bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure of the SLy1 SAM homodimer reveals a new interface for SAM domain self-association
Authors: Kukuk Laura , Dingley Andrew J. , Granzin Joachim , Nagel-Steger Luitgard , Thiagarajan-Rosenkranz Pallavi , Ciupka Daniel , Hänel Karen , Batra-Safferling Renu , Pacheco Victor , Stoldt Matthias , Pfeffer Klaus , Beer-Hammer Sandra , Willbold Dieter , Koenig Bernd W.
Published: January 2019

Sterile alpha motif (SAM) domains are protein interaction modules that are involved in a diverse range of biological functions such as transcriptional and translational regulation, cellular signalling, and regulation of developmental processes. SH3 domain-containing protein expressed in lymphocytes 1 (SLy1) is involved in immune regulation and contains a SAM domain of unknown function. In this report, the structure of the SLy1 SAM domain was solved and revealed that this SAM domain forms a symmetric homodimer through a novel interface. The interface consists primarily of the two long C-terminal helices, α5 and α5′, of the domains packing against each other. The dimerization is characterized by a dissociation constant in the lower micromolar range. A SLy1 SAM domain construct with an extended N-terminus containing five additional amino acids of the SLy1 sequence further increases the stability of the homodimer, making the SLy1 SAM dimer two orders of magnitude more stable than previously studied SAM homodimers, suggesting that the SLy1 SAM dimerization is of functional significance. The SLy1 SAM homodimer contains an exposed mid-loop surface on each monomer, which may provide a scaffold for mediating interactions with other SAM domain-containing proteins via a typical mid-loop–end-helix interface.
BLNCR is a long non-coding RNA adjacent to integrin beta-1 that is rapidly lost during epidermal progenitor cell differentiation
Authors: Tanis Sabine E. J. , Köksal Elif Senem , van Buggenum Jessie A. G. L. , Mulder Klaas W.
Published: January 2019

As our understanding of transcriptional regulation improves so does our appreciation of its complexity. Both coding and (long) non-coding RNAs provide cells with multiple levels of control and thereby flexibility to adapt gene expression to the environment. However, few long non-coding RNAs (lncRNAs) have been studied in human epidermal stem cells. Here, we characterized the expression of 26 lncRNAs in human epidermal keratinocytes, 7 of which we found to be dynamically expressed during differentiation. We performed in depth analysis of a lncRNA located proximal to the epidermal stem cell marker integrin beta-1 (ITGB1) and transcribed in the opposite direction. We dubbed this gene Beta1-adjacent long non-coding RNA, or BLNCR, and found that its expression is regulated by p63 and AP1 transcription factors. Furthermore, BLNCR expression is regulated downstream the integrin and EGF signaling pathways that are key to epidermal stem cell maintenance. Finally, we found that BLNCR expression is rapidly reduced upon induction of differentiation, preceding the down regulation of integrin beta-1 expression. These dynamics closely mirror the loss of proliferative and adhesion capacity of epidermal stem cells in colony formation assays. Together, these results suggest that loss of BLNCR expression marks the switch from a proliferative state towards terminal differentiation in human epidermal stem cells.
Potential role of host-derived quorum quenching in modulating bacterial colonization in the moon jellyfish Aurelia aurita
Authors: Weiland-Bräuer Nancy , Fischer Martin A. , Pinnow Nicole , Schmitz Ruth A.
Published: January 2019

Multicellular organisms can be regarded as metaorganisms, comprising of a macroscopic host interacting with associated microorganisms. Within this alliance, the host has to ensure attracting beneficial bacteria and defending against pathogens to establish and maintain a healthy homeostasis. Here, we obtained several lines of evidence arguing that Aurelia aurita uses interference with bacterial quorum sensing (QS) - quorum quenching (QQ) - as one host defense mechanism. Three A. aurita-derived proteins interfering with bacterial QS were identified by functionally screening a metagenomic library constructed from medusa-derived mucus. Native expression patterns of these host open reading frames (ORFs) differed in the diverse life stages (associated with different microbiota) pointing to a specific role in establishing the developmental stage-specific microbiota. Highly increased expression of all QQ-ORFs in germ-free animals further indicates their impact on the microbiota. Moreover, incubation of native animals with pathogenic bacteria induced expression of the identified QQ-ORFs arguing for a host defense strategy against confronting bacteria by interference with bacterial QS. In agreement, immobilized recombinant QQ proteins induced restructuring of polyp-associated microbiota through changing abundance and operational taxonomic unit composition. Thus, we hypothesize that additional to the immune system host-derived QQ-activities potentially control bacterial colonization.
Fast determination of omeprazole in extemporaneous suspensions used in paediatrics and stability studies
Authors: Kučerová Kateřina , Reiská Veronika , Švec František , Krčmová Lenka Kujovská , Matysová Ludmila
Published: January 2019

A simple and fast ultra-high-performance liquid chromatography method with UV detection for the separation and quantification of omeprazole and the impurities of omeprazole and methylparaben (the internal standard) in six extemporaneous suspensions has been developed and fully validated.
A protein amantadine-BODIPY assembly as a turn-on sensor for free copper(ii)
Authors: Zhang Peng-Li , Shao Jian , Li Xiao-Tong , Chen Qiu-Yun , Qu Ling-Ling
Published: January 2019

BOD-Ad@BSA nanoparticles () were used as the fluorescence sensor to distinguish free Cu2+ and Cu2+–protein complexes. We report a BOD-Ad@BSA-based method to detect the free Cu2+ content in fish samples without or with Cu2+ treatment.
The role of oxygen vacancies in water oxidation for perovskite cobalt oxide electrocatalysts: are more better?
Authors: Miao Xianbing , Wu Liang , Lin Yue , Yuan Xueyou , Zhao Jiyin , Yan Wensheng , Zhou Shiming , Shi Lei
Published: January 2019

