that HPSG, SBCG, and FCG belong to the same family of theories and that all claims to the contrary are unjustified.
LncRNA PVT1 predicts prognosis and regulates tumor growth in prostate cancer
Authors: Yang Jin , Li Cuirong , Mudd Ashley , Gu Xiao
Published: October 2017

Long non-coding RNA (lncRNA) plasmacytoma variant translocation 1(PVT1) was aberrantly expressed in various cancers and is associated with tumor prognosis. Here, we aim to investigate its function in prostate cancer. Small interfering RNA against PVT1 was transfected into prostate cancer cell lines and cell growth and apoptosis were analyzed. Our results showed that PVT1 was overexpressed in prostate cancer tissues and cells. Higher levels of PVT1 indicated poorer overall survival and disease-free survival. A significant association was found between PVT1 expression and tumor stage. Besides, PVT1 knockdown significantly inhibited prostate cancer growth in vivo and in vitro and promoted cell apoptosis. PVT1 knockdown also significantly upregulated the expression of cleaved caspase-3 and cleaved caspase-9, but downregulated the expression of c-Myc in prostate cancer cell lines. Our results suggest that PVT1 played an oncogenic role in prostate cancer and could be used as a potential biomarker for diagnosis of prostate cancer.
New triterpene saponins from the roots of Acacia macrostachya (Mimosaceae)
Authors: Tchoukoua Abdou , Tabopda Turibio Kuiate , Usukhbayar Narandulam , Kimura Ken-ichi , Kwon Eunsang , Momma Hiroyuki , Koseki Takuya , Shiono Yoshihito , Ngadjui Bonaventure Tchaleu
Published: October 2017

Four new oleanane-type saponins, macrostachyaosides A, B, C, and D (1–4) were isolated from the roots of Acacia macrostachya. Their structures were elucidated on the basis of extensive 1D- and 2D-NMR data and HR-ESI-MS analyses. At concentrations of 100 μM of each compounds, none of the tested compounds caused a significant growth reduction against HL60 cells.
Chromatin accessibility prediction via a hybrid deep convolutional neural network
Authors: Liu Qiao , Xia Fei , Yin Qijin , Jiang Rui
Published: October 2017

Motivation

A majority of known genetic variants associated with human-inherited diseases lie in non-coding regions that lack adequate interpretation, making it indispensable to systematically discover functional sites at the whole genome level and precisely decipher their implications in a comprehensive manner. Although computational approaches have been complementing high-throughput biological experiments towards the annotation of the human genome, it still remains a big challenge to accurately annotate regulatory elements in the context of a specific cell type via automatic learning of the DNA sequence code from large-scale sequencing data. Indeed, the development of an accurate and interpretable model to learn the DNA sequence signature and further enable the identification of causative genetic variants has become essential in both genomic and genetic studies.

Results

We proposed Deopen, a hybrid framework mainly based on a deep convolutional neural network, to automatically learn the regulatory code of DNA sequences and predict chromatin accessibility. In a series of comparison with existing methods, we show the superior performance of our model in not only the classification of accessible regions against background sequences sampled at random, but also the regression of DNase-seq signals. Besides, we further visualize the convolutional kernels and show the match of identified sequence signatures and known motifs. We finally demonstrate the sensitivity of our model in finding causative noncoding variants in the analysis of a breast cancer dataset. We expect to see wide applications of Deopen with either public or in-house chromatin accessibility data in the annotation of the human genome and the identification of non-coding variants associated with diseases.

Availability and implementation

Deopen is freely available at https://github.com/kimmo1019/Deopen.

Supplementary information

Supplementary data are available at Bioinformatics online.
Packing Curves on Surfaces with Few Intersections
Authors: Aougab Tarik , Biringer Ian , Gaster Jonah
Published: October 2017

Przytycki has shown that the size $\mathcal{N}_{k}(S)$ of a maximal collection of simple closed curves that pairwise intersect at most $k$ times on a topological surface $S$ grows at most as $|\chi(S)|^{k^{2}+k+1}$. In this article, we narrow Przytycki’s bounds, obtaining \[ \mathcal{N}_{k}(S) =O \left( \frac{ |\chi|^{3k}}{ ( \log |\chi| )^2 } \right)\!. \] In particular, the size of a maximal 1-system grows sub-cubically in $|\chi(S)|$. The proof uses a circle packing argument of Aougab and Souto and a bound for the number of curves of length at most $L$ on a hyperbolic surface. When the genus $g$ is fixed and the number of punctures $n$ grows, we use a different argument to show \[ \mathcal{N}_{k}(S) \leq O(n^{2k+2}). \] This may be improved when $k=2$, and we obtain the sharp estimate $\mathcal{N}_2(S)=\Theta(n^3)$.
Former Work Life and People With Dementia
Authors: Nordtug Bente , Torvik Karin , Brataas Hildfrid V. , Holen Are , Knizek Birthe Loa
Published: October 2017

