bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Yersinia Type III secretion effector YopM Is an E3 ubiquitin ligase that induced necrotic cell death by targeting NLRP3
Authors: Wei Congwen , Wang Ying , Du Zongmin , Guan Kai , Cao Ye , Yang Huiying , Zhou Pengyu , Wu Feixiang , Chen Jiankang , Wang Penghao , Zheng Zirui , Zhang Pingping , Zhang Yanhong , Ma Shengli , Yang Ruifu , Zhong Hui , He Xiang 
Published: December 2016

AbstractYersinia pestis uses type III effector proteins to target eukaryotic signaling systems. The Yersinia outer protein (Yop) M effector from the Y. pestis strain is a critical virulence determinant; however, its role in Y. pestis pathogenesis is just beginning to emerge. Here we first identify YopM as the structural mimic of the bacterial IpaH E3 ligase family in vitro, and establish that the conserved CLD motif in its N-terminal is responsible for the E3 ligase function. Furthermore, we show that NLRP3 is a novel target of the YopM protein. Specially, YopM associates with NLRP3, and its CLD ligase motif mediates the activating K63-linked ubiquitylation of NLRP3; as a result, YopM modulates NLRP3-mediated cell necrosis. Mutation of YopM E3 ligase motif dramatically reduces the ability of Y. pestis to induce HMGB1 release and cell necrosis, which ultimately contributes to bacterial virulence. In conclusion, this study has identified a previously unrecognized role for YopM E3 ligase activity in the regulation of host cell necrosis and plague pathogenesis.
Digenic mutations of human OCRL paralogs in Dent’s disease type 2 associated with Chiari I malformation
Authors: Duran Daniel , Jin Sheng Chih , DeSpenza Tyrone , Nelson-Williams Carol , Cogal Andrea G , Abrash Elizabeth W , Harris Peter C , Lieske John C , Shimshak Serena JE , Mane Shrikant , Bilguvar Kaya , DiLuna Michael L , Günel Murat , Lifton Richard P , Kahle Kristopher T 
Published: December 2016

AbstractOCRL1and its paralogINPP5Bencode phosphatidylinositol 5-phosphatases that localize to the primary cilium and have roles in ciliogenesis. Mutations inOCRL1cause the X-linked Dent disease type 2 (DD2; OMIM# 300555), characterized by low-molecular weight proteinuria, hypercalciuria, and the variable presence of cataracts, glaucoma and intellectual disability without structural brain anomalies. Disease-causing mutations inINPP5Bhave not been described in humans. Here, we report the case of an 11-year-old boy with short stature and an above-average IQ; severe proteinuria, hypercalciuria and osteopenia resulting in a vertebral compression fracture; and Chiari I malformation with cervico-thoracic syringohydromyelia requiring suboccipital decompression. Sequencing revealed a novel,de novoDD2-causing 462 bp deletion disrupting exon 3 ofOCRL1and a maternally inherited, extremely rare (ExAC allele frequency 8.4×10−6) damaging missense mutation inINPP5B(p.A51V). This mutation substitutes an evolutionarily conserved amino acid in the protein’s critical PH domain.In silicoanalyses of mutation impact predicted by SIFT, PolyPhen2, MetaSVM and CADD algorithms were all highly deleterious. Together, our findings report a novel association of DD2 with Chiari I malformation and syringohydromyelia, and document the effects of digenic mutation of humanOCRLparalogs. These findings lend genetic support to the hypothesis that impaired ciliogenesis may contribute to the development of Chiari I malformation, and implicates OCRL-dependent PIP3metabolism in this mechanism.
Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping
Authors: Bongiovanni Marie N. , Godet Julien , Horrocks Mathew H. , Tosatto Laura , Carr Alexander R. , Wirthensohn David C. , Ranasinghe Rohan T. , Lee Ji-Eun , Ponjavic Aleks , Fritz Joelle V. , Dobson Christopher M. , Klenerman David , Lee Steven F. 
Published: December 2016

