bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential NF2 Gene Status in Sporadic Vestibular Schwannomas and its Prognostic Impact on Tumour Growth Patterns
Authors: Chen Hongsai , Xue Lu , Wang Hantao , Wang Zhaoyan , Wu Hao 
Published: July 2017

AbstractThe great majority of sporadic vestibular schwannomas (VSs) are due to the inactivation of the NF2 gene. In this study, we found age-dependent differences in the clinical parameters of sporadic VSs. Young patients were characterized by progressive tumour behaviours, including earlier onset of initial symptoms, shorter symptom duration and larger tumour size. An increased rate of “two-hits” of both NF2 alleles, usually by mutation and allelic loss, was observed in young cases compared to older, and this correlated with the loss of protein and mRNA expression. In contrast, the tumours with a single mutation (referred to as ‘one-hit’) exhibited obvious expression levels. Moreover, a mixture of merlin-expressing tumour cells and non-expressing tumour cells was observed in ‘one-hit’ schwannomas, suggesting that a subset of ‘one-hit’ tumour cells was present in these tumours. To mimic the growth promoting effects by the second hit, we performed lentivirus-mediated NF2 knockdown in the ‘one-hit’ schwannoma cultures. Following the loss of NF2 expression, schwannoma cultures demonstrated increased proliferation rates. Above all, we have identified a correlation between the NF2 status and the growth patterns of sporadic VSs. The treatment decision-making, microsurgery or “wait and scan” strategy, should be carried out according to the tumour’s genetic background.
RLR-mediated antiviral innate immunity requires oxidative phosphorylation activity
Authors: Yoshizumi Takuma , Imamura Hiromi , Taku Tomohiro , Kuroki Takahiro , Kawaguchi Atsushi , Ishikawa Kaori , Nakada Kazuto , Koshiba Takumi 
Published: July 2017

AbstractMitochondria act as a platform for antiviral innate immunity, and the immune system depends on activation of the retinoic acid-inducible gene I (RIG-I)-like receptors (RLR) signaling pathway via an adaptor molecule, mitochondrial antiviral signaling. We report that RLR-mediated antiviral innate immunity requires oxidative phosphorylation (OXPHOS) activity, a prominent physiologic function of mitochondria. Cells lacking mitochondrial DNA or mutant cells with respiratory defects exhibited severely impaired virus-induced induction of interferons and proinflammatory cytokines. Recovery of the OXPHOS activity in these mutants, however, re-established RLR-mediated signal transduction. Using in vivo approaches, we found that mice with OXPHOS defects were highly susceptible to viral infection and exhibited significant lung inflammation. Studies to elucidate the molecular mechanism of OXPHOS-coupled immune activity revealed that optic atrophy 1, a mediator of mitochondrial fusion, contributes to regulate the antiviral immune response. Our findings provide evidence for functional coordination between RLR-mediated antiviral innate immunity and the mitochondrial energy-generating system in mammals.
Isotopic signature and nano-texture of cesium-rich micro-particles: Release of uranium and fission products from the Fukushima Daiichi Nuclear Power Plant
Authors: Imoto Junpei , Ochiai Asumi , Furuki Genki , Suetake Mizuki , Ikehara Ryohei , Horie Kenji , Takehara Mami , Yamasaki Shinya , Nanba Kenji , Ohnuki Toshihiko , Law Gareth T. W. , Grambow Bernd , Ewing Rodney C. , Utsunomiya Satoshi 
Published: July 2017

AbstractHighly radioactive cesium-rich microparticles (CsMPs) released from the Fukushima Daiichi Nuclear Power Plant (FDNPP) provide nano-scale chemical fingerprints of the 2011 tragedy. U, Cs, Ba, Rb, K, and Ca isotopic ratios were determined on three CsMPs (3.79–780 Bq) collected within ~10 km from the FDNPP to determine the CsMPs’ origin and mechanism of formation. Apart from crystalline Fe-pollucite, CsFeSi2O6 · nH2O, CsMPs are comprised mainly of Zn–Fe-oxide nanoparticles in a SiO2 glass matrix (up to ~30 wt% of Cs and ~1 wt% of U mainly associated with Zn–Fe-oxide). The 235U/238U values in two CsMPs: 0.030 (±0.005) and 0.029 (±0.003), are consistent with that of enriched nuclear fuel. The values are higher than the average burnup estimated by the ORIGEN code and lower than non-irradiated fuel, suggesting non-uniform volatilization of U from melted fuels with different levels of burnup, followed by sorption onto Zn–Fe-oxides. The nano-scale texture and isotopic analyses provide a partial record of the chemical reactions that occurred in the fuel during meltdown. Also, the CsMPs were an important medium of transport for the released radionuclides in a respirable form.
Beam propagation management in a fractional Schrödinger equation
Authors: Huang Changming , Dong Liangwei 
Published: July 2017