Twelve persons with dementia were interviewed about their former work lives. Their motivation for choosing their past work was influenced by values of their contemporary culture. Those who had come to terms with their illness had positive feelings about their past contributions in their former paid work. However, they often felt that unpaid work was taken for granted and not fully recognized by family or society. Some wrestled with accepting their illness; they were grieving their losses, regardless of former success. Caregivers may use parts of work narratives to elevate the self-esteem and quality of life of persons with dementia.
Thermal Ultra Short Photodynamic Therapy: Heating Fibroblasts During Sub–30-Minute Incubation of 5-Aminolevulinic Acid Increases Photodynamic Therapy–Induced Cell Death
Authors: Koo Eugene , Austin Evan , Mamalis Andrew , Jagdeo Jared
Published: October 2017

BACKGROUND

Actinic keratoses (AKs) prevalence was estimated at 39.5 million Americans in 2004, and the cost to treat AKs that year was approximately 1 billion dollars. Photodynamic therapy (PDT) is an FDA-approved therapy for the treatment of AK. Recent studies have focused on reducing PDT treatment time while maintaining efficacy.

OBJECTIVE

To investigate the use of thermal modulation to improve the efficacy of ultra short aminolevulinic acid (ALA) incubation PDT.

MATERIALS AND METHODS

Human dermal fibroblasts (HDFs) were incubated for 10, 15, or 20 minutes with 0.5-mM ALA at various temperatures (21, 24, 27, 30, 33, 36, 39, and 42°C). After ALA incubation, samples were treated for 1,000 seconds with blue light (417 ± 5 nm) resulting in a fluence of 10 J/cm2. Samples were collected and stained for apoptosis/necrosis with annexin-V and 7-aminoactinomycin D (7-AAD), then analyzed by flow cytometry.

RESULTS

Human dermal fibroblast treated with 10-minute ALA-PDT had no statistically significant changes in apoptosis at all temperatures. Human dermal fibroblast treated with 15- or 20-minute ALA-PDT had statistically significant increases in apoptosis at 39 and 42°C (p < .05).

CONCLUSION

These results suggest the use of thermal modulation may improve ultra short ALA incubation PDT efficacy.
Comparison of Moderate and High Energy of a Nano-Fractional Radiofrequency Treatment on a Photoaging Hairless Mice Model
Authors: Sun Wenjia , Zhang Chengfeng , Zhao Juemin , Wu Jiaqiang , Xiang Leihong
Published: October 2017

BACKGROUND

Fractional radiofrequency (FRF) has been widely used in skin rejuvenation. To explore optimal settings, it is important to compare different treatment parameters.

OBJECTIVE

This study was designed to compare the effect of moderate-energy and high-energy FRF treatment on a hairless mice model.

METHODS

Fifteen photoaged hairless mice were assigned to 3 groups: control, moderate energy, and high energy. Two treatment sessions (T × 1 and T × 2) were performed at 1-month interval. Transepidermal water loss was measured at baseline, immediately, 1, 2, and 4 weeks after T × 1. Skin samples were harvested before each treatment, 1 and 2 months after T × 2. Neocollagenesis was evaluated by hematoxylin and eosin staining, Masson staining, and immunohistochemistry analysis.

RESULTS

Transepidermal water loss of high-energy group was significantly higher than the moderate-energy group (p = .008) immediately after T × 1. Remarkable fibroblast proliferation was observed at 1 month after T × 1, followed by significant dermal thickening, and increase of Type I collagen and Type III collagen. There was no significant difference between 2 energy groups in fibroblast proliferation, dermal thickness, and collagen density.

CONCLUSION

The effect of moderate-energy treatment was comparable with that of high energy in neocollagenesis, whereas moderate energy yielded less damage to skin barrier function.
Bacterial Keratitis: Isolated Organisms and Antibiotic Resistance Patterns in San Francisco
Authors: Peng Michelle Y. , Cevallos Vicky , McLeod Stephen D. , Lietman Thomas M. , Rose-Nussbaumer Jennifer
Published: October 2017

Purpose:

Understanding the spectrum of pathogens in a given geographic region is important when deciding on empiric antibiotic therapy. In this study, we evaluate the spectrum of bacterial organisms cultured from corneal samples and their antibiotic sensitivities to guide initial treatment of keratitis.