AbstractSuper-resolution microscopy allows biological systems to be studied at the nanoscale, but has been restricted to providing only positional information. Here, we show that it is possible to perform multi-dimensional super-resolution imaging to determine both the position and the environmental properties of single-molecule fluorescent emitters. The method presented here exploits the solvatochromic and fluorogenic properties of nile red to extract both the emission spectrum and the position of each dye molecule simultaneously enabling mapping of the hydrophobicity of biological structures. We validated this by studying synthetic lipid vesicles of known composition. We then applied both to super-resolve the hydrophobicity of amyloid aggregates implicated in neurodegenerative diseases, and the hydrophobic changes in mammalian cell membranes. Our technique is easily implemented by inserting a transmission diffraction grating into the optical path of a localization-based super-resolution microscope, enabling all the information to be extracted simultaneously from a single image plane.
Current crowding mediated large contact noise in graphene field-effect transistors
Authors: Karnatak Paritosh , Sai T. Phanindra , Goswami Srijit , Ghatak Subhamoy , Kaushal Sanjeev , Ghosh Arindam 
Published: December 2016

AbstractThe impact of the intrinsic time-dependent fluctuations in the electrical resistance at the graphene–metal interface or the contact noise, on the performance of graphene field-effect transistors, can be as adverse as the contact resistance itself, but remains largely unexplored. Here we have investigated the contact noise in graphene field-effect transistors of varying device geometry and contact configuration, with carrier mobility ranging from 5,000 to 80,000 cm2V−1s−1. Our phenomenological model for contact noise because of current crowding in purely two-dimensional conductors confirms that the contacts dominate the measured resistance noise in all graphene field-effect transistors in the two-probe or invasive four-probe configurations, and surprisingly, also in nearly noninvasive four-probe (Hall bar) configuration in the high-mobility devices. The microscopic origin of contact noise is directly linked to the fluctuating electrostatic environment of the metal–channel interface, which could be generic to two-dimensional material-based electronic devices.
The E3 ubiquitin ligase TRIM31 attenuates NLRP3 inflammasome activation by promoting proteasomal degradation of NLRP3
Authors: Song Hui , Liu Bingyu , Huai Wanwan , Yu Zhongxia , Wang Wenwen , Zhao Jing , Han Lihui , Jiang Guosheng , Zhang Lining , Gao Chengjiang , Zhao Wei 
Published: December 2016

AbstractThe NLRP3 inflammasome has a fundamental role in host defence against microbial pathogens and its deregulation may cause diverse inflammatory diseases. NLRP3 protein expression is a rate-limiting step for inflammasome activation, thus its expression must be tightly controlled to maintain immune homeostasis and avoid detrimental effects. However, how NLRP3 expression is regulated remains largely unknown. In this study, we identify E3 ubiquitin ligase TRIM31 as a feedback suppressor of NLRP3 inflammasome. TRIM31 directly binds to NLRP3, promotes K48-linked polyubiquitination and proteasomal degradation of NLRP3. Consequently, TRIM31 deficiency enhances NLRP3 inflammasome activation and aggravates alum-induced peritonitis in vivo. Furthermore, TRIM31 deficiency attenuates the severity of dextran sodium sulfate (DSS)-induced colitis, an inflammatory bowel diseases model in which NLRP3 possesses protective roles. Thus, our research describes a mechanism by which TRIM31 limits NLRP3 inflammasome activity under physiological conditions and suggests TRIM31 as a potential therapeutic target for the intervention of NLRP3 inflammasome related diseases.
Optimal generation of spatially coherent soft X-ray isolated attosecond pulses in a gas-filled waveguide using two-color synthesized laser pulses
Authors: Jin Cheng , Hong Kyung-Han , Lin C. D. 
Published: December 2016

AbstractWe numerically demonstrate the generation of intense, low-divergence soft X-ray isolated attosecond pulses in a gas-filled hollow waveguide using synthesized few-cycle two-color laser waveforms. The waveform is a superposition of a fundamental and its second harmonic optimized such that highest harmonic yields are emitted from each atom. We then optimize the gas pressure and the length and radius of the waveguide such that bright coherent high-order harmonics with angular divergence smaller than 1 mrad are generated, for photon energy from the extreme ultraviolet to soft X-rays. By selecting a proper spectral range enhanced isolated attosecond pulses are generated. We study how dynamic phase matching caused by the interplay among waveguide mode, neutral atomic dispersion, and plasma effect is achieved at the optimal macroscopic conditions, by performing time-frequency analysis and by analyzing the evolution of the driving laser’s electric field during the propagation. Our results, when combined with the on-going push of high-repetition-rate lasers (sub- to few MHz’s) may eventually lead to the generation of high-flux, low-divergence soft X-ray tabletop isolated attosecond pulses for applications.
Effect of TREM-1 blockade and single nucleotide variants in experimental renal injury and kidney transplantation
Authors: Tammaro A. , Kers J. , Emal D. , Stroo I. , Teske G. J. D. , Butter L. M. , Claessen N. , Damman J. , Derive M. , Navis G. , Florquin S. , Leemans J. C. , Dessing M. C. 
Published: December 2016

