bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrafast nonlinear optical response of Dirac fermions in graphene
Authors: Baudisch Matthias , Marini Andrea , Cox Joel D. , Zhu Tony , Silva Francisco , Teichmann Stephan , Massicotte Mathieu , Koppens Frank , Levitov Leonid S. , García de Abajo F. Javier , Biegert Jens 
Published: March 2018

AbstractThe speed of solid-state electronic devices, determined by the temporal dynamics of charge carriers, could potentially reach unprecedented petahertz frequencies through direct manipulation by optical fields, consisting in a million-fold increase from state-of-the-art technology. In graphene, charge carrier manipulation is facilitated by exceptionally strong coupling to optical fields, from which stems an important back-action of photoexcited carriers. Here we investigate the instantaneous response of graphene to ultrafast optical fields, elucidating the role of hot carriers on sub-100 fs timescales. The measured nonlinear response and its dependence on interaction time and field polarization reveal the back-action of hot carriers over timescales commensurate with the optical field. An intuitive picture is given for the carrier trajectories in response to the optical-field polarization state. We note that the peculiar interplay between optical fields and charge carriers in graphene may also apply to surface states in topological insulators with similar Dirac cone dispersion relations.
p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage
Authors: Borisova Marina E. , Voigt Andrea , Tollenaere Maxim A. X. , Sahu Sanjeeb Kumar , Juretschke Thomas , Kreim Nastasja , Mailand Niels , Choudhary Chunaram , Bekker-Jensen Simon , Akutsu Masato , Wagner Sebastian A. , Beli Petra 
Published: March 2018

AbstractUltraviolet (UV) light radiation induces the formation of bulky photoproducts in the DNA that globally affect transcription and splicing. However, the signaling pathways and mechanisms that link UV-light-induced DNA damage to changes in RNA metabolism remain poorly understood. Here we employ quantitative phosphoproteomics and protein kinase inhibition to provide a systems view on protein phosphorylation patterns induced by UV light and uncover the dependencies of phosphorylation events on the canonical DNA damage signaling by ATM/ATR and the p38 MAP kinase pathway. We identify RNA-binding proteins as primary substrates and 14-3-3 as direct readers of p38-MK2-dependent phosphorylation induced by UV light. Mechanistically, we show that MK2 phosphorylates the RNA-binding subunit of the NELF complex NELFE on Serine 115. NELFE phosphorylation promotes the recruitment of 14-3-3 and rapid dissociation of the NELF complex from chromatin, which is accompanied by RNA polymerase II elongation.
CDK6 inhibits white to beige fat transition by suppressing RUNX1
Authors: Hou Xiaoli , Zhang Yongzhao , Li Wei , Hu Alexander J. , Luo Chi , Zhou Wenhui , Hu Jamie K. , Daniele Stefano G. , Wang Jinfeng , Sheng Jinghao , Fan Yongsheng , Greenberg Andrew S. , Farmer Stephen R. , Hu Miaofen G. 
Published: March 2018

AbstractWhereas white adipose tissue depots contribute to the development of metabolic diseases, brown and beige adipose tissue has beneficial metabolic effects. Here we show that CDK6 regulates beige adipocyte formation. We demonstrate that mice lacking the CDK6 protein or its kinase domain (K43M) exhibit significant increases beige cell formation, enhanced energy expenditure, better glucose tolerance, and improved insulin sensitivity, and are more resistant to high-fat diet-induced obesity. