bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineering Saccharomyces cerevisiae for geranylgeraniol overproduction by combinatorial design
Authors: Song Tian-Qing , Ding Ming-Zhu , Zhai Fang , Liu Duo , Liu Hong , Xiao Wen-Hai , Yuan Ying-Jin 
Published: November 2017

AbstractCombinatorial design is an effective strategy to acquire the optimal solution in complex systems. In this study, the combined effects of pathway combination, promoters’ strength fine-tuning, copy numbers and integration locus variations caused by δ-integration were explored in Saccharomyces cerevisiae using geranylgeraniol (GGOH) production as an example. Two GGOH biosynthetic pathway branches were constructed. In branch 1, GGOH was converted from isopentenyl pyrophosphate (IPP) and farnesyl diphosphate (FPP). In branch 2, GGOH was derived directly from IPP and dimethylallyl pyrophosphate (DMAPP). Regulated by 10 combinations of 11 diverse promoters, a fusion gene BTS1-ERG20, a heterologous geranylgeranyl diphosphate synthase from Sulfolobus acidocaldarius (GGPPSsa) and an endogenous N-terminal truncated gene 3-hydroxyl-3-methylglutaryl-CoA reductase isoenzyme 1 (tHMGR), were incorporated into yeast by δ-integration, leading to a series of GGOH producing strains with yields ranging from 18.45 mg/L to 161.82 mg/L. The yield was further increased to 437.52 mg/L by optimizing the fermentation medium. Consequently, the GGOH yield reached 1315.44 mg/L in a 5-L fermenter under carbon restriction strategy. Our study not only opens large opportunities for downstream diterpenes overproductions, but also demonstrates that pathway optimization based on combinatorial design is a promising strategy to engineer microbes for overproducing natural products with complex structure.
Navigability of temporal networks in hyperbolic space
Authors: Ortiz Elisenda , Starnini Michele , Serrano M. Ángeles 
Published: November 2017

AbstractInformation routing is one of the main tasks in many complex networks with a communication function. Maps produced by embedding the networks in hyperbolic space can assist this task enabling the implementation of efficient navigation strategies. However, only static maps have been considered so far, while navigation in more realistic situations, where the network structure may vary in time, remains largely unexplored. Here, we analyze the navigability of real networks by using greedy routing in hyperbolic space, where the nodes are subject to a stochastic activation-inactivation dynamics. We find that such dynamics enhances navigability with respect to the static case. Interestingly, there exists an optimal intermediate activation value, which ensures the best trade-off between the increase in the number of successful paths and a limited growth of their length. Contrary to expectations, the enhanced navigability is robust even when the most connected nodes inactivate with very high probability. Finally, our results indicate that some real networks are ultranavigable and remain highly navigable even if the network structure is extremely unsteady. These findings have important implications for the design and evaluation of efficient routing protocols that account for the temporal nature of real complex networks.
Investigation on thermodynamics of ion-slicing of GaN and heterogeneously integrating high-quality GaN films on CMOS compatible Si(100) substrates
Authors: Huang Kai , Jia Qi , You Tiangui , Zhang Runchun , Lin Jiajie , Zhang Shibin , Zhou Min , Zhang Bo , Yu Wenjie , Ou Xin , Wang Xi 
Published: November 2017

AbstractDie-to-wafer heterogeneous integration of single-crystalline GaN film with CMOS compatible Si(100) substrate using the ion-cutting technique has been demonstrated. The thermodynamics of GaN surface blistering is in-situ investigated via a thermal-stage optical microscopy, which indicates that the large activation energy (2.5 eV) and low H ions utilization ratio (~6%) might result in the extremely high H fluence required for the ion-slicing of GaN. The crystalline quality, surface topography and the microstructure of the GaN films are characterized in detail. The full width at half maximum (FWHM) for GaN (002) X-ray rocking curves is as low as 163 arcsec, corresponding to a density of threading dislocation of 5 × 107 cm−2. Different evolution of the implantation-induced damage was observed and a relationship between the damage evolution and implantation-induced damage is demonstrated. This work would be beneficial to understand the mechanism of ion-slicing of GaN and to provide a platform for the hybrid integration of GaN devices with standard Si CMOS process.
Suppression of the FA pathway combined with CHK1 inhibitor hypersensitize lung cancer cells to gemcitabine
Authors: Dai Chun-Hua , Wang Yi , Chen Ping , Jiang Qian , Lan Ting , Li Mei-Yu , Su Jin-Yu , Wu Yan , Li Jian 
Published: November 2017