AbstractRenal ischemia reperfusion (IR)-injury induces activation of innate immune response which sustains renal injury and contributes to the development of delayed graft function (DGF). Triggering receptor expressed on myeloid cells-1 (TREM-1) is a pro-inflammatory evolutionary conserved pattern recognition receptor expressed on a variety of innate immune cells. TREM-1 expression increases following acute and chronic renal injury. However, the function of TREM-1 in renal IR is still unclear. Here, we investigated expression and function of TREM-1 in a murine model of renal IR using different TREM-1 inhibitors: LP17, LR12 and TREM-1 fusion protein. In a human study, we analyzed the association of non-synonymous single nucleotide variants in the TREM1 gene in a cohort comprising 1263 matching donors and recipients with post-transplant outcomes, including DGF. Our findings demonstrated that, following murine IR, renal TREM-1 expression increased due to the influx of Trem1 mRNA expressing cells detected by in situ hybridization. However, TREM-1 interventions by means of LP17, LR12 and TREM-1 fusion protein did not ameliorate IR-induced injury. In the human renal transplant cohort, donor and recipient TREM1 gene variant p.Thr25Ser was not associated with DGF, nor with biopsy-proven rejection or death-censored graft failure. We conclude that TREM-1 does not play a major role during experimental renal IR and after kidney transplantation.
Evolution of the NET (NocA, Nlz, Elbow, TLP-1) protein family in metazoans: insights from expression data and phylogenetic analysis
Authors: Pereira Filipe , Duarte-Pereira Sara , Silva Raquel M. , da Costa Luís Teixeira , Pereira-Castro Isabel 
Published: December 2016

AbstractThe NET (for NocA, Nlz, Elbow, TLP-1) protein family is a group of conserved zinc finger proteins linked to embryonic development and recently associated with breast cancer. The members of this family act as transcriptional repressors interacting with both class I histone deacetylases and Groucho/TLE co-repressors. In Drosophila, the NET family members Elbow and NocA are vital for the development of tracheae, eyes, wings and legs, whereas in vertebrates ZNF703 and ZNF503 are important for the development of the nervous system, eyes and limbs. Despite the relevance of this protein family in embryogenesis and cancer, many aspects of its origin and evolution remain unknown. Here, we show that NET family members are present and expressed in multiple metazoan lineages, from cnidarians to vertebrates. We identified several protein domains conserved in all metazoan species or in specific taxonomic groups. Our phylogenetic analysis suggests that the NET family emerged in the last common ancestor of cnidarians and bilaterians and that several rounds of independent events of gene duplication occurred throughout evolution. Overall, we provide novel data on the expression and evolutionary history of the NET family that can be relevant to understanding its biological role in both normal conditions and disease.
Totally embedded hybrid thin films of carbon nanotubes and silver nanowires as flat homogenous flexible transparent conductors
Authors: Pillai Suresh Kumar Raman , Wang Jing , Wang Yilei , Sk Md Moniruzzaman , Prakoso Ari Bimo , Rusli  , Chan-Park Mary B. 
Published: December 2016

AbstractThere is a great need for viable alternatives to today’s transparent conductive film using largely indium tin oxide. We report the fabrication of a new type of flexible transparent conductive film using silver nanowires (AgNW) and single-walled carbon nanotube (SWCNT) networks which are fully embedded in a UV curable resin substrate. The hybrid SWCNTs-AgNWs film is relatively flat so that the RMS roughness of the top surface of the film is 3 nm. Addition of SWCNTs networks make the film resistance uniform; without SWCNTs, sheet resistance of the surface composed of just AgNWs in resin varies from 20 Ω/sq to 107 Ω/sq. With addition of SWCNTs embedded in the resin, sheet resistance of the hybrid film is 29 ± 5 Ω/sq and uniform across the 47 mm diameter film discs; further, the optimized film has 85% transparency. Our lamination-transfer UV process doesn’t need solvent for sacrificial substrate removal and leads to good mechanical interlocking of the nano-material networks. Additionally, electrochemical study of the film for supercapacitors application showed an impressive 10 times higher current in cyclic voltammograms compared to the control without SWCNTs. Our fabrication method is simple, cost effective and enables the large-scale fabrication of flat and flexible transparent conductive films.
Subchronic perfluorooctanesulfonate (PFOS) exposure induces elevated mutant frequency in an in vivo λ transgenic medaka mutation assay
Authors: Chen Yuanhong , Hu Wei , Huang Changjiang , Hua Shushan , Wei Qihao , Bai Chenglian , Chen Jiangfei , Norris Michelle B. , Winn Richard , Yang Dongren , Dong Qiaoxiang 
Published: December 2016