We demonstrate that high oxygen vacancies significantly weaken the oxygen-evolving activity for PrBaCo2O6−δ due to the formation of vacancy ordering.
Luminescent lanthanide (Eu(iii)) cross-linked supramolecular metallo co-polymeric hydrogels: the effect of ligand symmetry
Authors: Bradberry Samuel J. , Dee Garret , Kotova Oxana , McCoy Colin P. , Gunnlaugsson Thorfinnur
Published: January 2019

Two lanthanide luminescent naphthyl-dipicolinic amide (dpa) methacrylate monomers for the synthesis of grafted supramolecular co-polymer gels (hydrogels), and their use as additional crosslinks in robust covalently cross-linked HEMA hydrogels is presented.
A “turn-on” fluorescent probe for the detection of permanganate in aqueous media
Authors: Shi Genggongwo , Shahid Mushtaq Ahmed , Yousuf Muhammad , Mahmood Farzana , Rasheed Lubna , Bielawski Christopher W. , Kim Kwang S.
Published: January 2019

A novel carbazole-based probe exhibit fluorescence upon introduction to permanganate in aqueous media.
The functionality of surface hydroxyls on selective CH4 generation from photoreduction of CO2 over SiC nanosheets
Authors: Han Cheng , Lei Yongpeng , Wang Bing , Wu Chunzhi , Zhang Xiaoshan , Shen Shujin , Sun Lian , Tian Qiong , Feng Qingguo , Wang Yingde
Published: January 2019

The hydroxyls on SiC nanosheet provide local protons, stabilize the intermediates and localize the electrons for deep photoreduction of CO2.
Probing membrane asymmetry of ABC polymersomes
Authors: Konishcheva Evgeniia V. , Daubian Davy , Rigo Serena , Meier Wolfgang P.
Published: January 2019

We report the sensitivity of the membrane asymmetry of ABC (PEO-b-PCL-b-PMOXA) polymersomes towards the end-group modification of a shorter C block.
Conical intersections and intersystem crossings explain product formation in photochemical reactions of aryl azides
Authors: Soto Juan , Otero Juan C. , Avila Francisco J. , Peláez Daniel
Published: January 2019

Photochemistry of substituted aryl azides is governed by surface crossings. Internal conversion and intersystem crossing govern photodecomposition of 3-methoxyphenyl azide and 4-methoxyphenyl azide.
Thermodynamic stability of non-stoichiometric SrFeO3−δ: a hybrid DFT study
Authors: Heifets Eugene , Kotomin Eugene A. , Bagaturyants Alexander A. , Maier Joachim
Published: January 2019

Stability region for the only stable SrFeO2.5 phase is drawn as a function of temperature and oxygen gas partial pressure.
Mechanical properties of anhydrous oxalic acid and oxalic acid dihydrate
Authors: Colmenero Francisco
Published: January 2019

The mechanical properties of oxalic acid dihydrate and anhydrous oxalic acid (α and β polymorphic forms) were obtained by using rigorous theoretical solid-state methods based on density functional theory using plane waves and pseudopotentials.
Engineering ferroelectric instability to achieve ultralow thermal conductivity and high thermoelectric performance in Sn1−xGexTe
Authors: Banik Ananya , Ghosh Tanmoy , Arora Raagya , Dutta Moinak , Pandey Juhi , Acharya Somnath , Soni Ajay , Waghmare Umesh V. , Biswas Kanishka
Published: January 2019

Tailoring local structural distortions and the associated ferroelectric instability in SnTe via Ge alloying resulted in ultralow lattice thermal conductivity which boosts zT to 1.6 at 721 K.
Enhanced antibiotic removal through a dual-reaction-center Fenton-like process in 3D graphene based hydrogels
Authors: Zhuang Yuan , Liu Qiaozhi , Kong Yan , Shen Congcong , Hao Haotian , Dionysiou Dionysios D. , Shi Baoyou
Published: January 2019

Enhanced pollutant removal by FeOOH/RGO hydrogels relying on π–π and π–Fe interactions.
Experimental and theoretical studies of solvent polarity influence on the preparation of molecularly imprinted polymers for the removal of estradiol from water
Authors: Santos Xavier Leandro Pablo dos , Dias Ana Carolina , Baeta Bruno Eduardo Lobo , de Azevedo Santos Lucas , Ramalho Teodorico Castro , de Aquino Sérgio Francisco , da Silva Adilson Candido
Published: January 2019

Molecularly imprinted polymers synthesized by one-pot synthesis absorb β-estradiol quinoline efficiently and selectively.
Zinc(ii)–organic framework as a multi-responsive photoluminescence sensor for efficient and recyclable detection of pesticide 2,6-dichloro-4-nitroaniline, Fe(iii) and Cr(vi)
Authors: Guo Xiao-Yu , Dong Zhen-Peng , Zhao Fei , Liu Zhi-Liang , Wang Yan-Qin
Published: January 2019

A stable Zn-MOF acts as a multi-responsive luminescent sensor for efficient and recyclable detection of organochlorine pesticide 2,6-dichloro-4-nitroaniline, Fe(iii) and Cr(vi) with high selectivity and sensitivity.
Application of ZIF-8–graphene oxide sponge to a solid phase extraction method for the analysis of sex hormones in milk and milk products by high-performance liquid chromatography
Authors: Wang Xuemei , Wang Juan , Du Tongtong , Kou Haixia , Du Xinzhen , Lu Xiaoquan
Published: January 2019