AbstractThe combination of platinum and gemcitabine is one of the standard regimens in the treatment of advanced lung squamous carcinoma (LSC). Resistance to gemcitabine is main barrier to the successful treatment of LSC. In this study, we showed that suppression of the Fanconi anemia (FA) pathway increased the sensitivity of two LSC cell lines SK-MES-1 and KLN205 to gemcitabine. Moreover, we found that the CHK1 pathway and the FA pathway are functionally compensatory in the repair of DNA damage in the LSC cell lines. Inactivation of one of the two pathways led to DNA damage, triggering compensatory activation of other pathway. Furthermore, we demonstrated that FANCD2 depletion combined with CHK1 inhibitor MK-8776 significantly potentiated the cytotoxicity of gemcitabine to the two LSC cell lines, compared to individual FANCD2 depletion or MK-8776 treatment. The enhanced effect of gemcitabine-chemosensitization was accompanied by loss of DNA repair function and accumulation of DNA single strand breaks and double strand breaks, in parallel with obvious increase of caspase-3 dependent apoptosis. Our results indicate that the enhancement effect of FANCD2 depletion combined with CHK1 inhibitor in sensitizing the LCS cells to gemcitabine supports the FA pathway and CHK1 as two therapeutic targets for improvement of anti-tumor regimens in treatment of LSC.
Functional Group Effects on the Photoelectronic Properties of MXene (Sc2CT2, T = O, F, OH) and Their Possible Photocatalytic Activities
Authors: Xiong Kuangwei , Wang Peihong , Yang Guang , Liu Zhongfei , Zhang Haijun , Jin Shaowei , Xu Xin 
Published: November 2017

AbstractIn view of the diverse functional groups left on the MXene during the etching process, we computationally investigated the effects of surface-group types on the structural, electronic and optical properties of Sc2CT2 (T = -O, -OH, -F) MXenes. For all geometries of the Sc2CT2 MXenes, the geometry I of Sc2CT2, which has the functional groups locating above the opposite-side Sc atoms, are lowest-energy structure. Accordingly, the energetically favorable Sc2CF2-I, Sc2CO2-I and Sc2C(OH)2-I were selected for further evaluation of the photocatalytic activities. We found that the Sc2CO2-I is metallic, while Sc2CF2-I and Sc2C(OH)2 are semiconductors with visible-light absorptions and promising carrier mobilities. Compared with the Sc2C(OH)2-I, the Sc2CF2-I has not only more suitable band gap (1.91 eV), but also the higher redox capability of photo-activated carriers, which should have better photocatalytic performance.
A POCS super resolution restoration algorithm based on BM3D
Authors: Chen Jian , Wang WeiGuo , Liu TingXia , Zhang ZhenDong , Gao HuiBin 
Published: November 2017

AbstractThe inherent shortcoming of POCS (Projection Onto Convex Sets) is its sensitiveness to noise. The restoration quality of POCS based super resolution will severely decline when the noise is larger. In practical applications, the low resolution images generally include some kinds of noise, such as camera internal noise, transmission system noise and coherent noise. Therefore POCS cannot be used directly in super-resolution restoration for observed low resolution images. In order to solve the noise sensitive problem of the traditional POCS restoration algorithm, we firstly propose to optimize the BM3D (Block-Matching 3D) filtering by mean pre-screening of image blocks and limiting the number of image blocks. Then we combine the optimized BM3D filtering with POCS restoration in this paper. Experimental results show that the proposed POCS super resolution restoration algorithm based on BM3D can achieve better restoration effect when the low resolution images contain noise. Furthermore no noise can be perceived in the restored high resolution image basically.
Substrate Specificity and Allosteric Regulation of a d-Lactate Dehydrogenase from a Unicellular Cyanobacterium are Altered by an Amino Acid Substitution
Authors: Ito Shoki , Takeya Masahiro , Osanai Takashi 
Published: November 2017