AbstractPerfluorooctanesulfonate (PFOS) has been widely detected in the environment, wildlife and humans, but few studies have ever examined its mutagenic effect in vivo. In the present study, we use a transgenic fish model, the λ transgenic medaka, to evaluate the potential mutagenicity of PFOS in vivo following a subchronic exposure of 30 days. The mutant frequency of cII target gene was 3.46 × 10−5 in liver tissue from control fish, which increased by 1.4-fold to 4.86 × 10−5 in fish exposed to 6.7 μg/L PFOS, 1.55-fold to 5.36 × 10−5 in fish exposed to 27.6 μg/L PFOS, and 2.02-fold to 6.99 × 10−5 in fish exposed to 87.6 μg/L PFOS. This dose-dependent increase of mutant frequency was also accompanied with mutational spectrum changes associated with PFOS exposure. In particular, PFOS-induced mutation was characterized by +1 frameshift mutations, which increased from 0% in control fish to 13.2% in fish exposed to 27.6 μg/L PFOS and 14.6% in fish exposed to 87.6 μg/L PFOS. Our findings provide the first evidence of PFOS’s mutagenicity in an aquatic model system. Given the fact that most conventional mutagenic assays were negative for PFOS, we propose that PFOS-induced mutation in liver tissue of λ transgenic medaka may be mediated through compromised liver function.
Lipid-modified G4-decoy oligonucleotide anchored to nanoparticles: delivery and bioactivity in pancreatic cancer cells
Authors: Cogoi S. , Jakobsen U. , Pedersen E. B. , Vogel S. , Xodo L. E. 
Published: December 2016

AbstractKRAS is mutated in >90% of pancreatic ductal adenocarcinomas. As its inactivation leads to tumour regression, mutant KRAS is considered an attractive target for anticancer drugs. In this study we report a new delivery strategy for a G4-decoy oligonucleotide that sequesters MAZ, a transcription factor essential for KRAS transcription. It is based on the use of palmitoyl-oleyl-phosphatidylcholine (POPC) liposomes functionalized with lipid-modified G4-decoy oligonucleotides and a lipid-modified cell penetrating TAT peptide. The potency of the strategy in pancreatic cancer cells is demonstrated by cell cytometry, confocal microscopy, clonogenic and qRT-PCR assays.
Designing Multipolar Resonances in Dielectric Metamaterials
Authors: Butakov Nikita A. , Schuller Jon A. 
Published: December 2016

AbstractDielectric resonators form the building blocks of nano-scale optical antennas and metamaterials. Due to their multipolar resonant response and low intrinsic losses they offer design flexibility and high-efficiency performance. These resonators are typically described in terms of a spherical harmonic decomposition with Mie theory. In experimental realizations however, a departure from spherical symmetry and the use of high-index substrates leads to new features appearing in the multipolar response. To clarify this behavior, we present a systematic experimental and numerical characterization of Silicon disk resonators. We demonstrate that for disk resonators on low-index quartz substrates, the electric and magnetic dipole modes are easily identifiable across a wide range of aspect-ratios, but that higher order peaks cannot be unambiguously associated with any specific multipolar mode. On high-index Silicon substrates, even the fundamental dipole modes do not have a clear association. When arranged into arrays, resonances are shifted and pronounced preferential forward and backward scattering conditions appear, which are not as apparent in individual resonators and may be associated with interference between multipolar modes. These findings present new opportunities for engineering the multipolar scattering response of dielectric optical antennas and metamaterials, and provide a strategy for designing nano-optical components with unique functionalities.
Human adipose mesenchymal stem cell-derived exosomal-miRNAs are critical factors for inducing anti-proliferation signalling to A2780 and SKOV-3 ovarian cancer cells
Authors: Reza Abu Musa Md Talimur , Choi Yun-Jung , Yasuda Hideyo , Kim Jin-Hoi 
Published: December 2016

