bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial biofilms and the human skin microbiome
Authors: Brandwein Michael , Steinberg Doron , Meshner Shiri 
Published: November 2016

AbstractThe human skin microbiome plays an important role in both health and disease. Microbial biofilms are a well-characterized mode of surface-associated growth, which present community-like behaviors. Additionally, biofilms are a critical element in certain skin diseases. We review how the perception of the resident skin microbiota has evolved from the early linkages of certain microbes to disease states, to a more comprehensive and intricate understanding brought on by biofilm and microbiome revelations. Rapidly expanding arsenals of experimental methods are opening new horizons in the study of human–microbe and microbe–microbe interactions. Microbial community profiling has largely remained a separate discipline from that of biofilm research, yet the introduction of metatranscriptomics, metabolomics, and the ability to distinguish between dormant and active members of a community have all paved the road toward a convergent cognizance of the encounter between these two microbial disciplines.
Non-stimulated adrenal venous sampling using Dyna computed tomography in patients with primary aldosteronism
Authors: Chang Chin-Chen , Lee Bo-Ching , Liu Kao-Lang , Chang Yeun-Chung , Wu Vin-Cent , Huang Kuo-How 
Published: November 2016

AbstractIn this retrospective study, we aimed to examine the effect of applying Dyna computed tomography (CT) on the success rate of adrenal venous sampling (AVS) without adrenocorticotropic hormone stimulation. A total of 100 consecutive patients with primary aldosteronism who underwent AVS between May 2012 and July 2015 were enrolled. In all the cases, Dyna CT was used in AVS to validate catheter position in the right adrenal vein. A selectivity index (cortisoladrenal vein /cortisolinferior vena cava) of ≥2.0 of both adrenal veins were required for successful AVS. Dyna CT indicated misplaced catheters in 16 patients; of these patients, 75% (12/16) eventually had successful right AVS after catheter repositioning. The success rate of initial sampling at the right adrenal vein was 76% (76/100), which increased to 88% (88/100) after Dyna CT was applied (p < 0.001). The most common inadvertently catheterised vessels detected using Dyna CT were the accessory hepatic veins (56.3%, 9/16), followed by the renal capsular veins (37.5%, 6/16). The overall success rate of non-stimulated AVS using Dyna CT was 87% (87/100). Thus, the application of Dyna CT further increased the success rate of non-stimulated AVS.
Toward a new paradigm of DNA writing using a massively parallel sequencing platform and degenerate oligonucleotide
Authors: Hwang Byungjin , Bang Duhee 
Published: November 2016

AbstractAll synthetic DNA materials require prior programming of the building blocks of the oligonucleotide sequences. The development of a programmable microarray platform provides cost-effective and time-efficient solutions in the field of data storage using DNA. However, the scalability of the synthesis is not on par with the accelerating sequencing capacity. Here, we report on a new paradigm of generating genetic material (writing) using a degenerate oligonucleotide and optomechanical retrieval method that leverages sequencing (reading) throughput to generate the desired number of oligonucleotides. As a proof of concept, we demonstrate the feasibility of our concept in digital information storage in DNA. In simulation, the ability to store data is expected to exponentially increase with increase in degenerate space. The present study highlights the major framework change in conventional DNA writing paradigm as a sequencer itself can become a potential source of making genetic materials.
The trend and the disease prediction of vascular endothelial growth factor and placenta growth factor in nontuberculous mycobacterial lung disease
Authors: Lin Chou-Han , Shu Chin-Chung , Hsu Chia-Lin , Cheng Shih-Lung , Wang Jann-Yuan , Yu Chong-Jen , Lee Li-Na 
Published: November 2016