Methods:

We performed a retrospective case review of cultures from suspected infectious keratitis cases at the Francis I. Proctor Foundation, University of California, San Francisco, from 1996 through 2015. Logistic regression models were used to assess the risk of culturing methicillin-resistant Staphylococcus aureus (MRSA) from ulcers over time and the association between the year cultured and moxifloxacin resistance.

Results:

A total of 522 of 2203 (23.7%) cultures grew bacterial organisms believed to be the etiology of infection, with available antibiotic sensitivity data. Of these, 338 (65.3%) grew gram-positive organisms with the most common being methicillin-sensitive Staphylococcus aureus (20.1%, N = 105). One hundred eighty (34.7%) grew gram-negative species with Pseudomonas aeruginosa as the most prevalent organism (10.9%, N = 57). There was 1.13 increased odds of culturing MRSA for each 1-year increase in the culture date (P = 0.01) and 1.26 increased odds of culturing an organism resistant to moxifloxacin with each 1-year increase in the culture date after controlling for the infectious organism (P < 0.001).

Conclusions:

Gram-positive organisms are the most commonly identified etiology of microbial keratitis in this series. Approximately 35% of cultured organisms had variable susceptibility to moxifloxacin, and resistance seems to be increasing over time. The risk of culturing MRSA increased over time.
Recognizing and Managing Bullous Descemet Detachment Secondary to Accidental Hydroseparation During Phacoemulsification/Cataract Surgery by Relaxing Descemetotomy
Authors: Jacob Soosan , Agarwal Amar , Agarwal Athiya , Ai Saijimol
Published: October 2017

Purpose:

To report a new technique called relaxing Descemetotomy for treatment of bullous Descemet detachment (BDD) secondary to accidental hydroseparation of Descemet membrane (DM) during stromal hydration in cataract surgery.

Methods:

A clear corneal keratome entry was created close to the limbus extending inward to create a relaxing cut (ab externo relaxing Descemetotomy) on taut DM, thus creating an egress route for supra-Descemetic fluid (SDF). This was followed by pneumodescemetopexy to drain SDF internally.

Results:

Three patients with a history of unsuccessful pneumodescemetopexy and with planar or mildly convex separation of DM without break on anterior segment optical coherence tomography (ASOCT) underwent this procedure. All had successful reapposition of DM clinically and on ASOCT. All showed resolution of stromal edema and improved uncorrected and best-corrected visual acuity postoperatively.

Conclusions:

Rarely stromal hydration performed with an irrigating cannula positioned too close to the posterior stroma can result in hydroseparation of DM creating BDD, seen intraoperatively as a fluid wave propagating across the posterior aspect of the cornea. Large folds, free mobility, and DM tear classically seen with rhegmatogenous Descemet detachment are not seen clinically or on ASOCT in BDD. Pneumodescemetopexy alone cannot resolve BDD because without a DM tear, SDF cannot evacuate. Combining relaxing Descemetotomy with pneumodescemetopexy allows SDF to drain internally and Descemet detachment to resolve. This technique has numerous advantages over classical venting incisions in terms of ease, preferable limbal location, larger incision size, absence of complications such as visual axis scars, irregular astigmatism, epithelial ingrowth, infectious keratitis, etc.
Molecular Typing and Macrolide Resistance of Syphilis Cases in Manitoba, Canada, From 2012 to 2016
Authors: Shuel Michelle , Hayden Kristy , Kadkhoda Kamran , Tsang Raymond S.W.
Published: October 2017

Background

The province of Manitoba, Canada, with a population of approximately 1.3 million, has been experiencing increased incidence of syphilis cases since 2015. In this study, we examined the detection of Treponema pallidum DNA in 354 clinical samples from 2012 to 2016, and determined molecular types and mutations conferring resistance to azithromycin in the polymerase chain reaction (PCR)–positive samples.

Methods

T. pallidum DNA detection was done by PCR amplification of tpp47, bmp, and polA genes. Syphilis serology results were reviewed for the PCR-positive cases. Molecular typing of syphilis strains was done by analysis of the T, pallidum arp, tpr, and tp0548 gene targets as well as partial sequencing of the 23S rRNA gene for azithromycin resistance.

Results

Of the 354 samples tested, 74 individual cases were PCR positive. A result from the treponemal antibody chemiluminescent microparticle immunoassay test was positive in 72 of these cases and that from the Venereal Disease Research Laboratory testing was positive in 66. Mutations conferring resistance to azithromycin were found in all 74 PCR-positive samples. Molecular typing was completed on 57 PCR-positive samples, and 12 molecular types were identified with 14d/g found in 63.2%. Increased strain diversity was observed with 8 molecular types detected in 2016, whereas only 2 to 3 types were found in 2012 to 2014. A patient with 2 episodes of infection 9 months apart caused by different molecular strain types was also identified.