AbstractAn enigmatic question exists concerning the pro- or anti-cancer status of mesenchymal stem cells (MSCs). Despite growing interest, this question remains unanswered, and the debate became intensified with new evidences backing each side. Here, we showed that human adipose MSC (hAMSC)-derived conditioned medium (CM) exhibited inhibitory effects on A2780 human ovarian cancer cells by blocking the cell cycle, and activating mitochondria-mediated apoptosis signalling. Explicitly, we demonstrated that exosomes, an important biological component of hAMSC-CM, could restrain proliferation, wound-repair and colony formation ability of A2780 and SKOV-3 cancer cells. Furthermore, hAMSC-CM-derived exosomes induced apoptosis signalling by upregulating different pro-apoptotic signalling molecules, such as BAX, CASP9, and CASP3, as well as downregulating the anti-apoptotic protein BCL2. More specifically, cancer cells exhibited reduced viability following fresh or protease-digested exosome treatment; however, treatment with RNase-digested exosomes could not inhibit the proliferation of cancer cells. Additionally, sequencing of exosomal RNAs revealed a rich population of microRNAs (miRNAs), which exhibit anti-cancer activities by targeting different molecules associated with cancer survival. Our findings indicated that exosomal miRNAs are important players involved in the inhibitory influence of hAMSC-CM towards ovarian cancer cells. Therefore, we believe that these comprehensive results will provide advances concerning ovarian cancer research and treatment.
Epitaxy of highly ordered organic semiconductor crystallite networks supported by hexagonal boron nitride
Authors: Matković Aleksandar , Genser Jakob , Lüftner Daniel , Kratzer Markus , Gajić Radoš , Puschnig Peter , Teichert Christian 
Published: December 2016

AbstractThis study focuses on hexagonal boron nitride as an ultra-thin van der Waals dielectric substrate for the epitaxial growth of highly ordered crystalline networks of the organic semiconductor parahexaphenyl. Atomic force microscopy based morphology analysis combined with density functional theory simulations reveal their epitaxial relation. As a consequence, needle-like crystallites of parahexaphenyl grow with their long axes oriented five degrees off the hexagonal boron nitride zigzag directions. In addition, by tuning the deposition temperature and the thickness of hexagonal boron nitride, ordered networks of needle-like crystallites as long as several tens of micrometers can be obtained. A deeper understanding of the organic crystallites growth and ordering at ultra-thin van der Waals dielectric substrates will lead to grain boundary-free organic field effect devices, limited only by the intrinsic properties of the organic semiconductors.
Salt tolerance during germination and seedling growth of wild wheat Aegilops tauschii and its impact on the species range expansion
Authors: Saisho Daisuke , Takumi Shigeo , Matsuoka Yoshihiro 
Published: December 2016

AbstractAdaptation to edaphic stress may have a key role in plant species range expansion. Aegilops tauschii Coss., the common wheat’s D-genome progenitor native to the Transcaucasus-Middle East region, is a good model to study the relationships between soil salinity and plant distributions: one of its intraspecific sublineages, TauL1b, drove the long-distance eastward expansion of this species range reaching semi-arid-central Asia. Salt tolerance during germination and seedling growth was evaluated in 206 Ae. tauschii accessions by treating seeds with NaCl solutions differing in concentrations. Differences in natural variation patterns were analyzed between sublineages and associated with natural edaphic condition variables, and then compared with reproductive trait variation patterns. The natural variations observed in NaCl-induced-stress tolerance had clear geographic and genetic structure. Seedling growth significantly increased in the TauL1b accessions that were collected from salt-affected soil habitats, whereas germinability did not. Principal component analysis suggested that the NaCl-induced-stress tolerances and reproductive traits might have had a similar degree of influence on Ae. tauschii’s eastward range expansion. Adaptation to salt-affected soils through increased seedling growth was an important factor for the species’ successful colonization of the semi-arid central Asian habitats. TauL1b accessions might provide useful genetic resources for salt-tolerant wheat breeds.
Fractal Based Analysis of the Influence of Odorants on Heart Activity
Authors: Namazi Hamidreza , Kulish Vladimir V. 
Published: December 2016

AbstractAn important challenge in heart research is to make the relation between the features of external stimuli and heart activity. Olfactory stimulation is an important type of stimulation that affects the heart activity, which is mapped on Electrocardiogram (ECG) signal. Yet, no one has discovered any relation between the structures of olfactory stimuli and the ECG signal. This study investigates the relation between the structures of heart rate and the olfactory stimulus (odorant). We show that the complexity of the heart rate is coupled with the molecular complexity of the odorant, where more structurally complex odorant causes less fractal heart rate. Also, odorant having higher entropy causes the heart rate having lower approximate entropy. The method discussed here can be applied and investigated in case of patients with heart diseases as the rehabilitation purpose.