AbstractNontuberculous mycobacteria (NTM)-lung disease (LD) is an increasing health problem worldwide. The diagnosis of this disease remains difficult, however the application of placenta growth factor (PlGF) and vascular endothelial growth factor (VEGF) has not yet been studied. We screened patients with Mycobacterium avium complex or M. abscessus isolated from sputum, and enrolled 32 patients with NTM-LD and 93 with NTM pulmonary colonization. The NTM-LD group had a lower body mass index, higher proportion of bronchiectasis, more respiratory symptoms and pulmonary lesions, and higher titers of sputum acid-fast stain than the NTM pulmonary colonization group. The plasma level of PlGF was lower in the NTM-LD group than in the NTM colonization group, whereas the level of VEGF was higher in the NTM-LD group. In multivariable logistic regression analysis excluding NTM cultures, the predictive model for NTM-LD included sputum AFS titer, a nodular-bronchiectasis radiographic pattern, plasma VEGF/PlGF ratio, and chest radiographic score (VEGF/P1GF ratio became not significant as a factor in multivariable generalized linear model). The four-factor predictive index had good positive likelihood ratio and negative likelihood ratio for predicting NTM-LD in the patients with NTM in their sputum.
A new grading system for plant-available potassium using exhaustive cropping techniques combined with chemical analyses of soils
Authors: Li Ting , Wang Huoyan , Zhou Zijun , Chen Xiaoqin , Zhou Jianmin 
Published: November 2016

AbstractA new grading system for plant-available potassium (K) in soils based on K release rate from soils and plant growth indices was established. In the study, fourteen different agricultural soils from the southern subtropical to the northern temperate zones in China were analyzed by both chemical extraction methods and exhaustive cropping techniques. Based on the change trends in plant growth indices, relative biomass yields of 70% and 50%, K-deficient coefficients of 35 and 22 under conventional exhaustive experiments, and tissue K concentrations of 40 g kg−1 and 15 g kg−1 under intensive exhaustive experiments were obtained as critical values that represent different change trends. In addition, the extraction method using 0.2 mol L−1 sodium tetraphenylboron (NaTPB) suggested soil K release rates of 12 mg kg−1 min−1 and 0.4 mg kg−1 min−1 as turning points that illustrated three different release trends. Thus, plant-available K in soils was classified into three categories: high available K, medium available K and low available K, and grading criteria and measurement methods were also proposed. This work has increased our understanding of soil K bioavailability and has direct application in terms of routine assessment of agriculture soils.
Smart-aggregation imaging for single molecule localisation with SPAD cameras
Authors: Gyongy Istvan , Davies Amy , Dutton Neale A. W. , Duncan Rory R. , Rickman Colin , Henderson Robert K. , Dalgarno Paul A. 
Published: November 2016

AbstractSingle molecule localisation microscopy (SMLM) has become an essential part of the super-resolution toolbox for probing cellular structure and function. The rapid evolution of these techniques has outstripped detector development and faster, more sensitive cameras are required to further improve localisation certainty. Single-photon avalanche photodiode (SPAD) array cameras offer single-photon sensitivity, very high frame rates and zero readout noise, making them a potentially ideal detector for ultra-fast imaging and SMLM experiments. However, performance traditionally falls behind that of emCCD and sCMOS devices due to lower photon detection efficiency. Here we demonstrate, both experimentally and through simulations, that the sensitivity of a binary SPAD camera in SMLM experiments can be improved significantly by aggregating only frames containing signal, and that this leads to smaller datasets and competitive performance with that of existing detectors. The simulations also indicate that with predicted future advances in SPAD camera technology, SPAD devices will outperform existing scientific cameras when capturing fast temporal dynamics.
Improving the characterization of dissolved organic carbon in cloud water: Amino acids and their impact on the oxidant capacity
Authors: Bianco Angelica , Voyard Guillaume , Deguillaume Laurent , Mailhot Gilles , Brigante Marcello 
Published: November 2016

