bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atomic Scale Structural Characterization of Epitaxial (Cd,Cr)Te Magnetic Semiconductor
Authors: Bonef Bastien , Boukari Hervé , Grenier Adeline , Mouton Isabelle , Jouneau Pierre-Henri , Kinjo Hidekazu , Kuroda Shinji 
Published: June 2017

AbstractA detailed knowledge of the atomic structure of magnetic semiconductors is crucial to understanding their electronic and magnetic properties, which could enable spintronic applications. Energy-dispersive X-ray spectrometry (EDX) in the scanning transmission electron microscope and atom probe tomography (APT) experiments reveal the formation of Cr-rich regions in Cd1−xCrxTe layers grown by molecular beam epitaxy. These Cr-rich regions occur on a length scale of 6–10 nm at a nominal Cr composition of x=0.034 and evolve toward an ellipsoidal shape oriented along <111> directions at a composition of x=0.083. Statistical analysis of the APT reconstructed volume reveals that the Cr aggregation increases with the average Cr composition. The correlation with the magnetic properties of such (Cd,Cr)Te layers is discussed within the framework of strongly inhomogeneous materials. Finally, difficulties in accurately quantifying the Cr distribution in the CdTe matrix on an atomic scale by EDX and APT are discussed.
Open-source, community-driven microfluidics with Metafluidics
Authors: Kong David S , Thorsen Todd A , Babb Jonathan , Wick Scott T , Gam Jeremy J , Weiss Ron , Carr Peter A 
Published: June 2017

Abstract
Microfluidic devices have the potential to automate and miniaturize biological experiments, but open-source sharing of device designs has lagged behind sharing of other resources such as software. Synthetic biologists have used microfluidics for DNA assembly, cell-free expression, and cell culture, but a combination of expense, device complexity, and reliance on custom set-ups hampers their widespread adoption. We present Metafluidics, an open-source, community-driven repository that hosts digital design files, assembly specifications, and open-source software to enable users to build, configure, and operate a microfluidic device. We use Metafluidics to share designs and fabrication instructions for both a microfluidic ring-mixer device and a 32-channel tabletop microfluidic controller. This device and controller are applied to build genetic circuits using standard DNA assembly methods including ligation, Gateway, Gibson, and Golden Gate. Metafluidics is intended to enable a broad community of engineers, DIY enthusiasts, and other nontraditional participants with limited fabrication skills to contribute to microfluidic research.
Astronomical pacing of the global silica cycle recorded in Mesozoic bedded cherts
Authors: Ikeda Masayuki , Tada Ryuji , Ozaki Kazumi 
Published: June 2017

AbstractThe global silica cycle is an important component of the long-term climate system, yet its controlling factors are largely uncertain due to poorly constrained proxy records. Here we present a ∼70 Myr-long record of early Mesozoic biogenic silica (BSi) flux from radiolarian chert in Japan. Average low-mid-latitude BSi burial flux in the superocean Panthalassa is ∼90% of that of the modern global ocean and relative amplitude varied by ∼20–50% over the 100 kyr to 30 Myr orbital cycles during the early Mesozoic. We hypothesize that BSi in chert was a major sink for oceanic dissolved silica (DSi), with fluctuations proportional to DSi input from chemical weathering on timescales longer than the residence time of DSi (<∼100 Kyr). Chemical weathering rates estimated by the GEOCARBSULFvolc model support these hypotheses, excluding the volcanism-driven oceanic anoxic events of the Early-Middle Triassic and Toarcian that exceed model limits. We propose that the Mega monsoon of the supercontinent Pangea nonlinearly amplified the orbitally paced chemical weathering that drove BSi burial during the early Mesozoic greenhouse world.
Variation in auxin sensing guides AUX/IAA transcriptional repressor ubiquitylation and destruction
Authors: Winkler Martin , Niemeyer Michael , Hellmuth Antje , Janitza Philipp , Christ Gideon , Samodelov Sophia L. , Wilde Verona , Majovsky Petra , Trujillo Marco , Zurbriggen Matias D. , Hoehenwarter Wolfgang , Quint Marcel , Calderón Villalobos Luz Irina A. 
Published: June 2017