A zeolitic imidazolate framework-8 (ZIF-8) incorporating a graphene oxide sponge (GOS) nanocomposite (ZIF-8–GOS) was synthesized successfully by a simple one-pot preparation method.
Au nanoparticles supported on functionalized two-dimensional titanium carbide for the sensitive detection of nitrite
Authors: Zou Huiyan , Zhang Feifei , Wang Haiyan , Xia Jianfei , Gao Linna , Wang Zonghua
Published: January 2019

A novel electrochemical sensing platform based on a Au NPs/Ti3C2TX composite was constructed.
Applications of N′-monofunctionalised TsDPEN derivatives in asymmetric catalysis
Authors: Barrios-Rivera Jonathan , Xu Yingjian , Wills Martin
Published: January 2019

N′-Monoalkylated or N′-mono(thio)acylated(N-sulfonyl)-1,2-diphenylethylene-1,2-diamine (TsDPEN) derivatives are have found extensive applications in asymmetric catalysis of a wide range of synthetic applications.
Synthesis of cyano-substituted carbazoles via successive C–C/C–H cleavage
Authors: Yang Yajie , Huang Jiaqi , Tan Hailu , Kong Lingkai , Wang Mengdan , Yuan Yang , Li Yanzhong
Published: January 2019

Cs2CO3 promoted C–C σ-bond activation of α-cyano ketones followed by Fe-catalyzed selective C–H and/or C–C bond activations towards cyano carbazoles.
Tolerance of N2-heteroaryl modifications on guanine bases in a DNA G-quadruplex
Authors: Masaki Yoshiaki , Inde Takeshi , Maruyama Atsuya , Seio Kohji
Published: January 2019

To systematically determine the effect of N2-heteroaryl modification on the stability of G-quadruplex structures, six types of N2-heteroarylated deoxyguanosines were incorporated into oligonucleotides with intramolecular quadruplex-forming sequences obtained from the human telomere sequence.
Two unique copper cluster-based metal–organic frameworks with high performance for CO2 adsorption and separation
Authors: Yuan Jiaqi , Li Jiantang , Che Songtian , Li Guanghua , Liu Xinyao , Sun Xiaodong , Zou Lifei , Zhang Lirong , Liu Yunling
Published: January 2019

Two unique Cu cluster-based MOFs have been constructed. Compound 1 with high-density OMSs and LBSs exhibits high CO2 separation ability.
Real-time naked-eye recognizable temperature monitoring based on Ho3+ (or Tm3+)-activated NaYF4 upconversion nanowires via visual multicolor alteration
Authors: Li Dongdong , Lai Wen-Yong , Shen Xiaoqin , Shao Qiyue , Huang Wei
Published: January 2019

A naked-eye recognizable color change responding to external temperature stimuli by using upconversion-based nanomaterials of Ho3+ (or Tm3+)-activated NaYF4 upconversion nanowires.
Direct construction of 2,3-unsubstituted benzofurans and benzothiophenes via a metal-free catalyzed intramolecular Friedel–Crafts reaction
Authors: Ma Weimin , Huang Jiawei , Huang Xianyu , Meng Shulin , Yang Zhengwei , Li Chao , Wang Yue , Qi Ting , Li Baolin
Published: January 2019

A highly effective and straightforward method for the construction of 2,3-unsubstituted benzofurans and benzothiophenes has been developed.
Palladium-catalyzed annulation of N-alkoxy benzsulfonamides with arynes by C–H functionalization: access to dibenzosultams
Authors: Feng Simin , Li Shan , Li Jing , Wei Junfa
Published: January 2019

Palladium-catalyzed C–H/N–H functionalization of N-alkoxy benzsulfonamides with arynes provides dibenzosultams via C–C/C–N bond formation, accompanied by an unexpected N–O bond cleavage.
Experimental and theoretical investigation of intramolecular cooperativity in cyclic benzene trimer motif
Authors: Kumar Chakka Kiran , Deval Sathiyashivan Shankar , Masram Dhanraj T. , Jose K. V. Jovan , Sathiyendiran Malaichamy
Published: January 2019

A family of biaryl/alkylthiophene (R–R) benzimidazolyl-based tripodal molecules with cyclic benzene trimer (CBT) motif was synthesized and studied by NMR spectroscopy and MPW1PW91/6-311+G(d,p) theory.
Effect of tourmaline nanoparticles on the anticoagulation and cytotoxicity of poly(l-lactide-co-caprolactone) electrospun fibrous membranes
Authors: Zhao Tianyu , Zhang Hong , Li Pan , Liang Jinsheng
Published: January 2019

The hydrophilicity and anticoagulation of PLCL electrospun membranes were enhanced by the modification of well-dispersed TM NPs.
Solvothermal water-diethylene glycol synthesis of LiCoPO4and effects of surface treatments on lithium battery performance
Authors: Zhang Min , Garcia-Araez Nuria , Hector Andrew L. , Owen John R. , Palgrave Robert G. , Palmer Michael G. , Soulé Samantha
Published: January 2019

Solvothermal water-diethylene glycol synthesis of LiCoPO4, followed by thermal treatment under Ar, air, 5%H2/N2or NH3was investigated.
Self-organized nanocrystal rings formed by microemulsion for selective recognition of proteins and immunoassays
Authors: Liang Jing , Yu Lei , Lin Ziying , Song Keji , Zhang Jiejing , Zhang Jianfeng
Published: January 2019

Ordered nanocrystal rings were conveniently prepared by a microemulsion, which can further be applied for the recognition of proteins and immunoassays.
Supercritical water gasification of biomass: a state-of-the-art review of process parameters, reaction mechanisms and catalysis
Authors: Okolie Jude A. , Rana Rachita , Nanda Sonil , Dalai Ajay K. , Kozinski Janusz A.
Published: January 2019