AbstractLactate/lactic acid is an important chemical compound for the manufacturing of bioplastics. The unicellular cyanobacterium Synechocystis sp. PCC 6803 can produce lactate from carbon dioxide and possesses d-lactate dehydrogenase (Ddh). Here, we performed a biochemical analysis of the Ddh from this cyanobacterium (SyDdh) using recombinant proteins. SyDdh was classified into a cyanobacterial clade similar to those from Gram-negative bacteria, although it was distinct from them. SyDdh can use both pyruvate and oxaloacetate as a substrate and is activated by fructose-1,6-bisphosphate and repressed by divalent cations. An amino acid substitution based on multiple sequence alignment data revealed that the glutamine at position 14 and serine at position 234 are important for the allosteric regulation by Mg2+ and substrate specificity of SyDdh, respectively. These results reveal the characteristic biochemical properties of Ddh in a unicellular cyanobacterium, which are different from those of other bacterial Ddhs.
Near infrared light decreases synaptic vulnerability to amyloid beta oligomers
Authors: Comerota Michele M. , Krishnan Balaji , Taglialatela Giulio 
Published: November 2017

AbstractSynaptic dysfunction due to the disrupting binding of amyloid beta (Aβ) and tau oligomers is one of the earliest impairments in Alzheimer’s Disease (AD), driving initial cognitive deficits and clinical manifestation. Consequently, there is ample consensus that preventing early synaptic dysfunction would be an effective therapeutic strategy for AD. With this goal in mind, we investigated the effect of a treatment of mice with near infrared (NIR) light on synaptic vulnerability to Aβ oligomers. We found that Aβ oligomer binding to CNS synaptosomes isolated from wild type (wt) mice treated with NIR light was significantly reduced and the resulting suppression of long term potentiation (LTP) by Aβ oligomers was prevented. Similarly, APP transgenic mice treated with NIR showed a significant reduction of endogenous Aβ at CNS synapses. We further found that these phenomena were accompanied by increased synaptic mitochondrial membrane potential in both wt and Tg2576 mice. This study provides evidence that NIR light can effectively reduce synaptic vulnerability to damaging Aβ oligomers, thus furthering NIR light therapy as a viable treatment for AD.
The Mammalian Target of Rapamycin and DNA methyltransferase 1 axis mediates vascular endothelial dysfunction in response to disturbed flow
Authors: Zhang Yun-Peng , Huang Yi-Tao , Huang Tse-Shun , Pang Wei , Zhu Juan-Juan , Liu Yue-Feng , Tang Run-Ze , Zhao Chuan-Rong , Yao Wei-Juan , Li Yi-Shuan , Chien Shu , Zhou Jing 
Published: November 2017

AbstractThe earliest atherosclerotic lesions preferentially develop in arterial regions experienced disturbed blood flow, which induces endothelial expression of pro-atherogenic genes and the subsequent endothelial dysfunction. Our previous study has demonstrated an up-regulation of DNA methyltransferase 1 (DNMT1) and a global hypermethylation in vascular endothelium subjected to disturbed flow. Here, we determined that DNMT1-specific inhibition in arterial wall ameliorates the disturbed flow-induced atherosclerosis through, at least in part, targeting cell cycle regulator cyclin A and connective tissue growth factor (CTGF). We identified the signaling pathways mediating the flow-induction of DNMT1. Inhibition of the mammalian target of rapamycin (mTOR) suppressed the DNMT1 up-regulation both in vitro and in vivo. Together, our results demonstrate that disturbed flow influences endothelial function and induces atherosclerosis in an mTOR/DNMT1-dependent manner. The conclusions obtained from this study might facilitate further evaluation of the epigenetic regulation of endothelial function during the pathological development of atherosclerosis and offer novel prevention and therapeutic targets of this disease.
Impact of Lactobacillus reuteri colonization on gut microbiota, inflammation, and crying time in infant colic
Authors: Nation Monica L. , Dunne Eileen M. , Joseph Shayne J. , Mensah Fiona K. , Sung Valerie , Satzke Catherine , Tang Mimi L. K. 
Published: November 2017