AbstractAuxin is a small molecule morphogen that bridges SCFTIR1/AFB-AUX/IAA co-receptor interactions leading to ubiquitylation and proteasome-dependent degradation of AUX/IAA transcriptional repressors. Here, we systematically dissect auxin sensing by SCFTIR1-IAA6 and SCFTIR1-IAA19 co-receptor complexes, and assess IAA6/IAA19 ubiquitylation in vitro and IAA6/IAA19 degradation in vivo. We show that TIR1-IAA19 and TIR1-IAA6 have distinct auxin affinities that correlate with ubiquitylation and turnover dynamics of the AUX/IAA. We establish a system to track AUX/IAA ubiquitylation in IAA6 and IAA19 in vitro and show that it occurs in flexible hotspots in degron-flanking regions adorned with specific Lys residues. We propose that this signature is exploited during auxin-mediated SCFTIR1-AUX/IAA interactions. We present evidence for an evolving AUX/IAA repertoire, typified by the IAA6/IAA19 ohnologues, that discriminates the range of auxin concentrations found in plants. We postulate that the intrinsic flexibility of AUX/IAAs might bias their ubiquitylation and destruction kinetics enabling specific auxin responses.
Misfolded polypeptides are selectively recognized and transported toward aggresomes by a CED complex
Authors: Park Joori , Park Yeonkyoung , Ryu Incheol , Choi Mi-Hyun , Lee Hyo Jin , Oh Nara , Kim Kyutae , Kim Kyoung Mi , Choe Junho , Lee Cheolju , Baik Ja-Hyun , Kim Yoon Ki 
Published: June 2017

AbstractMisfolded polypeptides are rapidly cleared from cells via the ubiquitin–proteasome system (UPS). However, when the UPS is impaired, misfolded polypeptides form small cytoplasmic aggregates, which are sequestered into an aggresome and ultimately degraded by aggrephagy. Despite the relevance of the aggresome to neurodegenerative proteinopathies, the molecular mechanisms underlying aggresome formation remain unclear. Here we show that the CTIF–eEF1A1–DCTN1 (CED) complex functions in the surveillance of either pre-existing or newly synthesized polypeptides by linking two molecular events: selective recognition and aggresomal targeting of misfolded polypeptides. These events are accompanied by CTIF sequestration into the aggresome, preventing the additional synthesis of misfolded polypeptides from mRNAs bound by nuclear cap-binding complex. These events render cells more resistant to apoptosis induced by proteotoxic stresses. Collectively, our data provide compelling evidence for a previously unappreciated protein surveillance pathway and a regulatory gene expression network for coping with misfolded polypeptides.
Dissemination of antibiotic resistance genes from antibiotic producers to pathogens
Authors: Jiang Xinglin , Ellabaan Mostafa M. Hashim , Charusanti Pep , Munck Christian , Blin Kai , Tong Yaojun , Weber Tilmann , Sommer Morten O. A. , Lee Sang Yup 
Published: June 2017

AbstractIt has been hypothesized that some antibiotic resistance genes (ARGs) found in pathogenic bacteria derive from antibiotic-producing actinobacteria. Here we provide bioinformatic and experimental evidence supporting this hypothesis. We identify genes in proteobacteria, including some pathogens, that appear to be closely related to actinobacterial ARGs known to confer resistance against clinically important antibiotics. Furthermore, we identify two potential examples of recent horizontal transfer of actinobacterial ARGs to proteobacterial pathogens. Based on this bioinformatic evidence, we propose and experimentally test a ‘carry-back’ mechanism for the transfer, involving conjugative transfer of a carrier sequence from proteobacteria to actinobacteria, recombination of the carrier sequence with the actinobacterial ARG, followed by natural transformation of proteobacteria with the carrier-sandwiched ARG. Our results support the existence of ancient and, possibly, recent transfers of ARGs from antibiotic-producing actinobacteria to proteobacteria, and provide evidence for a defined mechanism.
Compartmentalized 3D Tissue Culture Arrays under Controlled Microfluidic Delivery
Authors: Gumuscu Burcu , Albers Hugo J. , van den Berg Albert , Eijkel Jan C. T. , van der Meer Andries D. 
Published: June 2017

AbstractWe demonstrate an in vitro microfluidic cell culture platform that consists of periodic 3D hydrogel compartments with controllable shapes. The microchip is composed of approximately 500 discontinuous collagen gel compartments locally patterned in between PDMS pillars, separated by microfluidic channels. The typical volume of each compartment is 7.5 nanoliters. The compartmentalized design of the microchip and continuous fluid delivery enable long-term culturing of Caco-2 human intestine cells. We found that the cells started to spontaneously grow into 3D folds on day 3 of the culture. On day 8, Caco-2 cells were co-cultured for 36 hours under microfluidic perfusion with intestinal bacteria (E. coli) which did not overgrow in the system, and adhered to the Caco-2 cells without affecting cell viability. Continuous perfusion enabled the preliminary evaluation of drug effects by treating the co-culture of Caco-2 and E. coli with 34 µg ml−1 chloramphenicol during 36 hours, resulting in the death of the bacteria. Caco-2 cells were also cultured in different compartment geometries with large and small hydrogel interfaces, leading to differences in proliferation and cell spreading profile of Caco-2 cells. The presented approach of compartmentalized cell culture with facile microfluidic control can substantially increase the throughput of in vitro drug screening in the future.
The correlation between the expression of genes involved in drug metabolism and the blood level of tacrolimus in liver transplant receipts
Authors: Wang Jianhai , Li Keqiu , Zhang Xiaoning , Teng Dahong , Ju Mingyan , Jing Yaqing , Zhao Yuxia , Li Guang 
Published: June 2017