The global energy demand has laid emphasis on the exploration of alternate sources of energy.
Multifunctional bipyramid-Au@ZnO core–shell nanoparticles as a cathode buffer layer for efficient non-fullerene inverted polymer solar cells with improved near-infrared photoresponse
Authors: Li Jinyan , Bai Yiming , Yang Bo , Zhang Jin , Chen Xiaohan , Hayat Tasawar , Alsaedi Ahmed , Yang Yun , Hou Jianhui , Tan Zhan'ao
Published: January 2019

How to enhance the light absorption of the photoactive layer with a limited thickness is still a big challenge.
Salen–porphyrin-based conjugated microporous polymer supported Pd nanoparticles: highly efficient heterogeneous catalysts for aqueous C–C coupling reactions
Authors: Ju Pengyao , Wu Shujie , Su Qing , Li Xiaodong , Liu Ziqian , Li Guanghua , Wu Qiaolin
Published: January 2019

Salen–porphyrin-based CMP supported Pd nanoparticles were employed as high-performance heterogeneous catalysts for aqueous Suzuki–Miyaura and Heck–Mizoroki coupling reactions.
High-loading individually dispersed NiCo2O4 anchoring on checkerboard-like C/CNT nanosheets as a binder-free high rate electrode for lithium storage
Authors: Wang Hanwei , Hu Lintong , Wang Chao , Sun Qingfeng , Li Huiqiao , Zhai Tianyou
Published: January 2019

This work design a new checkerboard-like TMO/C/CNT nanosheet anode, achieving an individually dispersion of nano-TMOs under an ultrahigh loading of 85.1%, which exhibits an excellent rate performance and cycling stability for LIBs.
Functional nanomaterials with unique enzyme-like characteristics for sensing applications
Authors: Song Wei , Zhao Bing , Wang Ce , Ozaki Yukihiro , Lu Xiaofeng
Published: January 2019

We highlight the recent developments in functional nanomaterials with unique enzyme-like characteristics for sensing applications.
Designing nanoparticles with improved tumor penetration: surface properties from the molecular architecture viewpoint
Authors: Zhang Long , Hao Pengyan , Yang Dejun , Feng Sheng , Peng Bo , Appelhans Dietmar , Zhang Tinghong , Zan Xingjie
Published: January 2019

Cancer is the second most common cause of death, and nanomedicine is regarded as one of the strategies that may revolutionize cancer treatments.
Enhancing the performance of photomultiplication-type organic photodetectors using solution-processed ZnO as an interfacial layer
Authors: Wang Jianbin , Zheng Qingdong
Published: January 2019

In comparison with PEDOT:PSS-based OPDs, ZnO-based OPDs show a broader spectral-response range with enhanced EQE, responsivity and detectivity.
Structure, luminescence and energy transfer in Ce3+ and Mn2+ codoped γ-AlON phosphors
Authors: Si Jiayong , Wang Le , Liu Lihong , Yi Wei , Cai Gemei , Takeda Takashi , Funahashi Shiro , Hirosaki Naoto , Xie Rong-Jun
Published: January 2019

Upon UV or blue light excitation, the codoped γ-AlON phosphor has higher luminescence intensity, quantum efficiency and thermal stability than the Mn2+-doped γ-AlON due to energy transfer and low total concentration of Ce3+ and Mn2+ ions.
Rare mutations of ADAM17 from TOFs induce hypertrophy in human embryonic stem cell-derived cardiomyocytes via HB-EGF signaling
Authors: Xie Yifang , Ma Anyun , Wang Boshi , Peng Rui , Jing Yingchun , Wang Deqian , Finnell Richard H. , Qiao Bin , Wang Yongming , Wang Hongyan , Zheng Yufang
Published: January 2019

Tetralogy of Fallot (TOF) is the most common cyanotic form of congenital heart defects (CHDs). The right ventricular hypertrophy is associated with the survival rate of patients with repaired TOF. However, very little is known concerning its genetic etiology. Based on mouse model studies, a disintergrin and metalloprotease 10/17 (ADAM10 and ADAM17) are the key enzymes for the NOTCH and ErbB pathways, which are critical pathways for heart development. Mutations in these two genes have not been previously reported in human TOF patients. In this study, we sequenced ADAM10 and ADAM17 in a Han Chinese CHD cohort comprised of 80 TOF patients, 286 other CHD patients, and 480 matched healthy controls. Three missense variants of ADAM17 were only identified in 80 TOF patients, two of which (Y42D and L659P) are novel and not found in the Exome Aggregation Consortium (ExAC) database. Point mutation knock-in (KI) and ADAM17 knock-out (KO) human embryonic stem cells (hESCs) were generated by CRISPR/Cas9 and programmed to differentiate into cardiomyocytes (CMs). Y42D or L659P KI cells or complete KO cells all developed hypertrophy with disorganized sarcomeres. RNA-seq results showed that phosphatidylinositide 3-kinases/protein kinase B (PI3K/Akt), which is downstream of epidermal growth factor receptor (EGFR) signaling, was affected in both ADAM17 KO and KI hESC-CMs. In vitro experiments showed that these two mutations are loss-of-function mutations in shedding heparin-binding EGF-like growth factor (HB-EGF) but not NOTCH signaling. Our results revealed that CM hypertrophy in TOF could be the result of mutations in ADAM17 which affects HB-EGF/ErbB signaling.
Multimodal supervised image translation
Authors: Ruan Congcong , Chen Dihu , Hu Haifeng
Published: January 2019