AbstractInfant colic is a distressing condition of unknown etiology. An aberrant gastrointestinal microbiota has been associated, and Lactobacillus reuteri supplementation has been shown to reduce crying and/or fussing time (‘crying time’) in some infants with colic. The relationship between L. reuteri gut colonization and crying time has not been examined. We investigated the relationship between L. reuteri colonization and fecal microbiota (microbial diversity and Escherichia coli), intestinal inflammation, and crying time in infants with colic, using a subset of 65 infants from the Baby Biotics trial, which randomized healthy term infants aged <13 weeks with infant colic to receive probiotic L. reuteri DSM 17938 (1 × 108 colony forming units) or placebo daily for 28 days. We observed an overall reduction in median crying time, regardless of L. reuteri colonization status (n = 14 colonized). There were no differences in E. coli colonization rates or densities, microbial diversity or intestinal inflammation by L. reuteri colonization status. We found that L. reuteri density positively correlated with crying time, and E. coli density negatively correlated with microbial diversity. As density of L. reuteri was associated with increased crying time, L. reuteri supplementation may not be an appropriate treatment for all infants with colic.
Acoustic frequency filter based on anisotropic topological phononic crystals
Authors: Chen Ze-Guo , Zhao Jiajun , Mei Jun , Wu Ying 
Published: November 2017

AbstractWe present a design of acoustic frequency filter based on a two-dimensional anisotropic phononic crystal. The anisotropic band structure exhibits either a directional or a combined (global + directional) bandgap at certain frequency regions, depending on the geometry. When the time-reversal symmetry is broken, it may introduce a topologically nontrivial bandgap. The induced nontrivial bandgap and the original directional bandgap result in various interesting wave propagation behaviors, such as frequency filter. We develop a tight-binding model to characterize the effective Hamiltonian of the system, from which the contribution of anisotropy is explicitly shown. Different from the isotropic cases, the Zeeman-type splitting is not linear and the anisotropic bandgap makes it possible to achieve anisotropic propagation characteristics along different directions and at different frequencies.
Oxygen drives benthic-pelagic decomposition pathways in shallow wetlands
Authors: van der Lee Gea H. , Kraak Michiel H. S. , Verdonschot Ralf C. M. , Vonk J. Arie , Verdonschot Piet F. M. 
Published: November 2017

AbstractOxygen availability is perceived as an important environmental factor limiting POM decomposition. In shallow wetlands, however, the impact of commonly observed anoxic conditions in the benthic layer on the relative contribution of microbes and invertebrates to POM decomposition remains largely unknown. Therefore, the aim of this study was to determine if dissolved oxygen drives benthic-pelagic decomposition pathways in shallow wetlands. Dissolved oxygen concentration, invertebrate community composition, microbial decomposition and invertebrate consumption were measured in the benthic and pelagic layer of 15 permanent drainage ditches. We showed that an increased duration of anoxic conditions in the benthic layer of the ditches was related to increased microbial decomposition in this layer, while invertebrate consumption decreased in the benthic layer and increased in the pelagic layer. The increased invertebrate consumption in the pelagic layer was related to the presence of amphipods. We concluded that anoxic conditions in the benthic layer of shallow wetlands relate to an increase in microbial decomposition and a decrease in invertebrate consumption, as detritivorous invertebrates move to the pelagic layer to consume particulate organic matter. This illustrates that environmental conditions, such as dissolved oxygen, may drive the relative importance of aquatic organisms to ecosystem functioning.
Tolerogenic dendritic cells are efficiently generated using minocycline and dexamethasone
Authors: Lee Jae-Hee , Park Chan-Su , Jang Sundong , Kim Ji-Wan , Kim Sang-Hyeon , Song Sukgil , Kim Kyungjae , Lee Chong-Kil 
Published: November 2017

AbstractTolerogenic dendritic cells (tDCs) represent a promising tool for cellular therapy against autoimmune diseases, allergies, and transplantation rejection. Numerous pharmacological agents are known to induce tDC generation. Minocycline, which has long been used as a broad-spectrum antibiotic, was recently shown to significantly increase the generation of DCs with regulatory properties. Here, we examined the effect of the combination of minocycline with dexamethasone, rapamycin, vitamin D3, and interleukin (IL)-10, which are all known inducers of tDC generation. The highest number of tDCs was generated when minocycline and dexamethasone were used together with granulocyte colony-stimulating factor (GM-SCF) and IL-4. The tolerogenicity of the minocycline/dexamethasone-conditioned tDCs was much better than or at least equal to those of the tDCs generated with either one of these agents, as assessed throughin vitrophenotypic and functional assays. In addition, pretreatment with MOG35-55 peptide-pulsed minocycline/dexamethasone-conditioned tDCs significantly ameliorated the clinical signs of experimental autoimmune encephalitis induced by MOG peptide injection in a murine model. These results confirmed that tDCs with potent tolerogenic properties could be efficiently generated by the combined use of minocycline and dexamethasone, along with GM-CSF and IL-4. Our results would help in the development ofex vivotDC-based immunotherapies.
An apelin receptor antagonist prevents pathological retinal angiogenesis with ischemic retinopathy in mice
Authors: Ishimaru Yuki , Shibagaki Fumiya , Yamamuro Akiko , Yoshioka Yasuhiro , Maeda Sadaaki 
Published: November 2017

