bluuebunny/crossref_metadata_2025_split huggingface dataset:
Active Adoption of Void Formation in Metal-Oxide for All Transparent Super-Performing Photodetectors
Authors: Patel Malkeshkumar , Kim Hong-Sik , Park Hyeong-Ho , Kim Joondong 
Published: May 2016

AbstractCould ‘defect-considered’ void formation in metal-oxide be actively used? Is it possible to realize stable void formation in a metal-oxide layer, beyond unexpected observations, for functional utilization? Herein we demonstrate the effective tailoring of void formation of NiO for ultra-sensitive UV photodetection. NiO was formed onto pre-sputtered ZnO for a large size and spontaneously formed abrupt p-NiO/n-ZnO heterojunction device. To form voids at an interface, rapid thermal process was performed, resulting in highly visible light transparency (85–95%). This heterojunction provides extremely low saturation current (<0.1 nA) with an extraordinary rectifying ratio value of over 3000 and works well without any additional metal electrodes. Under UV illumination, we can observe the fast photoresponse time (10 ms) along with the highest possible responsivity (1.8 A W−1) and excellent detectivity (2 × 1013 Jones) due to the existence of an intrinsic-void layer at the interface. We consider this as the first report on metal-oxide-based void formation (Kirkendall effect) for effective photoelectric device applications. We propose that the active adoption of ‘defect-considered’ Kirkendall-voids will open up a new era for metal-oxide based photoelectric devices.
Evaluation of the appropriateness of using glucometers for measuring the blood glucose levels in mice
Authors: Togashi Yu , Shirakawa Jun , Okuyama Tomoko , Yamazaki Shunsuke , Kyohara Mayu , Miyazawa Ayumi , Suzuki Takafumi , Hamada Mari , Terauchi Yasuo 
Published: May 2016

AbstractGlucometers are also widely used in diabetes research conducted using animal models. However, the appropriateness of measuring blood glucose levels using glucometers in animal models remains unclear. In this study, we evaluated the consistency between the blood glucose levels measured by 11 models of glucometers and plasma glucose levels measured by a laboratory biochemical test in blood samples collected by retro-orbital sinus puncture or tail-tip amputation. In both blood samples obtained by retro-orbital sinus puncture and those obtained by tail-tip amputation, 10 of the 11 models of glucometers yielded higher glucose values, while 1 yielded lower glucose values, than the plasma glucose values yielded by the laboratory test, the differences being in direct proportion to the plasma glucose values. Most glucometers recorded higher blood glucose levels after glucose loading and lower blood glucose levels after insulin loading in retro-orbital sinus blood as compared to tail vein blood. Our data suggest that the blood glucose levels measured by glucometers in mice tended to be higher than the plasma glucose levels yielded by the biochemical test under the hyperglycemic state, and that differences in the measured levels were observed according to the blood collection method depending on the glycemia status.
Large-scale rewiring of innate immunity circuitry and microRNA regulation during initial rice blast infection
Authors: Li Ze-Yuan , Xia Jing , Chen Zheng , Yu Yang , Li Quan-Feng , Zhang Yu-Chan , Zhang Jin-Ping , Wang Cong-Ying , Zhu Xiao-Yuan , Zhang Weixiong , Chen Yue-Qin 
Published: May 2016

AbstractRice blast is a recurrent fungal disease, and resistance to fungal infection is a complex trait. Therefore, a comprehensive examination of rice transcriptome and its variation during fungal infection is necessary to understand the complex gene regulatory networks. In this study, adopting Next-Generation Sequencing we profiled the transcriptomes and microRNAomes of rice varieties, one susceptible and the other resistant to M. oryzae, at multiple time points during the fungal infection. Our results revealed a substantial variation in the plant transcriptome and microRNAome as well as change to rice innate immunity during fungal infection. A number of putative R gene candidates were identified from a perturbed rice transcriptome analysis. The expression of genes and non-coding RNA molecules changed in both fungal resistant and susceptible plants during M. oryzae invasion discovered distinct pathways triggered in the susceptible and resistant plants. In addition, a number of fungus genes in the susceptible and resistant plants were constantly expressed at different time points, suggesting that they were likely to be the potential AVR genes. Our results revealed large-scale rewiring of innate immunity circuitry and microRNA regulation during initial rice blast infection, which would help to develop more robust blast-resistant rice plants.
Meta-q-plate for complex beam shaping
Authors: Ji Wei , Lee Chun-Hong , Chen Peng , Hu Wei , Ming Yang , Zhang Lijian , Lin Tsung-Hsien , Chigrinov Vladimir , Lu Yan-Qing 
Published: May 2016