Multimodal image‐to‐image translation is a class of vision and graphics problems where the goal is to learn a one‐to‐many mapping between the source domain and target domain. Given an image in the source domain, the model aims to produce as many diverse results as possible. It is an important and challenging problem in the task of image translation. To this end, recent works utilise Gaussian vectors to produce diverse results but with a small difference. It is because of the special probabilistic nature of Gaussian distribution. In this work, the authors propose linearly distributed latent codes instead of conventional Gaussian vectors, which control the style of generated images. Taking advantage of linear distribution, their model can produce much more diverse results and outperform the state‐of‐the‐art baselines in terms of diversity. Qualitative and quantitative comparisons against baselines demonstrate the effectiveness and superiority of their method.
Hydrophone based on 3D printed polypropylene (PP) piezoelectret
Authors: Palitó T.T.C. , Assagra Y.A.O. , Altafim R.A.P. , Carmo J.P. , Altafim R.A.C.
Published: January 2019

Every year, different areas of knowledge are becoming more interested in 3D‐printing technology. Recently, this technology was also proved to be feasible for creating sensitive materials such as piezoelectrets. This Letter extends the concept of a 3D printed piezoelectret to produce a pressure sensitive film that can be employed as an ultrasonic transducer for underwater applications, such as hydrophones. In order to achieve this, a two‐layer polypropylene film was printed using a filament‐based 3D printer. Afterwards, adhesive electrodes were attached on both sides of the film and electrical charging was applied. Later, the 3D printed film was mounted in a metal housing specially designed to keep the film in direct contact with the water and to isolate the electronic amplification. The validation was performed using a piezoelectric ceramic made of lead zirconate titanate (PZT), immersed in a water tank, to produce ultrasonic sweeps to be sensed by the 3D printed transducer. These tests revealed sensor sensitivities up to 600 mV and promote a precise detection of the acoustic resonance frequency of the PZT at 43.7 kHz.
Modelling and control for economy‐oriented car‐following problem of hybrid electric vehicle
Authors: Sun Yong , Wang Xiangyu , Li Liang , Shi Jialei , An Quan
Published: January 2019

For an intelligent hybrid electric vehicle (HEV), the economy‐oriented car‐following issue is a comprehensive problem of dynamic and economic performances, which involves in adaptive cruise control (ACC) and energy management strategy (EMS). In this study, three problems are formulated and analysed, which are a car‐following problem, HEV energy optimisation problem, and economy‐oriented HEV car‐following problem. In fact, the third problem includes the first and second problem. To describe the problems well, a novel efficiency model of HEV powertrain is proposed, and it is used to define the economic index for evaluation. The three problems can be solved by ACC, EMS, and combination of ACC and EMS. The comprehensive optimal solution for the third problem is analysed, which indicates that the fusion control is better than series control theoretically. Finally, a model predictive control method is used to compare the performances of fusion control with that of series control for a specific driving cycle. The results show that the fuel consumption of fusion control is less than that of series control by ∼5%.
ISRF: interest semantic reasoning based fog firewall for information‐centric Internet of Vehicles
Authors: Liu Yi , Wu Jun , Li Jianhua , Yang Wu , Chen Hao , Li Gaolei
Published: January 2019

Nowadays, Internet of Vehicles (IoV) has attracted lots of attention as an important component of intelligent transportation. Meanwhile, information‐centric network is a meaningful next‐generation network with content‐oriented attributes, which has been introduced into IoV for more flexible services. In information‐centric IoV, there are abundant semantic features because of the content big data in the network layer. As very few works of information‐centric IoV consider semantic models, current security approaches in information‐centric IoV cannot defence against efficiently novel threats with penetrated malicious content and semantic obfuscation, especially at the network edge. Thus an efficient firewall is a must for information‐centric IoV. However, existing firewalls based on traditional computing resources cannot detect content threats implicated in semantics at the edge of networks. In this study, the authors propose an interest semantic reasoning based fog firewall for information‐centric IoV. Firstly, a fog firewall is proposed to construct an edge isolation for information‐centric IoV. Moreover, interest semantic reasoning with context weight and knowledge graph is proposed to mine implicit relations and illegal knowledge in names and contents. Based on knowledge constructed from reasoning, it aims to perceive threats from interest packet in information‐centric IoV. Simulations verify its feasibility and efficiency of the proposed scheme.
Enhanced photocatalytic activity and cycle stability driven by ultrasonic vibration for ferroelectric photocatalysts
Authors: Zhang Xiaoshan , Huan Yu , Li Kai , Tian Hui , Shen Hengtao , Li Min , Li Hangyu , Wei Tao
Published: January 2019

Ferroelectric materials have been applied in the photocatalytic field due to the internal electric field generated by the spontaneous polarisation. In this study, it is found that the ferroelectric BaTiO3 catalysts exhibit the excellent photocatalytic property and cycle stability under ultrasonic vibration. In addition, the degraded photocatalytic activity after several cycling tests can resurrect if the BaTiO3 sample is treated by ultrasonic before photocatalytic reaction. The enhanced photocatalytic activity and cycle stability are ascribed to the variational spontaneous polarisation under external strain for ferroelectric materials. Under ultrasonic vibration, the high‐frequency alternating strain applied on the BaTiO3 grain changes the internal polarisation electric field. Due to the fast changing polarisation electric field, there is no enough time to form the depolarisation electric field in the BaTiO3 grain. Therefore, the effective electric field existed in BaTiO3 grain is large and can effectively promote the separation the photo‐generated electrons/holes; thus improving the photocatalytic activity. It is suggested that ultrasonic vibration is an efficient method to improve the photocatalytic properties and cycle stability of the ferroelectric photocatalysts.
Smoothing control strategy of wind and photovoltaic output power fluctuation by considering the state of health of battery energy storage system
Authors: Lamsal Dipesh , Sreeram Victor , Mishra Yateendra , Kumar Deepak
Published: January 2019

