bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endosomal phosphatidylserine is critical for the YAP signalling pathway in proliferating cells
Authors: Matsudaira Tatsuyuki , Mukai Kojiro , Noguchi Taishin , Hasegawa Junya , Hatta Tomohisa , Iemura Shun-ichiro , Natsume Tohru , Miyamura Norio , Nishina Hiroshi , Nakayama Jun , Semba Kentaro , Tomita Takuya , Murata Shigeo , Arai Hiroyuki , Taguchi Tomohiko 
Published: October 2017

AbstractYes-associated protein (YAP) is a recently discovered growth-promoting transcription coactivator that has been shown to regulate the malignancy of various cancers. How YAP is regulated is not fully understood. Here, we show that one of the factors regulating YAP is phosphatidylserine (PS) in recycling endosomes (REs). We use proximity biotinylation to find proteins proximal to PS. Among these proteins are YAP and multiple proteins related to YAP signalling. Knockdown of ATP8A1 (an RE PS-flippase) or evectin-2 (an RE-resident protein) and masking of PS in the cytoplasmic leaflet of membranes, all suppress nuclear localization of YAP and YAP-dependent transcription. ATP8A1 knockdown increases the phosphorylated (activated) form of Lats1 that phosphorylates and inactivates YAP, whereas evectin-2 knockdown reduces the ubiquitination and increased the level of Lats1. The proliferation of YAP-dependent metastatic cancer cells is suppressed by knockdown of ATP8A1 or evectin-2. These results suggest a link between a membrane phospholipid and cell proliferation.
DNA Ligase C and Prim-PolC participate in base excision repair in mycobacteria
Authors: Płociński Przemysław , Brissett Nigel C. , Bianchi Julie , Brzostek Anna , Korycka-Machała Małgorzata , Dziembowski Andrzej , Dziadek Jarosław , Doherty Aidan J. 
Published: October 2017

AbstractProkaryotic Ligase D is a conserved DNA repair apparatus processing DNA double-strand breaks in stationary phase. An orthologous Ligase C (LigC) complex also co-exists in many bacterial species but its function is unknown. Here we show that the LigC complex interacts with core BER enzymes in vivo and demonstrate that together these factors constitute an excision repair apparatus capable of repairing damaged bases and abasic sites. The polymerase component, which contains a conserved C-terminal structural loop, preferentially binds to and fills-in short gapped DNA intermediates with RNA and LigC ligates the resulting nicks to complete repair. Components of the LigC complex, like LigD, are expressed upon entry into stationary phase and cells lacking either of these pathways exhibit increased sensitivity to oxidising genotoxins. Together, these findings establish that the LigC complex is directly involved in an excision repair pathway(s) that repairs DNA damage with ribonucleotides during stationary phase.
Realizing and manipulating space-time inversion symmetric topological semimetal bands with superconducting quantum circuits
Authors: Tan Xinsheng , Zhao Yuxin , Liu Qiang , Xue Guangming , Yu Haifeng , Wang Z. D. , Yu Yang 
Published: October 2017

AbstractSymmetries of space-inversion (P), time-reversal (T), as well as the joint space–time inversion (PT) are fundamental and significantly important in physics. Here we have experimentally realized the joint PT invariant $${\Bbb Z}_2$$

Z

2

-type topological semimetal-bands, via an analogy between the momentum space and a controllable parameter space in superconducting quantum circuits. By measuring the whole energy spectrum of the system, we clearly imaged an exotic tunable gapless band structure typical of topological semimetals. Two topological quantum phase transitions, from a topological semimetal to two kinds of insulators, can be manipulated by continuously tuning the different parameters in the experimental setup, one of which captures the $${\Bbb Z}_2$$

Z

2

topology of the PT semimetal via merging a pair of nontrivial $${\Bbb Z}_2$$

Z

2

Dirac points. Remarkably, the topological robustness was demonstrated unambiguously, by adding a perturbation that breaks only the individual T and P symmetries but keeps the joint PT symmetry. In contrast, when another kind of PT-violating perturbation is introduced, a topologically trivial insulator gap is fully opened.
SCARA5 plays a critical role in the commitment of mesenchymal stem cells to adipogenesis
Authors: Lee Hyemin , Lee Yoo Jeong , Choi Hyeonjin , Seok Jo Woon , Yoon Bo Kyung , Kim Daeun , Han Ji Yoon , Lee Yoseob , Kim Hyo Jung , Kim Jae-woo 
Published: October 2017