AbstractGeneralization of Fractional Schrödinger equation (FSE) into optics is fundamentally important, since optics usually provides a fertile ground where FSE-related phenomena can be effectively observed. Beam propagation management is a topic of considerable interest in the field of optics. Here, we put forward a simple scheme for the realization of propagation management of light beams by introducing a double-barrier potential into the FSE. Transmission, partial transmission/reflection, and total reflection of light fields can be controlled by varying the potential depth. Oblique input beams with arbitrary distributions obey the same propagation dynamics. Some unique properties, including strong self-healing ability, high capacity of resisting disturbance, beam reshaping, and Goos-Hänchen-like shift are revealed. Theoretical analysis results are qualitatively in agreements with the numerical findings. This work opens up new possibilities for beam management and can be generalized into other fields involving fractional effects.
Generation of clade- and symbiont-specific antibodies to characterize marker molecules during Cnidaria-Symbiodinium endosymbiosis
Authors: Huang Kao-Jean , Huang Zi-Yu , Lin Ching-Yen , Wang Li-Hsueh , Chou Pin-Hsiang , Chen Chii-Shiarng , Li Hsing-Hui 
Published: July 2017

AbstractThe endosymbiosis between cnidarians and dinoflagellates is responsible for the formation of coral reefs. Changes in molecules have been identified during the process of cnidaria-Symbiodiniumendosymbiosis. However, the complexity of the molecular interaction has prevented the establishment of a mechanistic explanation of cellular regulation in this mutualistic symbiosis. To date, no marker molecules have been identified to specifically represent the symbiotic status. Because the endosymbiotic association occurs in the symbiotic gastrodermal cells (SGCs), whole cells of isolated SGCs were used as an antigen to generate monoclonal antibodies (mAb) to screen possible molecular candidates of symbiotic markers. The results showed that one of the generated monoclonal antibodies, 2–6F, specifically recognized clade C symbioticSymbiodiniumbut not its free-living counterpart or otherSymbiodiniumclades. The expression levels of 2–6F mAb-recognized proteins are highly correlated with the symbiotic status, and these proteins were characterized asN-linked glycoproteins via treatment with peptide N-glycosidase F. Furthermore, their glycan moieties were markedly different from those of free-livingSymbiodinium, potentially suggesting host regulation of post-translational modification. Consequently, the 2–6F mAb can be used to detect the symbiotic state of corals and investigate the complex molecular interactions in cnidaria-Symbiodiniumendosymbiosis.
Three‐dimensional high‐isolated dual‐band balun using double‐sided parallel‐strip line with inserted conductor plane
Authors: Yao Lidan , Wu Yongle , Li Mingxing , Liu Yuanan 
Published: July 2017

A novel three‐dimensional high‐isolated dual‐band balun is proposed for the first time. A horizontal feeding plane, a vertically mounted plane, and four grounded resistors constitute the entire structure. By introducing the double‐sided parallel‐strip line with an inserted conductor plane to the middle of the vertical plane, the output matching and isolation, frequency‐independent phase difference, and complete ground in the bottom layer of the horizontal plane are perfectly integrated in this novel balun. To prove this conception, a practical balun operating at 1.3/2.5 GHz is designed. As expected, remarkable consistency between the simulation and measurement is obtained.
An 80 au cavity in the disk around HD 34282
Authors: van der Plas G. , Ménard F. , Canovas H. , Avenhaus H. , Casassus S. , Pinte C. , Caceres C. , Cieza L. 
Published: July 2017