The output power of wind and photovoltaic (PV) systems contain fluctuations due to the intermittent nature of solar irradiance and wind speed. It is required to smooth the fluctuated power before supplying it to the grid. Here, a fuzzy‐based discrete Kalman filter approach is proposed for smoothing output power fluctuations of the wind and PV generation systems using a battery energy storage system. The proposed approach incorporates the state of health of the battery as a feedback to not only obtain smooth output power but also improve the battery health by adaptively regulating the battery power. The effectiveness of the proposed approach is verified by evaluating the power fluctuation rates and performance indices.
Extending the event-weighted pulsation search to very faint gamma-ray sources
Authors: Bruel P.
Published: January 2019

Context. Because of the relatively broad angular resolution of current gamma-ray instruments in the MeV–GeV energy range, the photons of a given source are mixed with those coming from nearby sources or diffuse background. This source confusion seriously hampers the search for pulsation from faint sources.

Aims. Statistical tests for pulsation can be made significantly more sensitive when the probability that a photon comes from the pulsar is used as a weight. However, computing this probability requires knowledge of the spectral model of all sources in the region of interest, including the pulsar itself. This is not possible for very faint pulsars that are not detected as gamma-ray sources or whose spectrum is not measured precisely enough. Extending the event-weighted pulsation search to such very faint gamma-ray sources would allow improving our knowledge of the gamma-ray pulsar population.

Methods. We present two methods that overcome this limitation by scanning the spectral parameter space, while minimizing the number of trials. The first one approximates the source to background ratio yielding a simple estimate of the weight while the second one makes use of the full spatial and spectral information of the region of interest around the pulsar.

Results. We tested these new methods on a sample of 144 gamma-ray pulsars already detected by the Fermi Large Area Telescope data. Both methods detect pulsation from all pulsars of the sample, including the ones for which no significant phase-averaged gamma-ray emission is detected.
Brownian dynamics investigation of the Boltzmann superposition principle for orthogonal superposition rheology
Authors: Metri Vishal , Briels W. J.
Published: January 2019

The most general linear equation describing the stress response at time t to a time-dependent shearing perturbation may be written as the integral over the past history t′ of a time dependent relaxation modulus, depending on t − t′, multiplied by the perturbing shear rate at time t′. This is in agreement with the Boltzmann superposition principle, which says that the stress response of a system to a time dependent shearing deformation may be written as the sum of responses to a sequence of step-strain perturbations in the past. In equilibrium rheology, the Boltzmann superposition principle gives rise to the equality of the shear relaxation modulus, obtained from oscillatory experiments, and the stress relaxation modulus measured after a step-strain perturbation. In this paper, we describe the results of Brownian dynamics simulations of a simple soft matter system showing that the same conclusion does not hold when the system is steadily sheared in a direction perpendicular to the probing flows, and with a gradient parallel to that of the probing deformations, as in orthogonal superposition rheology. In fact, we find that the oscillatory relaxation modulus differs from the step-strain modulus even for the smallest orthogonal shear flows that we could simulate. We do find, however, that the initial or plateau levels of both methods agree and provide an equation relating the plateau value to the perturbation of the pair-function.
Exaggerated post exercise hypotension following concentric but not eccentric resistance exercise: Implications for metabolism
Authors: Stavres Jon , Fischer Stephen M , McDaniel John
Published: January 2019

Post exercise hypotension (PEH) is primarily attributed to post‐exercise vasodilation via central and peripheral mechanisms. However, the specific contribution of metabolic cost during exercise, independent of force production, is less clear. This study aimed to use isolated concentric and eccentric exercise to examine the role of metabolic activity in eliciting PEH, independent of total work. Twelve participants (6 male) completed upper and lower body concentric (CONC), eccentric (ECC), and traditional (TRAD) exercise sessions matched for work (3 × 10 in TRAD and 3 × 20 in CONC and ECC; all at 65% 1RM). Blood pressure was collected at baseline and every 15 min after exercise for 120 min. Brachial blood flow and vascular conductance were also assessed at baseline, immediately after exercise, and every 30 min after exercise. ⩒O2 was lower during ECC compared to CONC and TRAD (−2.7 mL/Kg/min ± 0.4 and −2.2 mL/Kg/min ± 0.4, respectively p < 0.001). CONC augmented the PEH response (Peak ΔMAP −3.3 mmHg ± 0.9 [mean ± SE], p = 0.006) through 75 min of recovery and ECC elicited a post‐exercise hypertensive response through 120 min of recovery (Peak ΔMAP +4.5 mmHg ± 0.8, p < 0.001). CONC and TRAD elicited greater increases in brachial blood flow post exercise than ECC (Peak Δ brachial flow +190.4 mL/min ± 32.3, +202.3 mL/min ± 39.2, and 69.6 mL/min ± 19.8, respectively, p ≤ 0.005), while conductance increased immediately post exercise in all conditions and then decreased throughout recovery following ECC (−32.9 mL/min/mmHg ± 9.3, p = 0.005). These data suggest that more metabolically demanding concentric exercise augments PEH compared to work‐matched eccentric exercise.
President Obama, poverty, and the scope and limits of social policy change
Authors: Waddan Alex
Published: January 2019