AbstractOptical beam shaping plays a key role in optics and photonics. In this work, meta-q-plate featured by arbitrarily space-variant optical axes is proposed and demonstrated via liquid crystal photoalignment based on a polarization-sensitive alignment agent and a dynamic micro-lithography system. Meta-q-plates with multiple-, azimuthally/radially variant topological charges and initial azimuthal angles are fabricated. Accordingly, complex beams with elliptical, asymmetrical, multi-ringed and hurricane transverse profiles are generated, making the manipulation of optical vortex up to an unprecedented flexibility. The evolution, handedness and Michelson interferogram of the hurricane one are theoretically analysed and experimentally verified. The design facilitates the manipulation of polarization and spatial degrees of freedom of light in a point-to-point manner. The realization of meta-q-plate drastically enhances the capability of beam shaping and may pave a bright way towards optical manipulations, OAM based informatics, quantum optics and other fields.
Population transcriptomics uncovers the regulation of gene expression variation in adaptation to changing environment
Authors: Xu Qin , Zhu Caiyun , Fan Yangyang , Song Zhihong , Xing Shilai , Liu Wei , Yan Juan , Sang Tao 
Published: May 2016

AbstractExpression variation plays an important role in plant adaptation, but little is known about the factors impacting the expression variation when population adapts to changing environment. We used RNA-seq data from 80 individuals in 14 Miscanthus lutarioriparius populations, which were transplanted into a harsh environment from native habitat, to investigate the expression level, expression diversity and genetic diversity for genes expressed in both environments. The expression level of genes with lower expression level or without SNP tended to be more changeable in new environment, which suggested highly expressed genes experienced stronger purifying selection than those at lower level. Low proportion of genes with population effect confirmed the weak population structure and frequent gene flow in these populations. Meanwhile, the number of genes with environment effect was the most frequent compared with that with population effect. Our results showed that environment and genetic diversity were the main factors determining gene expression variation in population. This study could facilitate understanding the mechanisms of global gene expression variation when plant population adapts to changing environment.
Cleavage Site Localization Differentially Controls Interleukin-6 Receptor Proteolysis by ADAM10 and ADAM17
Authors: Riethmueller Steffen , Ehlers Johanna C. , Lokau Juliane , Düsterhöft Stefan , Knittler Katharina , Dombrowsky Gregor , Grötzinger Joachim , Rabe Björn , Rose-John Stefan , Garbers Christoph 
Published: May 2016

AbstractLimited proteolysis of the Interleukin-6 Receptor (IL-6R) leads to the release of the IL-6R ectodomain. Binding of the cytokine IL-6 to the soluble IL-6R (sIL-6R) results in an agonistic IL-6/sIL-6R complex, which activates cells via gp130 irrespective of whether the cells express the IL-6R itself. This signaling pathway has been termed trans-signaling and is thought to mainly account for the pro-inflammatory properties of IL-6. A Disintegrin And Metalloprotease 10 (ADAM10) and ADAM17 are the major proteases that cleave the IL-6R. We have previously shown that deletion of a ten amino acid long stretch within the stalk region including the cleavage site prevents ADAM17-mediated cleavage, whereas the receptor retained its full biological activity. In the present study, we show that deletion of a triple serine (3S) motif (Ser-359 to Ser-361) adjacent to the cleavage site is sufficient to prevent IL-6R cleavage by ADAM17, but not ADAM10. We find that the impaired shedding is caused by the reduced distance between the cleavage site and the plasma membrane. Positioning of the cleavage site in greater distance towards the plasma membrane abrogates ADAM17-mediated shedding and reveals a novel cleavage site of ADAM10. Our findings underline functional differences in IL-6R proteolysis by ADAM10 and ADAM17.
Touch uses frictional cues to discriminate flat materials
Authors: Gueorguiev David , Bochereau Séréna , Mouraux André , Hayward Vincent , Thonnard Jean-Louis 
Published: May 2016