AbstractImmunosuppressive medications, such as tacrolimus and mycophenolate mofetil, are commonly used for reducing the risk of organ rejection in receipts of allogeneic organ transplant. The optimal dosages of these drugs are required for preventing rejection and avoiding toxicity to receipts. This study aimed to identify the correlation between the expression profiling of genes involved in drug metabolism and the blood level of tacrolimus in liver transplant receipts. Sixty-four liver transplant receipts were enrolled in this retrospective study. Receipts were divided into low (2–5.9 ng/ml) and high (6–15 ng/ml) tacrolimus groups. Clinical assessment showed that the blood level of tacrolimus was inversely correlated with the liver function evaluated by blood levels of total bilirubin and creatinine. Compared to the high tacrolimus group, expression levels of six cytochrome P450 enzymes, CYP1A1, CYP2B6, CYP3A5, CYP4A11, CYP19A1, and CYP17A1 were significantly higher in the low tacrolimus group. The expression levels of these genes were negatively correlated with the tacrolimus blood level. Enzyme assays showed that CYP3A5 and CYP17A1 exerted direct metabolic effects on tacrolimus and mycophenolate mofetil, respectively. These results support clinical application of this expression profiling of genes in drug metabolism for selection of immunosuppressive medications and optimal dosages for organ transplant receipts.
Variable thermal expansion of glass-ceramics containing Ba1−xSrxZn2Si2O7
Authors: Thieme Christian , Schlesier Martin , Oji Dike Eze , Rüssel Christian 
Published: June 2017

AbstractUp to now, the thermal expansion behavior of multiphase glass-ceramics cannot be predicted reliably because of the nescience about the formation of the type and concentration of crystalline phases. In the system BaO-SrO-ZnO-SiO2, recently a new phase based on Ba1−xSrxZn2Si2O7 solid solutions was found, which exhibits unexpected low and highly anisotropic thermal expansion, which can be used for an adjustment of the thermal expansion properties. In the case of sealing materials for high-temperature reactors, the formation of this phase should be avoided. Hence, in this manuscript the concentration thresholds in which these solid solutions precipitate from glasses were determined. The phase analysis was correlated with the thermal expansion behavior of the glass-ceramics. Depending on the Ba/Sr-ratio of the glasses and the considered temperature range, the coefficients of thermal expansion of the glass-ceramics vary between 19.4·10−6 K−1 and 4.8·10−6 K−1. The concentration thresholds in which the as mentioned phases form via crystallization of glasses differ strongly from the literature values obtained via conventional ceramic mixed oxide route.
Deep-sequencing of Marburg virus genome during sequential mouse passaging and cell-culture adaptation reveals extensive changes over time
Authors: Wei Haiyan , Audet Jonathan , Wong Gary , He Shihua , Huang Xueyong , Cutts Todd , Theriault Steven , Xu Bianli , Kobinger Gary , Qiu Xiangguo 
Published: June 2017

AbstractMarburg virus (MARV) has caused outbreaks of filoviral hemorrhagic fever since its discovery in 1967. The largest and deadliest outbreak occurred in Angola in 2005, with 252 cases and 227 deaths. In 2014, we developed a mouse-adapted MARV, Angola variant through serial passaging in mice. The mouse-adapted MARV exhibits many of the hallmarks of MARV disease in humans. By applying deep-sequencing to every passage of the virus, we are able to study virus evolution in this host with surprising precision. We show that two regions go through substantial changes: the intergenic region between NP and VP35, as well as the first 100 amino acids of the VP40 protein. Our results also reveal that there were profound changes during the production of the final virus stock in cell culture. Overall, our results show that a handful of regions carry most of the mutations acquired during the adaptation of the virus to a new host and that many mutations become fixed very early during the adaptation process.
New insight into the function of wheat glutenin proteins as investigated with two series of genetic mutants
Authors: Wang Zhaojun , Li Yiwen , Yang Yushuang , Liu Xin , Qin Huanju , Dong Zhenying , Zheng Shuhai , Zhang Kunpu , Wang Daowen 
Published: June 2017