There has been a growing discussion in recent years about rising inequality in the U.S. Yet, this discourse, in focusing on the fortunes of the top 1%, distracted attention from the design of policy initiatives aimed at improving socio-economic conditions for the poor. This paper examines the development of anti-poverty politics and policy in the US during the Obama era. It analyses how effective the strategies and programmes adopted were and asks how they fit with models of policy change. The paper illustrates that the Obama administration did adopt an array of anti-poverty measures in the stimulus bill, but these built on existing programmes rather than create new ones and much of the effort was stymied by institutional obstacles. The expansion of the Medicaid program, which was part of the ACA, was also muted by institutional opposition, but it was a more path breaking reform than is often appreciated.
Methionine triggers Ppz-mediated dephosphorylation of Art1 to promote cargo-specific endocytosis
Authors: Lee Sora , Ho Hsuan-Chung , Tumolo Jessica M. , Hsu Pi-Chiang , MacGurn Jason A.
Published: January 2019

Regulation of plasma membrane (PM) protein abundance by selective endocytosis is critical for cellular adaptation to stress or changing nutrient availability. One example involves rapid endocytic turnover of Mup1, a yeast methionine transporter, in response to increased methionine availability. Here, we report that methionine triggers rapid translocation of the ubiquitin ligase adaptor Art1 to the PM and dephosphorylation of Art1 at specific threonine residues. This methionine-induced dephosphorylation of Art1 is mediated by Ppz phosphatases, and analysis of phosphomimetic and phosphorylation-defective variants of Art1 indicates that these events toggle Art1 recognition of Mup1 at the PM. Importantly, we find that Ppz phosphatases are dispensable for Art1 PM translocation, but are required for Art1 interaction with Mup1. Based on our findings, we propose that methionine influx triggers Art1 translocation to the PM, followed by Ppz-mediated dephosphorylation which promotes cargo recognition at the PM.
The Effects of Farm Subsidies on Farm Exports in the United States
Authors: Tong Lan Anh , Pham Cong S , Ulubaşoğlu Mehmet A
Published: January 2019

We estimate the elasticity of U.S. farm exports to U.S. farm subsidies using a gravity model of state‐level farm exports to 100 major trading destinations for the period 1999 to 2011. Our identification strategy exploits the within‐state variation that is free of endogeneity bias in the levels and trends of farm subsidies and farm exports. We find that a 1% decrease in farm subsidies would reduce U.S. farm exports by 0.40% per annum. This equivalently means that the complete abolishment of the farm subsidy program would reduce U.S. farm exports by approximately $15.3 billion per year. Importantly, we document robust evidence that amber box subsidy programs such as counter‐cyclical payments and marketing loan gains have the strongest effect on farm exports, while green box subsidy payments, such as direct payments have negligible effects. Finally, subsidy payments affect exports only in agricultural commodities, not in livestock. Our subsidy elasticity estimates are statistically significant, stable, and economically meaningful, and are vitally needed by U.S. and global policymakers in the face of critical domestic and international developments.
TOPAS: network-based structural alignment of RNA sequences
Authors: Chen Chun-Chi , Jeong Hyundoo , Qian Xiaoning , Yoon Byung-Jun
Published: January 2019

Motivation

For many RNA families, the secondary structure is known to be better conserved among the member RNAs compared to the primary sequence. For this reason, it is important to consider the underlying folding structures when aligning RNA sequences, especially for those with relatively low sequence identity. Given a set of RNAs with unknown structures, simultaneous RNA alignment and folding algorithms aim to accurately align the RNAs by jointly predicting their consensus secondary structure and the optimal sequence alignment. Despite the improved accuracy of the resulting alignment, the computational complexity of simultaneous alignment and folding for a pair of RNAs is O(N6), which is too costly to be used for large-scale analysis.

Results

In order to address this shortcoming, in this work, we propose a novel network-based scheme for pairwise structural alignment of RNAs. The proposed algorithm, TOPAS, builds on the concept of topological networks that provide structural maps of the RNAs to be aligned. For each RNA sequence, TOPAS first constructs a topological network based on the predicted folding structure, which consists of sequential edges and structural edges weighted by the base-pairing probabilities. The obtained networks can then be efficiently aligned by using probabilistic network alignment techniques, thereby yielding the structural alignment of the RNAs. The computational complexity of our proposed method is significantly lower than that of the Sankoff-style dynamic programming approach, while yielding favorable alignment results. Furthermore, another important advantage of the proposed algorithm is its capability of handling RNAs with pseudoknots while predicting the RNA structural alignment. We demonstrate that TOPAS generally outperforms previous RNA structural alignment methods on RNA benchmarks in terms of both speed and accuracy.

Availability and implementation

Source code of TOPAS and the benchmark data used in this paper are available at https://github.com/bjyoontamu/TOPAS.
Streamlined analysis of LINCS L1000 data with the slinky package for R
Authors: Kort Eric J , Jovinge Stefan
Published: January 2019

The L1000 dataset from the NIH LINCS program holds the promise to deconvolute a wide range of biological questions in transcriptional space. However, using this large and decentralized dataset presents its own challenges. The slinky package was created to streamline the process of identifying samples of interest and their corresponding control samples, and loading their associated expression data and metadata. The package can integrate with workflows leveraging the BioConductor collection of tools by encapsulating the L1000 data as a SummarizedExperiment object.

Availability and implementation

Slinky is freely available as an R package at http://bioconductor.org/packages/slinky
Sstack: an R package for stacking with applications to scenarios involving sequential addition of samples and features
Authors: Matlock Kevin , Rahman Raziur , Ghosh Souparno , Pal Ranadip
Published: January 2019

Biological processes are characterized by a variety of different genomic feature sets. However, often times when building models, portions of these features are missing for a subset of the dataset. We provide a modeling framework to effectively integrate this type of heterogeneous data to improve prediction accuracy. To test our methodology, we have stacked data from the Cancer Cell Line Encyclopedia to increase the accuracy of drug sensitivity prediction. The package addresses the dynamic regime of information integration involving sequential addition of features and samples.