AbstractPathological retinal angiogenesis is caused by the progression of ischemic retinal diseases and can result in retinal detachment and irreversible blindness. This neovascularization is initiated from the retinal veins and their associated capillaries and involves the overgrowth of vascular endothelial cells. Since expression of the apelin receptor (APJ) is restricted to the veins and proliferative endothelial cells during physiological retinal angiogenesis, in the present study, we investigated the effect of APJ inhibition on pathological retinal angiogenesis in a mouse model of oxygen-induced retinopathy (OIR). In vitro experiments revealed that ML221, an APJ antagonist, suppressed cultured-endothelial cell proliferation in a dose-dependent manner. Intraperitoneal administration of ML221 inhibited pathological angiogenesis but enhanced the recovery of normal vessels into the ischemic regions in the retina of the OIR model mice. ML221 did not affect the expression levels of vascular endothelial growth factor (VEGF) and its receptor (VEGFR2) in the retina. APJ was highly expressed in the endothelial cells within abnormal vessels but was only detected in small amounts in morphologically normal vessels. These results suggest that APJ inhibitors selectively prevent pathological retinal angiogenesis and that the drugs targeting APJ may be new a candidate for treating ischemic retinopathy.
Developing Appreciation for Sarcasm and Sarcastic Gossip: It Depends on Perspective
Authors: Glenwright Melanie , Tapley Brent , Rano Jacqueline K. S. , Pexman Penny M. 
Published: November 2017

Background
Speakers use sarcasm to criticize others and to be funny; the indirectness of sarcasm protects the addressee's face (Brown & Levinson, 1987). Thus, appreciation of sarcasm depends on the ability to consider perspectives.

Purpose
We investigated development of this ability from late childhood into adulthood and examined effects of interpretive perspective and parties present.

Method
We presented 9- to 10-year-olds, 13- to 14-year-olds, and adults with sarcastic and literal remarks in three parties–present conditions: private evaluation, public evaluation, and gossip. Participants interpreted the speaker's attitude and humor from the addressee's perspective and, when appropriate, from the bystander's perspective.

Results
Children showed no influence of interpretive perspective or parties present on appreciation of the speaker's attitude or humor. Adolescents and adults, however, shifted their interpretations, judging that addressees have less favorable views of criticisms than bystanders. Further, adolescents and adults differed in their perceptions of the social functions of gossip, with adolescents showing more positive attitudes than adults toward sarcastic gossip.

Conclusions
We suggest that adults' disapproval of sarcastic gossip shows a deeper understanding of the utility of sarcasm's face-saving function. Thus, the ability to modulate appreciation of sarcasm according to interpretive perspective and parties present continues to develop in adolescence and into adulthood.
A Method to Administer Agents to the Larynx in an Awake Large Animal
Authors: Durkes Abigail , Sivasankar M. Preeti 
Published: November 2017

Purpose
This research note describes an adapted experimental methodology to administer an exogenous agent to the larynx and upper airway of awake animals. The exogenous agent could be a perturbation. In the current study, the agent was isotonic saline. Isotonic saline was selected because it is safe, of similar composition to extracellular fluid, and used in voice studies. The described approach allowed large animals such as pigs to be comfortably restrained without chemical sedation or anesthesia for extended periods while receiving the agent.

Method
Six Sinclair pigs were successfully trained with positive reinforcement to voluntarily enter and then be restrained in a Panepinto Sling. Once restrained, the pigs accepted a nose cone that delivered nebulized isotonic saline. This procedure was repeated 3 times per day for 20 days. At the end of the study, the larynx and airway tissues were excised and examined using histology and transmission electron microscopy.

Results
Pathology related to the procedure (i.e., nebulized inhaled isotonic saline or stress) was not identified in any examined tissues.

Conclusions
This methodology allowed for repeated application of exogenous agents to awake, unstressed animals. This method can be used repeatedly in the laboratory to test various therapeutics for safety, toxicity, and dosage. Future studies will specifically manipulate the type of agent to further our understanding of laryngeal pathobiology.