AbstractIn a forced-choice task, we asked human participants to discriminate by touch alone glass plates from transparent polymethyl methacrylate (PMMA) plastic plates. While the surfaces were flat and did not exhibit geometric features beyond a few tens of nanometres, the materials differed by their molecular structures. They produced similar coefficients of friction and thermal effects were controlled. Most participants performed well above chance and participants with dry fingers discriminated the materials especially well. Current models of tactile surface perception appeal to surface topography and cannot explain our results. A correlation analysis between detailed measurements of the interfacial forces and discrimination performance suggested that the perceptual task depended on the transitory contact phase leading to full slip. This result demonstrates that differences in interfacial mechanics between the finger and a material can be sensed by touch and that the evanescent mechanics that take place before the onset of steady slip have perceptual value.
Rational design of mutations that change the aggregation rate of a protein while maintaining its native structure and stability
Authors: Camilloni Carlo , Sala Benedetta Maria , Sormanni Pietro , Porcari Riccardo , Corazza Alessandra , De Rosa Matteo , Zanini Stefano , Barbiroli Alberto , Esposito Gennaro , Bolognesi Martino , Bellotti Vittorio , Vendruscolo Michele , Ricagno Stefano 
Published: May 2016

AbstractA wide range of human diseases is associated with mutations that, destabilizing proteins native state, promote their aggregation. However, the mechanisms leading from folded to aggregated states are still incompletely understood. To investigate these mechanisms, we used a combination of NMR spectroscopy and molecular dynamics simulations to compare the native state dynamics of Beta-2 microglobulin (β2m), whose aggregation is associated with dialysis-related amyloidosis, and its aggregation-resistant mutant W60G. Our results indicate that W60G low aggregation propensity can be explained, beyond its higher stability, by an increased average protection of the aggregation-prone residues at its surface. To validate these findings, we designed β2m variants that alter the aggregation-prone exposed surface of wild-type and W60G β2m modifying their aggregation propensity. These results allowed us to pinpoint the role of dynamics in β2m aggregation and to provide a new strategy to tune protein aggregation by modulating the exposure of aggregation-prone residues.
Generation and gene expression profiling of 48 transcription-factor-inducible mouse embryonic stem cell lines
Authors: Yamamizu Kohei , Sharov Alexei A. , Piao Yulan , Amano Misa , Yu Hong , Nishiyama Akira , Dudekula Dawood B. , Schlessinger David , Ko Minoru S. H. 
Published: May 2016

AbstractMouse embryonic stem cells (ESCs) can differentiate into a wide range – and possibly all cell types in vitro, and thus provide an ideal platform to study systematically the action of transcription factors (TFs) in cell differentiation. Previously, we have generated and analyzed 137 TF-inducible mouse ESC lines. As an extension of this “NIA Mouse ESC Bank,” we generated and characterized 48 additional mouse ESC lines, in which single TFs in each line could be induced in a doxycycline-controllable manner. Together, with the previous ESC lines, the bank now comprises 185 TF-manipulable ESC lines (>10% of all mouse TFs). Global gene expression (transcriptome) profiling revealed that the induction of individual TFs in mouse ESCs for 48 hours shifts their transcriptomes toward specific differentiation fates (e.g., neural lineages by Myt1 Isl1, and St18; mesodermal lineages by Pitx1, Pitx2, Barhl2, and Lmx1a; white blood cells by Myb, Etv2, and Tbx6, and ovary by Pitx1, Pitx2, and Dmrtc2). These data also provide and lists of inferred target genes of each TF and possible functions of these TFs. The results demonstrate the utility of mouse ESC lines and their transcriptome data for understanding the mechanism of cell differentiation and the function of TFs.
9.5 mW fully integrated K‐band on–off keying receiver with −47.6 dBm sensitivity and 600 Mbit/s data rate in 90 nm CMOS
Authors: Chiou H.‐K. , Chien K.‐H. 
Published: May 2016

A K‐band on–off keying (OOK) receiver implemented in tsmcTM 90 nm CMOS process is proposed. The proposed OOK receiver consists of a two‐stage wideband low‐noise amplifier, a single‐to‐differential envelop detector with RC lowpass filter and a 62.6 dB three‐stage variable gain amplifier and DC offset compensation circuit. The OOK receiver achieved a sensitivity of −47.6 dBm at 600 Mbit/s data rate under a pseudo‐random binary sequence 29–1 pattern. The receiver consumes a low power of 9.5 mW, which minimum average power is only 15.86 nW at the input power of −47.6 dBm. The chip area including test pads is 1 × 0.81 mm2.
Amine functionalised hydroxyapatite nanoparticles for anti‐angiogenesis gene therapy of breast cancer
Authors: Xu Hongjie , Wei Dajun , Gai Xiaodong , Jiang Ying 
Published: May 2016