Availability and implementation

The framework has been implemented as a R package Sstack, which can be downloaded from https://cran.r-project.org/web/packages/Sstack/index.html, where further explanation of the package is available.

Supplementary information

Supplementary data are available at Bioinformatics online.
TopoLink: evaluation of structural models using chemical crosslinking distance constraints
Authors: Ferrari Allan J R , Clasen Milan A , Kurt Louise , Carvalho Paulo C , Gozzo Fabio C , Martínez Leandro
Published: January 2019

A software was developed to evaluate structural models using chemical crosslinking experiments. The user provides the types of linkers used and their reactivity, and the observed crosslinks and dead-ends. The software computes the minimum length of a physically inspired linker that connects the reactive atoms of interest, and reports the consistency of each distance with the experimental observation. Statistics on model consistency with the links are provided. Tools to evaluate the correlation of crosslinks in ensembles of models were developed. TopoLink was used to evaluate the potential crosslinks of all structures of the CATH database. The number of crosslinks expected as a function of protein size and linker length can be used as guide for experimental design.

Availability and implementation

TopoLink is available as free software at http://m3g.iqm.unicamp.br/topolink, and distributed as source code with a user-friendly graphical interface for Windows. A web server is also provided.

Supplementary information

Supplementary data are available at Bioinformatics online.
PopCluster: an algorithm to identify genetic variants with ethnicity-dependent effects
Authors: Gurinovich Anastasia , Bae Harold , Farrell John J , Andersen Stacy L , Monti Stefano , Puca Annibale , Atzmon Gil , Barzilai Nir , Perls Thomas T , Sebastiani Paola
Published: January 2019

Motivation

Over the last decade, more diverse populations have been included in genome-wide association studies. If a genetic variant has a varying effect on a phenotype in different populations, genome-wide association studies applied to a dataset as a whole may not pinpoint such differences. It is especially important to be able to identify population-specific effects of genetic variants in studies that would eventually lead to development of diagnostic tests or drug discovery.

Results

In this paper, we propose PopCluster: an algorithm to automatically discover subsets of individuals in which the genetic effects of a variant are statistically different. PopCluster provides a simple framework to directly analyze genotype data without prior knowledge of subjects’ ethnicities. PopCluster combines logistic regression modeling, principal component analysis, hierarchical clustering and a recursive bottom-up tree parsing procedure. The evaluation of PopCluster suggests that the algorithm has a stable low false positive rate (∼4%) and high true positive rate (>80%) in simulations with large differences in allele frequencies between cases and controls. Application of PopCluster to data from genetic studies of longevity discovers ethnicity-dependent heterogeneity in the association of rs3764814 (USP42) with the phenotype.

Availability and implementation

PopCluster was implemented using the R programming language, PLINK and Eigensoft software, and can be found at the following GitHub repository: https://github.com/gurinovich/PopCluster with instructions on its installation and usage.

Supplementary information

Supplementary data are available at Bioinformatics online.
The intestine responds to heart failure by enhanced mitochondrial fusion through glucagon-like peptide-1 signalling
Authors: Naruse Genki , Kanamori Hiromitsu , Yoshida Akihiro , Minatoguchi Shingo , Kawaguchi Tomonori , Iwasa Masamitsu , Yamada Yoshihisa , Mikami Atsushi , Kawasaki Masanori , Nishigaki Kazuhiko , Minatoguchi Shinya
Published: January 2019

Aims

Glucagon-like peptide-1 (GLP-1) is a neuroendocrine hormone secreted by the intestine. Its receptor (GLP-1R) is expressed in various organs, including the heart. However, the dynamics and function of the GLP-1 signal in heart failure remains unclear. We investigated the impact of the cardio-intestinal association on hypertensive heart failure using miglitol, an α-glucosidase inhibitor known to stimulate intestinal GLP-1 production.

Methods and results

Dahl salt-sensitive (DS) rats fed a high-salt diet were assigned to miglitol, exendin (9-39) (GLP-1R blocker) and untreated control groups and treated for 11 weeks. Control DS rats showed marked hypertension and cardiac dysfunction with left ventricular dilatation accompanied by elevated plasma GLP-1 levels and increased cardiac GLP-1R expression as compared with age-matched Dahl salt-resistant (DR) rats. Miglitol further increased plasma GLP-1 levels, suppressed adverse cardiac remodelling, and mitigated cardiac dysfunction. In cardiomyocytes from miglitol-treated DS hearts, mitochondrial size was significantly larger with denser cristae than in cardiomyocytes from control DS hearts. The change in mitochondrial morphology reflected enhanced mitochondrial fusion mediated by protein kinase A activation leading to phosphorylation of dynamin-related protein 1, expression of mitofusin-1 and OPA-1, and increased myocardial adenosine triphosphate (ATP) content. GLP-1R blockade with exendin (9-39) exacerbated cardiac dysfunction and led to fragmented mitochondria with disarrayed cristae in cardiomyocytes and reduction of myocardial ATP content. In cultured cardiomyocytes, GLP-1 increased expression of mitochondrial fusion-related proteins and ATP content. When GLP-1 and exendin (9-39) were administered together, their effects cancelled out.

Conclusions

Increased intestinal GLP-1 secretion is an adaptive response to heart failure that is enhanced by miglitol. This could be an effective strategy for treating heart failure through regulation of mitochondrial dynamics.