AbstractMesenchymal stem cells have the capacity to give rise to multiple cell types, such as adipocytes, osteoblasts, chondrocytes, and myocytes. However, the molecular events responsible for the lineage specification and differentiation of mesenchymal stem cells remain unclear. Using gene expression profile studies, we determined that Scavenger receptor class A, member 5 (SCARA5) is a novel mediator of adipocyte commitment. SCARA5 was expressed at a higher level in committed A33 preadipocyte cells compared to C3H10T1/2 pluripotent stem cells. Gain- and loss-of-function studies likewise revealed that SCARA5 acts as a mediator of adipocyte commitment and differentiation in both A33 and C3H10T1/2 cells. RNAi-mediated knockdown of SCARA5 in A33 cells markedly inhibited the adipogenic potential, whereas overexpression of SCARA5 enhanced adipocyte differentiation in C3H10T1/2 cells. We also demonstrated that the focal adhesion kinase (FAK) and ERK signaling pathways is associated with the SCARA5-mediated response, thereby modulating adipocyte lineage commitment and adipocyte differentiation. Additionally, glucocorticoids induced the expression of SCARA5 in differentiating adipocytes through glucocorticoids response elements (GRE) in the SCARA5 promoter. Taken together, our study demonstrates that SCARA5 is a positive regulator in adipocyte lineage commitment and early adipogenesis in mesenchymal stem cells.
Rotational dynamics and dynamical transition of water inside hydrophobic pores of carbon nanotubes
Authors: Kyakuno Haruka , Matsuda Kazuyuki , Nakai Yusuke , Ichimura Ryota , Saito Takeshi , Miyata Yasumitsu , Hata Kenji , Maniwa Yutaka 
Published: October 2017

AbstractWater in a nanoconfined geometry has attracted great interest from the viewpoint of not only basic science but also nanofluidic applications. Here, the rotational dynamics of water inside single-walled carbon nanotubes (SWCNTs) with mean diameters larger than ca. 1.4 nm were investigated systematically using 2H nuclear magnetic resonance spectroscopy with high-purity SWCNTs and molecular dynamics calculations. The results were compared with those for hydrophilic pores. It was found that faster water dynamics could be achieved by increasing the hydrophobicity of the pore walls and decreasing the pore diameters. These results suggest a strategy that paves the way for emerging high-performance filtration/separation devices. Upon cooling below 220 K, it was found that water undergoes a transition from fast to slow dynamics states. These results strongly suggest that the observed transition is linked to a liquid-liquid crossover or transition proposed in a two-liquid states scenario for bulk water.
Tracking the impact of depression in a perspective-taking task
Authors: Ferguson Heather J. , Cane James 
Published: October 2017

AbstractResearch has identified impairments in Theory of Mind (ToM) abilities in depressed patients, particularly in relation to tasks involving empathetic responses and belief reasoning. We aimed to build on this research by exploring the relationship between depressed mood and cognitive ToM, specifically visual perspective-taking ability. High and low depressed participants were eye-tracked as they completed a perspective-taking task, in which they followed the instructions of a ‘director’ to move target objects (e.g. a “teapot with spots on”) around a grid, in the presence of a temporarily-ambiguous competitor object (e.g. a “teapot with stars on”). Importantly, some of the objects in the grid were occluded from the director’s (but not the participant’s) view. Results revealed no group-based difference in participants’ ability to use perspective cues to identify the target object. All participants were faster to select the target object when the competitor was only available to the participant, compared to when the competitor was mutually available to the participant and director. Eye-tracking measures supported this pattern, revealing that perspective directed participants’ visual search immediately upon hearing the ambiguous object’s name (e.g. “teapot”). We discuss how these results fit with previous studies that have shown a negative relationship between depression and ToM.
Blood levels of D-amino acid oxidase vs. D-amino acids in reflecting cognitive aging
Authors: Lin Chieh-Hsin , Yang Hui-Ting , Chiu Chih-Chiang , Lane Hsien-Yuan 
Published: October 2017