A functionalised hydroxyapatite (HAP) nanoparticles based drug delivery system (DDS) [anti‐angiogenesis (ANG)/amine functionalised HAP (NHAP) nanoparticles] composed of HAP nanoparticles and therapeutic ANG plasmid was successfully developed for gene therapy of breast cancer. ANG/NHAP nanoparticles displayed nano‐sized diameter of around 50 nm and effective plasmid condensation ability. Cellular assays on MCF‐7 cells further confirmed high transfection and ANG efficacy as well as low cytotoxicity of ANG/NHAP nanoparticles, which suggested that ANG/NHAP nanoparticles might be a safe and effective DDS for potential breast cancer gene therapy.
Seascapes are not landscapes: an analysis performed using Bernhard Riemann's rules
Authors: Manderson John Pilling 
Published: May 2016

AbstractApplied seascape ecology rests on paradigms of terrestrial landscape ecology. Patches defined by persistent seabed features are the basic units of analysis. Persistent oceanographic features provide context while dynamic features are usually ignored. Should seascape ecology rest on terrestrial paradigms? I use Reimann’s rules of analysis to identify differences between seascapes and landscapes. Reimann’s method uses hypotheses about system function to guide the development of models of system components based upon fundamental “laws”. The method forced me to avoid using terrestrial analogies in understanding of organism-habitat relationships. The fundamental laws applying to all organisms were the conservative metabolic requirements underlying individual performance and population growth. Physical properties of the environment; specifically those dictating strategies available to organisms meeting metabolic requirements, were the “laws” applying to the external environment. Organisms living in the ocean’s liquid meet most metabolic requirements using strong habitat selection for properties of the liquid that are controlled by “fast”, often episodic, atmospheric and tidal forces. Seascapes are therefor primarily driven by dynamic hydrography including mixing processes. In contrast, most terrestrial organisms are decoupled by gravity and physiological regulation from an atmospheric fluid that is metabolically more challenging. They show strong habitat selection for many essential metabolic materials concentrated on the land surface where slower biogeochemical processes including soil development drive ecological dynamics. Living in a liquid is different from living in a gas and resource use management in the oceans needs to be tuned to seascapes dynamics that is driven primarily by hydrodynamics and secondarily by seabed processes. Advances in ocean observing and data assimilative circulation models now permit the rapid development of applied seascape ecology. This development is essential now that changes in global climate are being rapidly translated into changes in the dynamics of the ocean hydrosphere that structures and controls ecological dynamics within seascapes.
SU Lyncis, a hard X-ray bright M giant: clues point to a large hidden population of symbiotic stars
Authors: Mukai K. , Luna G. J. M. , Cusumano G. , Segreto A. , Munari U. , Sokoloski J. L. , Lucy A. B. , Nelson T. , Nuñez N. E. 
Published: May 2016

Abstract
Symbiotic star surveys have traditionally relied almost exclusively on low resolution optical spectroscopy. However, we can obtain a more reliable estimate of their total Galactic population by using all available signatures of the symbiotic phenomenon. Here we report the discovery of a hard X-ray source, 4PBC J0642.9+5528, in the Swift hard X-ray all-sky survey, and identify it with a poorly studied red giant, SU Lyn, using pointed Swift observations and ground-based optical spectroscopy. The X-ray spectrum, the optical to UV spectrum, and the rapid UV variability of SU Lyn are all consistent with our interpretation that it is a symbiotic star containing an accreting white dwarf. The symbiotic nature of SU Lyn went unnoticed until now, because it does not exhibit emission lines strong enough to be obvious in low resolution spectra. We argue that symbiotic stars without shell-burning have weak emission lines, and that the current lists of symbiotic stars are biased in favour of shell-burning systems. We conclude that the true population of symbiotic stars has been underestimated, potentially by a large factor.
Donor-Derived Coccidioides immitis Endocarditis and Disseminated Infection in the Setting of Solid Organ Transplantation
Authors: Nelson Joanna K. , Giraldeau Genevieve , Montoya Jose G. , Deresinski Stan , Ho Dora Y. , Pham Michael 
Published: May 2016