Conclusions

The finding of an increase in genetic diversity in the strains in this study and an increase in macrolide resistance compared with previous Canadian reports highlighted the need for continued surveillance including strain characterization.
Development of proteolytically stable N-methylated peptide inhibitors of aggregation of the amylin peptide implicated in type 2 diabetes
Authors: Obasse Idira , Taylor Mark , Fullwood Nigel J. , Allsop David
Published: October 2017

Islet amyloid polypeptide, also known as amylin, is the main component of the amyloid deposits present in approximately 90% of people with type 2 diabetes mellitus (T2DM). In this disease, amylin aggregates into multimeric β-pleated sheet structures which cause damage to pancreatic islet β-cells. Inhibitors of early-stage amylin aggregation could therefore provide a disease-modifying treatment for T2DM. In this study, overlapping peptides were designed to target the ‘binding’ region (RLANFLVHSS, residues 11–20) of human amylin, and their effects on amyloid fibril formation were determined by thioflavin-T assay. The first generation peptides showed less than 50% inhibition of aggregation, but a second generation peptide (H
2
N-RGANFLVHGR-CONH
2
) showed strong inhibitory effects on amylin aggregation, and this was confirmed by negative stain electron microscopy. Cytotoxicity studies revealed that this peptide protected human pancreatic 1.4E7 (ECACC 10070102) insulin-secreting cells from the toxic effects of human amylin. Unlike the retro-inverso version of this peptide, which stimulated aggregation, two N-methylated peptides (H
2
N-RGAmNFmLVmHGR-CONH
2
and H
2
N-RGANmFLmVHmR-CONH
2
) gave very clear dose-dependent inhibition of fibril formation. These two peptides were also stable against a range of different proteolytic enzymes, and in human plasma. These N-methylated peptides could provide a novel treatment for slowing progression of T2DM.
Mechanism of biosurfactant adsorption to oil/water interfaces from millisecond scale tensiometry measurements
Authors: Kong Lingling , Saar Kadi Liis , Jacquat Raphael , Hong Liu , Levin Aviad , Gang Hongze , Ye Ruqiang , Mu Bozhong , Knowles Tuomas P. J.
Published: October 2017

Many biological molecules are by their nature amphiphilic and have the ability to act as surfactants, stabilizing interfaces between aqueous and immiscible oil phases. In this paper, we explore the adsorption kinetics of surfactin, a naturally occurring cyclic lipopeptide, at hexadecane/water interfaces and compare and contrast its adsorption behaviour with that of synthetic alkyl benzene sulfonate isomers, through direct measurements of changes in interfacial tension upon surfactant adsorption. We access millisecond time resolution in kinetic measurements by making use of droplet microfluidics to probe the interfacial tension of hexadecane droplets dispersed in a continuous water phase through monitoring their deformation when the droplets are exposed to shear flows in a microfluidic channel with regular corrugations. Our results reveal that surfactin rapidly adsorbs to the interface, thus the interfacial tension equilibrates within 300 ms, while the synthetic surfactants used undergo adsorption processes at an approximately one order of magnitude longer timescale. The approach presented may provide opportunities for understanding and modulating the adsorption mechanism of amphiphiles on a variety of interfaces in the context of life sciences and industrial applications.
Factors affecting the physical stability (aggregation) of peptide therapeutics
Authors: Zapadka Karolina L. , Becher Frederik J. , Gomes dos Santos A. L. , Jackson Sophie E.
Published: October 2017

The number of biological therapeutic agents in the clinic and development pipeline has increased dramatically over the last decade and the number will undoubtedly continue to increase in the coming years. Despite this fact, there are considerable challenges in the development, production and formulation of such biologics particularly with respect to their physical stabilities. There are many cases where self-association to form either amorphous aggregates or highly structured fibrillar species limits their use. Here, we review the numerous factors that influence the physical stability of peptides including both intrinsic and external factors, wherever possible illustrating these with examples that are of therapeutic interest. The effects of sequence, concentration, pH, net charge, excipients, chemical degradation and modification, surfaces and interfaces, and impurities are all discussed. In addition, the effects of physical parameters such as pressure, temperature, agitation and lyophilization are described. We provide an overview of the structures of aggregates formed, as well as our current knowledge of the mechanisms for their formation.