AbstractImproving our understanding of cloud chemistry depends on achieving better chemical characterization (90% of the organic carbon [OC] fraction remains uncharacterized) and, consequently, assessing the reactivity of this complex system. In this manuscript, we report for the first time the concentrations of 16 amino acids (AAs) in 25 cloud water samples. The concentrations of individual AAs ranged from a few nM up to ~2.0 μM, and the average contribution of AAs corresponded to 9.1% (4.4 to 21.6%) of the dissolved OC (DOC) concentration. Considering their occurrence and concentrations, AAs were expected to represent an important hydroxyl radical (HO•) sink in aqueous cloud samples. In this work, we estimated that approximately 17% (from 7 to 36%) of the hydroxyl radical-scavenging ability of the DOC could be attributed to the presence of AAs, whereas comparing the AAs suggested that an average of 51% (from 22 to 80%) of their reactivity with HO• could account for the presence of tryptophan. These results clearly demonstrate that the occurrence and reactivity of AAs must be considered to better estimate the chemical composition and oxidant capacity of the cloud aqueous phase.
Driving Pest Insect Populations: Agricultural Chemicals Lead to an Adaptive Syndrome in Nilaparvata Lugens Stål (Hemiptera: Delphacidae)
Authors: You Lin-Lin , Wu You , Xu Bing , Ding Jun , Ge Lin-Quan , Yang Guo-Qin , Song Qi-Sheng , Stanley David , Wu Jin-Cai 
Published: November 2016

AbstractThe brown planthopper (BPH) is a devastating pest of rice throughout Asia. In this paper we document the BPH biogeographic range expansion in China over the 20-year period, 1992 to 2012. We posed the hypothesis that the range expansion is due to a syndrome of adaptations to the continuous presence of agricultural chemicals (insecticides and a fungicide) over the last 40 years. With respect to biogeography, BPH ranges have expanded by 13% from 1992 to 1997 and by another 3% from 1997 to 2012. In our view, such expansions may follow primarily from the enhancing effects of JGM, among other agricultural chemicals, and from global warming. JGM treatments led to increased thermotolerance, recorded as decreased mortality under heat stress at 40 ± 1 °C (down from 80% to 55%) and increased fecundity (by 49%) at 34 °C. At the molecular level, JGM treatments led to increased abundances of mRNA encoding Acetyl Co-A carboxylase (Acc) (up 25%) and Hsp70 (up 32%) in experimental BPH. RNAi silencing ofHsp70andAcceliminated the JGM effects on fecundity and silencingHsp70reduced JGM-induced thermotolerance. Integrated with global climate change scenarios, such syndromes in pest insect species have potential for regional- and global-scale agricultural disasters.
A simplified computational memory model from information processing
Authors: Zhang Lanhua , Zhang Dongsheng , Deng Yuqin , Ding Xiaoqian , Wang Yan , Tang Yiyuan , Sun Baoliang 
Published: November 2016

AbstractThis paper is intended to propose a computational model for memory from the view of information processing. The model, called simplified memory information retrieval network (SMIRN), is a bi-modular hierarchical functional memory network by abstracting memory function and simulating memory information processing. At first meta-memory is defined to express the neuron or brain cortices based on the biology and graph theories, and we develop an intra-modular network with the modeling algorithm by mapping the node and edge, and then the bi-modular network is delineated with intra-modular and inter-modular. At last a polynomial retrieval algorithm is introduced. In this paper we simulate the memory phenomena and functions of memorization and strengthening by information processing algorithms. The theoretical analysis and the simulation results show that the model is in accordance with the memory phenomena from information processing view.
Generation of macroscopic Schrödinger cat state in diamond mechanical resonator
Authors: Hou Qizhe , Yang Wanli , Chen Changyong , Yin Zhangqi 
Published: November 2016

AbstractWe propose a scheme to generate macroscopic Schrödinger cat state (SCS) in diamond mechanical resonator (DMR) via the dynamical strain-mediated coupling mechanism. In our model, the direct coupling between the nitrogen-vacancy (NV) center and lattice strain field enables coherent spin–phonon interactions in the quantum regime. Based on a cyclic Δ-type transition structure of the NV center constructed by combining the quantized mechanical strain field and a pair of external microwave fields, the populations of the different energy levels can be selectively transferred by controlling microwave fields, and the SCS can be created by adjusting the controllable parameters of the system. Furthermore, we demonstrate the nonclassicality of the mechanical SCS both in non-dissipative case and dissipative case. The experimental feasibility and challenge are justified using currently available technology.
DNA barcoding of Mobulid Ray Gill Rakers for Implementing CITES on Elasmobranch in China
Authors: Zeng Yan , Wu Zhongze , Zhang Chunguang , Meng Zhibin , Jiang Zhigang , Zhang Jie 
Published: November 2016