AbstractFeasible peripheral biomarker for Alzheimer’s disease (AD) is lacking. Dysregulation of N-methyl-D-aspartate (NMDA) receptor is implicated in the pathogenesis of AD. D-amino acid oxidase (DAO) and amino acids can regulate the NMDA receptor function. This study aimed to examine whether peripheral DAO and amino acids levels are characteristic of age-related cognitive decline. We enrolled 397 individuals (including amnestic mild cognitive impairment (MCI), mild AD, moderate to severe AD, and healthy elderly). DAO levels in the serum were measured using ELISA. Amino acids levels in serum were measured by high performance liquid chromatography. Severity of the cognitive deficits in subjects was assessed using Clinical Dementia Rating Scale (CDR). The DAO levels increased with the severity of the cognitive deficits. DAO levels were significantly associated with D-glutamate and D-serine levels. The Receiver Operating Characteristics analysis of DAO levels for AD patients vs. healthy controls determined the optimal cutoff value, 30.10, with high sensitivity (0.842) and specificity (0.889) (area under curve = 0.928). This is the first study indicating that the peripheral DAO levels may increase with age-related cognitive decline. The finding supports the hypofunction of NMDA receptor hypothesis in AD. Whether DAO could serve as a potential surrogate biomarker needs further studies.
Bile acid TUDCA improves insulin clearance by increasing the expression of insulin-degrading enzyme in the liver of obese mice
Authors: Vettorazzi Jean Franciesco , Kurauti Mirian Ayumi , Soares Gabriela Moreira , Borck Patricia Cristine , Ferreira Sandra Mara , Branco Renato Chaves Souto , Michelone Luciana de Souza Lima , Boschero Antonio Carlos , Junior Jose Maria Costa , Carneiro Everardo Magalhães 
Published: October 2017

AbstractDisruption of insulin secretion and clearance both contribute to obesity-induced hyperinsulinemia, though reduced insulin clearance seems to be the main factor. The liver is the major site for insulin degradation, a process mainly coordinated by the insulin-degrading enzyme (IDE). The beneficial effects of taurine conjugated bile acid (TUDCA) on insulin secretion as well as insulin sensitivity have been recently described. However, the possible role of TUDCA in insulin clearance had not yet been explored. Here, we demonstrated that 15 days treatment with TUDCA reestablished plasma insulin to physiological concentrations in high fat diet (HFD) mice, a phenomenon associated with increased insulin clearance and liver IDE expression. TUDCA also increased IDE expression in human hepatic cell line HepG2. This effect was not observed in the presence of an inhibitor of the hepatic membrane bile acid receptor, S1PR2, nor when its downstream proteins were inhibited, including IR, PI3K and Akt. These results indicate that treatment with TUDCA may be helpful to counteract obesity-induced hyperinsulinemia through increasing insulin clearance, likely through enhanced liver IDE expression in a mechanism dependent on S1PR2-Insulin pathway activation.
Aerobic degradation of crude oil by microorganisms in soils from four geographic regions of China
Authors: Liu Qinglong , Tang Jingchun , Gao Kai , Gurav Ranjit , Giesy John P. 
Published: October 2017

AbstractA microcosm experiment was conducted for 112 d by spiking petroleum hydrocarbons into soils from four regions of China. Molecular analyses of soils from microcosms revealed changes in taxonomic diversity and oil catabolic genes of microbial communities. Degradation of total petroleum hydrocarbons (TPHs) in Sand from the Bohai Sea (SS) and Northeast China (NE) exhibited greater microbial mineralization than those of the Dagang Oilfield (DG) and Xiamen (XM). High-throughput sequencing and denaturing gradient gel electrophoresis (DGGE) profiles demonstrated an obvious reconstruction of the bacterial community in all soils. The dominant phylum of the XM with clay soil texture was Firmicutes instead of Proteobacteria in others (DG, SS, and NE) with silty or sandy soil texture. Abundances of alkane monooxygenase gene AlkB increased by 10- to 1000-fold, relative to initial values, and were positively correlated with rates of degradation of TPHs and n-alkanes C13-C30. Abundances of naphthalene dioxygenase gene Nah were positively correlated with degradation of naphthalene and total tricyclic PAHs. Redundancy analysis (RDA) showed that abiotic process derived from geographical heterogeneity was the primary effect on bioremediation of soils contaminated with oil. The optimization of abiotic and biotic factors should be the focus of future bioremediation of oil contaminated soil.
Sustained accuracy improvement in intraocular lens power calculation with the application of quality control circle
Authors: Lin Lei , Chang Pingjun , Xie Jialu , Li Zhangliang , Zhang Hongfang , Lu Fan , Zhao Yun-e 
Published: October 2017