Context. Large cavities in disks are important testing grounds for the mechanisms proposed to drive disk evolution and dispersion, such as dynamical clearing by planets and photoevaporation.
Aims. We aim to resolve the large cavity in the disk around HD 34282, whose presence has been predicted by previous studies modeling the spectral energy distribution of the disk.
Methods. Using ALMA band 7 observations we studied HD 34282 with a spatial resolution of 0.10″ × 0.17′′ at 345 GHz.
Results. We resolve the disk around HD 34282 into a ring between 0.24′′ and 1.15′′ (78+7-11 and 374+33-54 au adopting a distance of 325+29-47 pc). The emission in this ring shows azimuthal asymmetry centered at a radial distance of 0.46′′ and a position angle of 135° and an azimuthal FWHM of 51°. We detect CO emission both inside the disk cavity and as far out as 2.7 times the radial extent of the dust emission.
Conclusions. Both the large disk cavity and the azimuthal structure in the disk around HD 34282 can be explained by the presence of a 50 Mjup brown dwarf companion at a separation of ≈0.1′′.
Group augmentation, collective action, and territorial boundary patrols by male chimpanzees
Authors: Langergraber Kevin E. , Watts David P. , Vigilant Linda , Mitani John C. 
Published: July 2017

SignificanceMany animals, especially humans, carry out activities collectively because the benefits of doing so exceed those that can be achieved individually. But how can collective action evolve when individuals receive the benefits of cooperation regardless of whether they pay the costs of participation? Collective action may be especially difficult to achieve when groups are large, because each individual’s contribution has a small effect on the outcome. We show that group augmentation theory helps explain one of the most striking examples of collective action in nonhuman primates, territorial boundary patrolling by male chimpanzees: Males bear the short-term costs of patrolling even when they have little to gain immediately because patrolling enhances group size, increasing the male’s chances of future reproduction.
Heart Rate Variability and Cognitive Function In Middle-Age Adults: The Coronary Artery Risk Development in Young Adults
Authors: Zeki Al Hazzouri Adina , Elfassy Tali , Carnethon Mercedes R , Lloyd-Jones Donald M , Yaffe Kristine 
Published: July 2017

Abstract

BACKGROUND
Low heart rate variability (HRV), a marker of cardiac autonomic dysfunction, has been associated with major risk factors of cognitive impairment. Yet, the direct association of HRV with cognitive function remains relatively unexplored, particularly in midlife.

METHODS
In 2005, 2 measures of short-term HRV, the SD of normal-to-normal intervals (SDNN) and the root mean square of successive differences (RMSSD), were calculated for participants of the Coronary Artery Risk Development in Young Adults study, and then categorized into quartiles. Five years later, 3 cognitive tests were administered for verbal memory (“Rey Auditory-Verbal Learning Test”, RAVLT, range 0–15), processing speed (“Digit Symbol Substitution Test”, DSST, range 0–133), and executive function (“Stroop interference”).

RESULTS
Two thousand one hundred and eighteen participants (57.7% female, 42.2% Black) with a mean baseline age of 45.3 years were included in this analysis. In demographic-adjusted models, compared to participants with quartile 1 SDNN (lowest quartile), participants in the upper quartiles of SDNN scored better on the DSST (quartile 4: β = 1.83 points better, P = 0.03; and quartile 3: β = 1.95 points better, P = 0.03) and on the stroop (quartile 3: β = 1.19 points better, P &lt; 0.05; and quartile2: β = 1.44 points better, P = 0.02). After adjusting for behavioral and cardiovascular risk factors, higher quartile SDNN remained significantly associated with better stroop score (quartile 3: β = 1.21 points better, P = 0.04; and quartile 2: β = 1.72 points better, P &lt; 0.01) but not with DSST. There was no association between quartile of RMSSD and cognitive function, from fully adjusted models.

CONCLUSIONS
Our findings suggest that higher quartile SDDN is associated with better executive function in midlife, above, and beyond cardiovascular risk factors.
Coccidioidomycosis A Cause of Sarcoidosis
Authors: Kuberski Tim , Yourison Isaac 
Published: July 2017

Abstract

Background
Sarcoidosis is a granulomatous disease of unknown etiology and coccidioidomycosis is a granulomatous fungal infection endemic to the southwestern United States. Clinical observations on patients with sarcoidosis and coccidioidomycosis simultaneously led to the hypothesis that sarcoidosis can be caused by the fungus Coccidioides.