AbstractAmong the three major food crops (rice, wheat and maize), wheat is unique in accumulating gluten proteins in its grains. Of these proteins, the high and low molecular weight glutenin subunits (HMW-GSs and LMW-GSs) form glutenin macropolymers that are vital for the diverse end-uses of wheat grains. In this work, we developed a new series of deletion mutants lacking one or two of the threeGlu-1loci (Glu-A1,-B1and -D1) specifying HMW-GSs. Comparative analysis of single and double deletion mutants reinforced the suggestion thatGlu-D1(encoding the HMW-GSs 1Dx2 and 1Dy12) has the largest effects on the parameters related to gluten and dough functionalities and breadmaking quality. Consistent with this suggestion, the deletion mutants lackingGlu-D1or its combination withGlu-A1orGlu-B1generally exhibited strong decreases in functional glutenin macropolymers (FGMPs) and in the incorporation of HMW-GSs and LMW-GSs into FGMPs. Further examination of two knockout mutants missing 1Dx2 or 1Dy12 showed that 1Dx2 was clearly more effective than 1Dy12 in promoting FGMPs by enabling the incorporation of more HMW-GSs and LMW-GSs into FGMPs. The new insight obtained and the mutants developed by us may aid further research on the control of wheat end-use quality by glutenin proteins.
Strong 3D and 1D magnetism in hexagonal Fe-chalcogenides FeS and FeSe vs. weak magnetism in hexagonal FeTe
Authors: Parker David S. 
Published: June 2017

AbstractWe present a comparative theoretical study of the hexagonal forms of the Fe-chalcogenides FeS, FeSe and FeTe with their better known tetragonal forms. While the tetragonal forms exhibit only an incipient antiferromagnetism and experimentally show superconductivity when doped, the hexagonal forms of FeS and FeSe display a robust magnetism. We show that this strong magnetism arises from a van Hove singularity associated with the direct Fe-Fe c-axis chains in the generally more three-dimensional NiAs structure. We also find that hexagonal FeTe is much less magnetic than the other two hexagonal materials, so that unconventional magnetically-mediated superconductivity is possible, although a large T
c
value is unlikely.
Fiber Optic Sensor for Real-Time Sensing of Silica Scale Formation in Geothermal Water
Authors: Okazaki Takuya , Orii Tatsuya , Ueda Akira , Ozawa Akiko , Kuramitz Hideki 
Published: June 2017

AbstractWe present a novel fiber optic sensor for real-time sensing of silica scale formation in geothermal water. The sensor is fabricated by removing the cladding of a multimode fiber to expose the core to detect the scale-formation-induced refractive index change. A simple experimental setup was constructed to measure the transmittance response using white light as a source and a spectroscopy detector. A field test was performed on geothermal water containing 980 mg/L dissolved silica at 93 °C in Sumikawa Geothermal Power Plant, Japan. The transmittance response of the fiber sensor decreased due to the formation of silica scale on the fiber core from geothermal water. An application of this sensor in the evaluation of scale inhibitors was demonstrated. In geothermal water containing a pH modifier, the change of transmittance response decreased with pH decrease. The effectiveness of a polyelectrolyte inhibitor in prevention of silica scale formation was easily detectable using the fiber sensor in geothermal water.
Capacity limit for faster-than-Nyquist non-orthogonal frequency-division multiplexing signaling
Authors: Zhou Ji , Qiao Yaojun , Yang Zhanyu , Cheng Qixiang , Wang Qi , Guo Mengqi , Tang Xizi 
Published: June 2017

AbstractFaster-than-Nyquist (FTN) signal achieves higher spectral efficiency and capacity compared to Nyquist signal due to its smaller pulse interval or narrower subcarrier spacing. Shannon limit typically defines the upper-limit capacity of Nyquist signal. To the best of our knowledge, the mathematical expression for the capacity limit of FTN non-orthogonal frequency-division multiplexing (NOFDM) signal is first demonstrated in this paper. The mathematical expression shows that FTN NOFDM signal has the potential to achieve a higher capacity limit compared to Nyquist signal. In this paper, we demonstrate the principle of FTN NOFDM by taking fractional cosine transform-based NOFDM (FrCT-NOFDM) for instance. FrCT-NOFDM is first proposed and implemented by both simulation and experiment. When the bandwidth compression factor α is set to 0.8 in FrCT-NOFDM, the subcarrier spacing is equal to 40% of the symbol rate per subcarrier, thus the transmission rate is about 25% faster than Nyquist rate. FTN NOFDM with higher capacity would be promising in the future communication systems, especially in the bandwidth-limited applications.
In-situ Electrodeposition of Highly Active Silver Catalyst on Carbon Fiber Papers as Binder Free Cathodes for Aluminum-air Battery
Authors: Hong Qingshui , Lu Huimin 
Published: June 2017