AbstractAccurate intraocular lens (IOL) power calculation is always a challenge in ophthalmology, and unoptimized process may lead to inaccurate refractive outcomes. Quality control circle (QCC) has shown its success in many fields as a process management tool. However, its efficacy in ophthalmology remains unclear. Here we utilized the QCC method to optimize the process and evaluate its efficacy in improving the accuracy of IOL power calculation. After the QCC application, the percentage of eyes with achieved refractive outcomes within 0.5 diopter significantly increased from 63.2% to 80.8% calculated by Haigis formula and 59.2% to 75.8% by SRK/T formula in patients with normal axial length (AL) (22 mm ≤ AL < 26 mm). Although there were no statistically significant differences in patients with long AL by the two formulas (p = 0.886 and 0.726), we achieved an accuracy of 75% with the application of the PhacoOptics software, which was significantly higher than that using the other two formulas (p < 0.001). Our findings indicated that QCC optimized and standardized the process of IOL power calculation, thus improved the accuracy of IOL power calculation in patients who underwent cataract surgery.
Exosomes Derived from HIV-1 Infected DCs Mediate Viral trans-Infection via Fibronectin and Galectin-3
Authors: Kulkarni Rutuja , Prasad Anil 
Published: October 2017

AbstractExosomes are membrane enclosed nano-sized vesicles actively released into the extracellular milieu that can harbor genomic, proteomic and lipid cargos. Functionally, they are shown to regulate cell-cell communication and transmission of pathogens. Though studies have implicated a role for exosomes in HIV-1 pathogenesis, their mechanisms are not well defined. Here, we characterized exosomes derived from uninfected or HIV-1 infected T-cells and DCs. We demonstrate substantial differences in morphological, molecular and biogenesis machinery between exosomes derived from these two immune cell types. In addition, exosomes derived from HIV-1 infected DCs were 4 fold more infective than either cell free HIV-1 or exosomes derived from T-cells. Molecular analysis of exosomes detected the presence of fibronectin and galectin-3 in those derived from DCs, whereas T-cell exosomes lacked these molecules. Addition of anti-fibronectin antibody and β-lactose, a galectin-3 antagonist, significantly blocked DC exosome-mediated HIV-1 infection of T-cells. We also observed increased gene expression of the pro-inflammatory cytokines IFN-γ, TNF-α, IL-1β and RANTES and activation of p38/Stat pathways in T-cells exposed to exosomes derived from HIV-1 infected DCs. Our study provides insight into the role of exosomes in HIV pathogenesis and suggests they can be a target in development of novel therapeutic strategies against viral infection.
Development of a multiplex Endopep-MS assay for simultaneous detection of botulinum toxins A, B and E
Authors: Rosen Osnat , Feldberg Liron , Yamin Tamar Shamai , Dor Eyal , Barnea Ada , Weissberg Avi , Zichel Ran 
Published: October 2017

AbstractBotulinum neurotoxins (BoNTs) are bacterial proteins that cause botulism, a life-threatening disease. The Endopep-MS assay permits rapid detection and serotypic differential diagnosis of BoNTs. The serotype-specific nature of this assay requires that each serum sample be aliquoted and individually tested, which in addition to the limited volume of clinical samples, especially in infants, points to the need for a multiplex assay. However, previous attempts to develop such an assay have been challenging, mainly due to inhibition of BoNT/A activity by the BoNT/E peptide substrate. BoNT/A and BoNT/E share the same native target protein as their substrate. We hypothesized that the steric interference between the BoNT/A and BoNT/E substrate peptides is responsible for the difficulty in simultaneously assaying these two toxins. To explore the basis for steric interference, we used the reported structure of BoNT/A in complex with SNAP-25 and modelled the structure of BoNT/E with SNAP-25. Following this thorough structural analysis, we designed a new peptide substrate for BoNT/A that maintained the assay sensitivity and allowed, for the first time, simultaneous detection of the three most abundant human botulinum serotypes. Adopting the multiplex assay will minimize the required sample volume and assay time for botulinum detection while maintaining the superior Endopep-MS assay performance.
How goats avoid ingesting noxious insects while feeding
Authors: Berman Tali S. , Ben-Ari Matan , Glasser Tzach A. , Gish Moshe , Inbar Moshe 
Published: October 2017