Methods
Two patients with sarcoidosis and coccidioidomycosis were studied, one prospectively (ie, a patient with sarcoidosis was predicted to develop coccidioidomycosis) and the other retrospectively (ie, a patient with coccidioidomycosis develops sarcoidosis). In addition, a literature review found 5 patients with these 2 diseases, and they were analyzed to establish an archived relationship between the 2 entities. In addition, polymerase chain reaction (PCR) testing for Coccidioides deoxyribonucleic acid (DNA) was performed on tissue from 15 Arizona patients diagnosed with sarcoidosis.

Results
Patient 1 was diagnosed with sarcoid in Arizona and followed prospectively. There was no evidence for coccidioidomycosis at diagnosis. This patient was observed for 8 years before he was documented to have disseminated coccidioidomycosis. Patient 2 was retrospectively studied. He was diagnosed with disseminated coccidioidomycosis, but after 3 years, while on antifungal therapy, he developed respiratory failure. A lung biopsy was consistent with sarcoidosis with no evidence of Coccidioides; cultures, histopathology, and serology were all negative. Paradoxically, PCR testing for Coccidioides DNA on tissue taken at the time of the sarcoidosis diagnosis were all negative, including Patient 2 who had proven coccidioidomycosis.

Conclusions
The 2 study patients and 5 case reports from the literature support the hypothesis that Coccidioides can cause sarcoidosis in Arizona. There are similar reports in the literature that Histoplasma can be associated with sarcoidosis. Based on these observations, we propose that sarcoidosis can be caused by endemic fungi in different areas of the United States, coccidioidomycosis in the Southwest and histoplasmosis in the Midwest.
Accurate Immune Repertoire Sequencing Reveals Malaria Infection Driven Antibody Lineage Diversification in Young Children
Authors: Wendel Ben S. , He Chenfeng , Qu Mingjuan , Wu Di , Hernandez Stefany M. , Ma Ke-Yue , Liu Eugene W. , Xiao Jun , Crompton Peter D. , Pierce Susan K. , Ren Pengyu , Chen Keke , Jiang Ning 
Published: July 2017

ABSTRACTAccurately measuring antibody repertoire sequence composition in a small amount of blood is challenging yet important to the understanding of the repertoire response to infections and vaccinations. Here, we describe an accurate and high-coverage repertoire sequencing method, MIDCIRS, which uses as few as 1,000 naïve B cells. Using it, we studied age-related antibody repertoire development and diversification before and during acute malaria in infants (< 12 months old) and toddlers (12 – 47 months old) with 4-8 ml of blood draws. Unexpectedly, we discovered high levels of somatic hypermutation (SHM) in infants as young as three months old. Antibody clonal lineage analysis revealed that both infants and toddlers increase SHM levels upon infection and memory B cells isolated from pre-malaria samples in malaria-experienced individuals continue to induce SHMs upon malaria rechallenge. These results highlight the vast potential of antibody repertoire diversification in infants and toddlers that has not been realized previously.
GEM: A manifold learning based framework for reconstructing spatial organizations of chromosomes
Authors: Zhu Guangxiang , Deng Wenxuan , Hu Hailin , Ma Rui , Zhang Sai , Yang Jinglin , Peng Jian , Kaplan Tommy , Zeng Jianyang 
Published: July 2017