AbstractThe Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) has been counted on for conserving threatened marine fish since it regulates the commercial international trade of these species. Implementation of the international treaty for Mantas included on CITES Appendix II is challenging due to insufficient information on species identification and markets management. To fill the gap in such aspects, we identified five species of Mobulid rays (Mobula spps. and Manta spp) by using COI and NADH2 mtDNA markers in dried ray gill rakers from Chinese markets, namely, Mobula japonica (representing 54.8% of the sample set), M. tarapacana (14.4%), M. kuhlii (13.3%), M. thurstoni (6.4%), along with Manta birostris (11.2%; CITES Appendix II). The utilization and conservation statuses of these species were discussed. Based on combination of DNA barcodes and key morphological characters, we developed a three-step process for identifying the gill rakers of Mobulid rays which has been adopted by frontline enforcement in China. We hope that our work can serve as a foundation and basis to reinforce objectives of international treaties, regulation of consumer-driven markets, regional cooperation, and national fishery management on endangered elasmobranchs in China as well as related countries.
Edge effects reverse facilitation by a widespread foundation species
Authors: Jurgens Laura J. , Gaylord Brian 
Published: November 2016

AbstractDense aggregations of foundation species often mitigate environmental stresses for organisms living among them. Considerable work documents such benefits by comparing conditions inside versus outside these biogenic habitats. However, environmental gradients commonly arise across the extent of even single patches of habitat-forming species, including cases where stresses diverge between habitat interiors and edges. We ask here whether such edge effects could alter how habitat-forming species influence residents, potentially changing the strength or direction of interactions (i.e., from stress amelioration to exacerbation). We take as a model system the classic marine foundation species, Mytilus californianus, the California mussel. Results demonstrate that mussel beds both increase and decrease thermal stresses. Over a distance of 6 to 10 cm from the bed interior to its upper surface, peak temperatures climb from as much as 20 °C below to 5 °C above those of adjacent bedrock. This directional shift in temperature modification affects interactions with juvenile mussels, such that thermal stresses and associated mortality risk are higher at the bed surface, but substantially reduced deeper within the adult matrix. These findings provide a case example of how stress gradients generated across biogenic habitats can markedly alter ecological interactions even within a single habitat patch.
Genetic variations in the PI3K-PTEN-AKT-mTOR pathway are associated with distant metastasis in nasopharyngeal carcinoma patients treated with intensity-modulated radiation therapy
Authors: Guo Qiaojuan , Lu Tianzhu , Chen Yan , Su Ying , Zheng Yuhong , Chen Zeng , Chen Chao , Lin Shaojun , Pan Jianji , Yuan Xianglin 
Published: November 2016

AbstractDistant metastasis is the primary failure pattern of nasopharyngeal carcinoma(NPC) in intensity-modulated radiation therapy(IMRT) era. This study was conducted to find the impact of genetic variations in the phosphatidylinositol 3-kinase(PI3K)/phosphatase and tensin homologue(PTEN)/v-akt murine thymoma viral oncogene homologue(AKT)/mammalian target of rapamycin(mTOR) pathway on the risk of distant metastasis in NPC. We genotyped 16 single-nucleotide polymorphisms(SNPs) in five core genes in this pathway from 496 patients treated by IMRT with or without chemotherapy. The relationships between genetic polymorphisms and distant progression were evaluated. We observed that two loci in the AKT1 gene(rs3803300 and rs2494738 alone or combined) were associated with prognosis, with patients carrying at least one variant allele had significantly reduced risk of distant failure, especially in N2-3 group. In addition, we found that genetic variation may had some joint effect with N classification in recursive-partitioning analysis(RPA) analysis, with which patients were stratified into four different risk subgroups (RPA model): RPA1(low risk), RPA2(moderate risk), RPA3(high risk) and RPA4(highest risk). Our findings suggested that genetic variations within the PI3K signaling pathway modulate the development and invasion of NPC patients. Further research is needed to replicate the study in other centers and races, and to unravel the functional significance of these polymorphisms.
High Energy Particle Radiation-associated Oncogenic Transformation in Normal Mice: Insight into the Connection between Activation of Oncotargets and Oncogene Addiction
Authors: Aravindan Natarajan , Aravindan Sheeja , Manickam Krishnan , Natarajan Mohan 
Published: November 2016