AbstractAs mammalian herbivores feed, they often encounter noxious insects on plants. It is unknown how they handle such insects. We experimentally examined the behavioural responses of goats to the noxious spring-webworm (Ocnogyna loewii), and manipulated their sensory perception to reveal the process of insect detection. Goats did not avoid plants with webworms, demonstrating a remarkable ability to sort them apart from the plant (98% of webworms survived). Initial detection of webworms involved tactile stimulation, done by repeatedly touching the leaves with the muzzle. This enabled them to pick webworm-free leaves. If the goats picked up leaves with a webworm, they shook or discarded the leaf. They spat out webworms that entered their mouths, after detecting them by touch and taste. By using their keen senses and efficient behaviours, goats are able to feed while accurately excluding insects. These findings highlight the importance of direct interactions between mammalian herbivores and insects.
High Quantum Yield Green-Emitting Carbon Dots for Fe(ІІІ) Detection, Biocompatible Fluorescent Ink and Cellular Imaging
Authors: Khan Waheed Ullah , Wang Deyin , Zhang Wei , Tang Zuobin , Ma Xinlong , Ding Xin , Du Shanshan , Wang Yuhua 
Published: October 2017

AbstractIn the present work, we reported the luminescence of a green-emitting carbon dots (CDs) synthesized via solid state reaction method using diammonium hydrogen citrate and urea as a starting materials. The obtained green-emitting CDs shows strong absorption in the 350–450 nm region and gives intense green emission (λmax = 537 nm) with quantum yield as high as 46.4% under 420 nm excitation. The obtained green-emitting CDs also demonstrates high photo-stability, which is evidenced by the fact that its emission intensity almost has no change under irradiation by a 365 nm UV lamp for 2 hours. Moreover, the obtained green-emitting CDs shows high sensitivity and selectivity for the detection of Fe3+, and their emission intensity response towards Fe3+ ions is highly linear (R2 = 0.995) over the concentration range from 25 to 300 µM, which could provide an effective platform for detection of Fe3+. Mostly important, we further demonstrate that such photoluminescent green-emitting CDs exhibits low toxicity and are biocompatible for use with in cellular imaging. Combining with low cytotoxicity, good water solubility and excellent luminescence properties, green-emitting CDs could be used as a biocompatible fluorescent ink in future applications.
Intelligibility of Noise-Adapted and Clear Speech in Child, Young Adult, and Older Adult Talkers
Authors: Smiljanic Rajka , Gilbert Rachael C. 
Published: October 2017

Purpose
This study examined intelligibility of conversational and clear speech sentences produced in quiet and in noise by children, young adults, and older adults. Relative talker intelligibility was assessed across speaking styles.

Method
Sixty-one young adult participants listened to sentences mixed with speech-shaped noise at −5 dB signal-to-noise ratio. The analyses examined percent correct scores across conversational, clear, and noise-adapted conditions and the three talker groups. Correlation analyses examined whether talker intelligibility is consistent across speaking style adaptations.

Results
Noise-adapted and clear speech significantly enhanced intelligibility for young adult listeners. The intelligibility improvement varied across the three talker groups. Notably, intelligibility benefit was smallest for children's speaking style modifications. Listeners also perceived speech produced in noise by older adults to be less intelligible compared to the younger talkers. Talker intelligibility was correlated strongly between conversational and clear speech in quiet, but not for conversational speech produced in quiet and in noise.

Conclusions
Results provide evidence that intelligibility variation related to age and communicative barrier has the potential to aid clinical decision making for individuals with speech disorders, particularly dysarthria.
Predicting Intelligibility Gains in Dysarthria Through Automated Speech Feature Analysis
Authors: Fletcher Annalise R. , Wisler Alan A. , McAuliffe Megan J. , Lansford Kaitlin L. , Liss Julie M. 
Published: October 2017

PurposeBehavioral speech modifications have variable effects on the intelligibility of speakers with dysarthria. In the companion article, a significant relationship was found between measures of speakers' baseline speech and their intelligibility gains following cues to speak louder and reduce rate (Fletcher, McAuliffe, Lansford, Sinex, & Liss, 2017). This study reexamines these features and assesses whether automated acoustic assessments can also be used to predict intelligibility gains.MethodFifty speakers (7 older individuals and 43 with dysarthria) read a passage in habitual, loud, and slow speaking modes. Automated measurements of long-term average spectra, envelope modulation spectra, and Mel-frequency cepstral coefficients were extracted from short segments of participants' baseline speech. Intelligibility gains were statistically modeled, and the predictive power of the baseline speech measures was assessed using cross-validation.ResultsStatistical models could predict the intelligibility gains of speakers they had not been trained on. The automated acoustic features were better able to predict speakers' improvement in the loud condition than the manual measures reported in the companion article.ConclusionsThese acoustic analyses present a promising tool for rapidly assessing treatment options. Automated measures of baseline speech patterns may enable more selective inclusion criteria and stronger group outcomes within treatment studies.