AbstractDecoding the spatial organizations of chromosomes has crucial implications for studying eukaryotic gene regulation. Recently, Chromosomal conformation capture based technologies, such as Hi-C, have been widely used to uncover the interaction frequencies of genomic loci in high-throughput and genome-wide manner and provide new insights into the folding of three-dimensional (3D) genome structure. In this paper, we develop a novel manifold learning framework, called GEM (Genomic organization reconstructor based on conformationalEnergy andManifold learning), to elucidate the underlying 3D spatial organizations of chromosomes from Hi-C data. Unlike previous chromatin structure reconstruction methods, which explicitly assume specific relationships between Hi-C interaction frequencies and spatial distances between distal genomic loci, GEM is able to reconstruct an ensemble of chromatin conformations by directly embedding the neigh-boring affinities from Hi-C space into 3D Euclidean space based on a manifold learning strategy that considers both the fitness of Hi-C data and the biophysical feasibility of the modeled structures, which are measured by the conformational energy derived from our current biophysical knowledge about the 3D polymer model. Extensive validation tests on both simulated interaction frequency data and experimental Hi-C data of yeast and human demonstrated that GEM not only greatly outperformed other state-of-art modeling methods but also reconstructed accurate chromatin structures that agreed well with the hold-out or independent Hi-C data and sparse geometric restraints derived from the previous fluorescencein situhybridization (FISH) studies. In addition, as GEM can generate accurate spatial organizations of chromosomes by integrating both experimentally-derived spatial contacts and conformational energy, we for the first time extended our modeling method to recover long-range genomic interactions that are missing from the original Hi-C data. All these results indicated that GEM can provide a physically and physiologically valid 3D representations of the organizations of chromosomes and thus serve as an effective and useful genome structure reconstructor.
DddY is a bacterial dimethylsulfoniopropionate lyase representing a new cupin enzyme superfamily with unknown primary function
Authors: Lei Lei , Alcolombri Uria , Tawfik Dan S 
Published: July 2017

AbstractDimethylsulfide (DMS) is released at rates of >107tons annually and plays a key role in the oceanic sulfur cycle and ecology. Marine bacteria, algae, and possibly other organisms, release DMS via cleavage of dimethylsulfoniopropionate (DMSP). Different genes encoding proteins with DMSP lyase activity are known belonging to different superfamilies and exhibiting highly variable levels of DMSP lyase activity. DddY shows the highest activity among all reported bacterial lyases yet is poorly characterized. Here, we describe the characterization of recombinant DddY is from different marine bacteria. We found that DddY activity demands a transition metal ion cofactor. DddY also shares two sequence motifs with other bacterial lyases assigned as cupin-like enzymes, DddQ, DddL, DddK, and DddW. These cupin motif residues are essential for DddY activity, as for the other cupin DMSP lyases, and all these enzymes are characterized by a common metal-chelator inhibitor (TPEN). Analysis of all sequences carrying these cupin motifs defined a superfamily: Cupin-DLL (DMSP lyases and lyase-like). The DMSP lyase families are sporadically distributed suggesting that DMSP lyases evolved within this superfamily independently along multiple lineages. However, the specific activity levels, genomic context analysis, and systematic profiling of substrate selectivity as described in the accompanying paper, indicate that for only some of these families, most distinctly DddY and DddL, DMSP lyase is the primary, native activity. In other families, foremost DddQ, DMSP lyase seems to be merely a promiscuous activity. The native function of DddQ, and of nearly all members of this newly identified Cupin-DLL superfamily, remains unknown.AbbreviationsDMSPdimethylsulfoniopropionateDMSdimethylsulfidecupin-DLLcupin DMSP lyase and lyase-likeFundingFinancial support by the Estate of Mark Scher, and the Sasson & Marjorie Peress Philanthropic Fund, are gratefully acknowledged. D.S.T. is the Nella and Leon Benoziyo Professor of Biochemistry.
A computational modelling framework to quantify the effects of passaging cell lines
Authors: Jin Wang , Penington Catherine J , McCue Scott W , Simpson Matthew J 
Published: July 2017

AbstractIn vitrocell culture is routinely used to grow and supply a sufficiently large number of cells for various types of cell biology experiments. Previous experimental studies report that cell characteristics evolve as the passage number increases, and various cell lines can behave differently at high passage numbers. To provide insight into the putative mechanisms that might give rise to these differences, we performin silicoexperiments using a random walk model to mimic thein vitrocell culture process. Our results show that it is possible for the average proliferation rate to either increase or decrease as the passaging process takes place, and this is due to a competition between the initial heterogeneity and the degree to which passaging damages the cells. We also simulate a suite of scratch assays with cells from near–homogeneous and heterogeneous cell lines, at both high and low passage numbers. Although it is common in the literature to report experimental results without disclosing the passage number, our results show that we obtain significantly different closure rates when performingin silicoscratch assays using cells with different passage numbers. Therefore, we suggest that the passage number should always be reported to ensure that the experiment is as reproducible as possible. Furthermore, our modelling also suggests some avenues for further experimental examination that could be used to validate or refine our simulation results.