AbstractCarbon fiber papers supported Ag catalysts (Ag/CFP) with different coverage of electro-active site are prepared by electrochemical deposition and used as binder free cathodes in primary aluminum-air (Al-air) battery. Scanning Electron Microscopy and X-ray Diffraction studies are carried out to characterize the as-prepared Ag/CFP air cathodes. Oxygen reduction reaction (ORR) activities on these air cathodes in alkaline solutions are systematic studied. A newly designed aluminum-air cell is used to further determine the cathodes performance under real operation condition and during the test, the Ag/CFP electrodes show outstanding catalytic activity for ORR in concentrated alkaline electrolyte, and no obvious activity degradation is observed after long-time discharge. The electrochemical test results display the dependence of coverage of the electro-active Ag on the catalytic performance of the air cathodes. The resulting primary Al-air battery made from the best-performing cathode shows an impressive discharge peak power density, outperforming that of using commercial nano-manganese catalyst air electrodes.
Highly phosphorylated functionalized rice starch produced by transgenic rice expressing the potato GWD1 gene
Authors: Chen Yaling , Sun Xiao , Zhou Xin , Hebelstrup Kim H. , Blennow Andreas , Bao Jinsong 
Published: June 2017

AbstractStarch phosphorylation occurs naturally during starch metabolism in the plant and is catalysed by glucan water dikinases (GWD1) and phosphoglucan water dikinase/glucan water dikinase 3 (PWD/GWD3). We generated six stable individual transgenic lines by over-expressing the potato GWD1 in rice. Transgenic rice grain starch had 9-fold higher 6-phospho (6-P) monoesters and double amounts of 3-phospho (3-P) monoesters, respectively, compared to control grain. The shape and topography of the transgenic starch granules were moderately altered including surface pores and less well defined edges. The gelatinization temperatures of both rice flour and extracted starch were significantly lower than those of the control and hence negatively correlated with the starch phosphate content. The 6-P content was positively correlated with amylose content and relatively long amylopectin chains with DP25-36, and the 3-P content was positively correlated with short chains of DP6-12. The starch pasting temperature, peak viscosity and the breakdown were lower but the setback was higher for transgenic rice flour. The 6-P content was negatively correlated with texture adhesiveness but positively correlated with the cohesiveness of rice flour gels. Our data demonstrate a way forward to employ a starch bioengineering approach for clean modification of starch, opening up completely new applications for rice starch.
Allopregnanolone mediates the exacerbation of Tourette-like responses by acute stress in mouse models
Authors: Mosher Laura J. , Godar Sean C. , Nelson Marianela , Fowler Stephen C. , Pinna Graziano , Bortolato Marco 
Published: June 2017

AbstractTourette syndrome (TS) is a neuropsychiatric disorder characterized by multiple tics and sensorimotor abnormalities, the severity of which is typically increased by stress. The neurobiological underpinnings of this exacerbation, however, remain elusive. We recently reported that spatial confinement (SC), a moderate environmental stressor, increases tic-like responses and elicits TS-like sensorimotor gating deficits in the D1CT-7 mouse, one of the best-validated models of TS. Here, we hypothesized that these adverse effects may be mediated by neurosteroids, given their well-documented role in stress-response orchestration. Indeed, SC increased the levels of progesterone, as well as its derivatives 5α-dihydroprogesterone and allopregnanolone, in the prefrontal cortex (PFC) of D1CT-7 mice. Among these steroids, however, only allopregnanolone (5–15 mg/kg, IP) dose-dependently exacerbated TS-like manifestations in D1CT-7, but not wild-type littermates; these effects were countered by the benchmark anti-tic therapy haloperidol (0.3 mg/kg, IP). Furthermore, the phenotypic effects of spatial confinement in D1CT-7 mice were suppressed by finasteride (25–50 mg/kg, IP), an inhibitor of the main rate-limiting enzyme in allopregnanolone synthesis. These findings collectively suggest that stress may exacerbate TS symptoms by promoting allopregnanolone synthesis in the PFC, and corroborate previous clinical results pointing to finasteride as a novel therapeutic avenue to curb symptom fluctuations in TS.