Abstract
Background.  Endocarditis is a rare manifestation of infection with Coccidioides. This is the first reported case of donor-derived Coccidioides endocarditis obtained from a heart transplant.
Methods.  We present a unique case of donor-derived Coccidioides immitis endocarditis and disseminated infection in a heart transplant patient. We also conducted a review of the literature to identify other cases of donor-derived coccidioidomycosis in solid organ transplant recipients and reviewed their clinical characteristics.
Results.  Fifteen prior cases of donor-derived coccidioidomycosis were identified. A majority of these cases were diagnosed by positive culture (83%). Mortality was high at 58%.
Conclusions.  Clinicians should maintain a high index of suspicion for disseminated coccidioidomycosis in patients who received transplants with organs from donors with a history of residing in endemic regions.
Consensus Phylogenetic trees of Fifteen Prokaryotic Aminoacyl-tRNA Synthetase Polypeptides based on Euclidean Geometry of All-Pairs Distances and Concatenation
Authors: Bargaje Rhishikesh , Kumar M.Milner , Modak Sohan Prabhakar 
Published: May 2016

AbstractBackgroundMost molecular phylogenetic trees depict the relative closeness or the extent of similarity among a set of taxa based on comparison of sequences of homologous genes or proteins. Since the tree topology for individual monogenic traits varies among the same set of organisms and does not overlap taxonomic hierarchy, hence there is a need to generate multidimensional phylogenetic trees.ResultsPhylogenetic trees were constructed for 119 prokaryotes representing 2 phyla under Archaea and 11 phyla under Bacteria after comparing multiple sequence alignments for 15 different aminoacyl-tRNA synthetase polypeptides. The topology of Neighbor Joining (NJ) trees for individual tRNA synthetase polypeptides varied substantially. We use Euclidean geometry to estimate all-pairs distances in order to construct phylogenetic trees. Further, we used a novel “Taxonomic fidelity” algorithm to estimate clade by clade similarity between the phylogenetic tree and the taxonomic tree. We find that, as compared to trees for individual tRNA synthetase polypeptides and rDNA sequences, the topology of our Euclidean tree and that for aligned and concatenated sequences of 15 proteins are closer to the taxonomic trees and offer the best consensus. We have also aligned sequences after concatenation, and find that by changing the order of sequence joining prior to alignment, the tree topologies vary. In contrast, changing the types of polypeptides in the grouping for Euclidean trees does not affect the tree topologies.ConclusionsWe show that a consensus phylogenetic tree of 15 polypeptides from 14 aminoacyl-tRNA synthetases for 119 prokaryotes using Euclidean geometry exhibits better taxonomic fidelity than trees for individual tRNA synthetase polypeptides as well as 16S rDNA. We have also examined Euclidean N-dimensional trees for 15 tRNA synthetase polypeptides which give the same topology as that constructed after amalgamating 3-dimensional Euclidean trees for groups of 3 polypeptides. Euclidean N-dimensional trees offer a reliable future to multi-genic molecular phylogenetics.
Methods for High-Throughput Drug Combination Screening and Synergy Scoring
Authors: He Liye , Kulesskiy Evgeny , Saarela Jani , Turunen Laura , Wennerberg Krister , Aittokallio Tero , Tang Jing 
Published: May 2016

AbstractGene products or pathways that are aberrantly activated in cancer but not in normal tissue hold great promises for being effective and safe anticancer therapeutic targets. Many targeted drugs have entered clinical trials but so far showed limited efficacy mostly due to variability in treatment responses and often rapidly emerging resistance. Towards more effective treatment options, we will critically need multi-targeted drugs or drug combinations, which selectively inhibit the cancer cells and block distinct escape mechanisms for the cells to become resistant. Functional profiling of drug combinations requires careful experimental design and robust data analysis approaches. At the Institute for Molecular Medicine Finland (FIMM), we have developed an experimental-computational pipeline for high-throughput screening of drug combination effects in cancer cells. The integration of automated screening techniques with advanced synergy scoring tools allows for efficient and reliable detection of synergistic drug interactions within a specific window of concentrations, hence accelerating the identification of potential drug combinations for further confirmatory studies.