AbstractConcerns on high-energy particle radiation-induced tumorigenic transformation of normal tissue in astronauts, and in cancer patients undergoing radiotherapy, emphasizes the significance of elucidating the mechanisms involved in radiogenic transformation processes. Mostly used genetically modified or tumor-prone models are less reliable in determining human health risk in space or protracted post-treatment normal tissue toxicity. Here, in wild type C57BL/6 mice, we related the deregulation of distinctive set of tissue-specific oncotargets in major organs upon 56Fe (600 MeV/amu; 0.5 Gy/min; 0.8 Gy) particle radiation and compared the response with low LET γ-radiation (137Cs; 0.5 Gy/min; 2 Gy). One of the novel findings is the ‘tissue-independent’ activation of TAL2 upon high-energy radiation, and thus qualifies TAL2 as a potential biomarker for particle and other qualities of radiation. Heightened expression of TAL2 gene transcript, which sustained over four weeks post-irradiation foster the concept of oncogene addiction signaling in radiogenic transformation. The positive/negative expression of other selected oncotargets that expresses tissue-dependent manner indicated their role as a secondary driving force that addresses the diversity of tissue-dependent characteristics of tumorigenesis. This study, while reporting novel findings on radiogenic transformation of normal tissue when exposed to particle radiation, it also provides a platform for further investigation into different radiation quality, LET and dose/dose rate effect in healthy organs.
Origin of long-lived quantum coherence and excitation dynamics in pigment-protein complexes
Authors: Zhang Zhedong , Wang Jin 
Published: November 2016

AbstractWe explore the mechanism for the long-lived quantum coherence by considering the discrete phonon modes: these vibrational modes effectively weaken the exciton-environment interaction, due to the new composite (polaron) formed by excitons and vibrons. This subsequently demonstrates the role of vibrational coherence which greatly contributes to long-lived feature of the excitonic coherence that has been observed in femtosecond experiments. The estimation of the timescale of coherence elongated by vibrational modes is given in an analytical manner. To test the validity of our theory, we study the pigment-protein complex in detail by exploring the energy transfer and coherence dynamics. The ground-state vibrational coherence generated by incoherent radiations is shown to be long-survived and is demonstrated to be significant in promoting the excitation energy transfer. This is attributed to the nonequilibriumness of the system caused by the detailed-balance-breaking, which funnels the downhill migration of excitons.
Intestinal tuft cells regulate the ATM mediated DNA Damage response via Dclk1 dependent mechanism for crypt restitution following radiation injury
Authors: Chandrakesan Parthasarathy , May Randal , Weygant Nathaniel , Qu Dongfeng , Berry William L. , Sureban Sripathi M. , Ali Naushad , Rao Chinthalapally , Huycke Mark , Bronze Michael S. , Houchen Courtney W. 
Published: November 2016

AbstractCrypt epithelial survival and regeneration after injury require highly coordinated complex interplay between resident stem cells and diverse cell types. The function of Dclk1 expressing tuft cells regulating intestinal epithelial DNA damage response for cell survival/self-renewal after radiation-induced injury is unclear. Intestinal epithelial cells (IECs) were isolated and purified and utilized for experimental analysis. We found that small intestinal crypts of VillinCre;Dclk1f/f mice were hypoplastic and more apoptotic 24 h post-total body irradiation, a time when stem cell survival is p53-independent. Injury-induced ATM mediated DNA damage response, pro-survival genes, stem cell markers, and self-renewal ability for survival and restitution were reduced in the isolated intestinal epithelial cells. An even greater reduction in these signaling pathways was observed 3.5 days post-TBI, when peak crypt regeneration occurs. We found that interaction with Dclk1 is critical for ATM and COX2 activation in response to injury. We determined that Dclk1 expressing tuft cells regulate the whole intestinal epithelial cells following injury through paracrine mechanism. These findings suggest that intestinal tuft cells play an important role in regulating the ATM mediated DNA damage response, for epithelial cell survival/self-renewal via a Dclk1 dependent mechanism, and these processes are indispensable for restitution and function after severe radiation-induced injury.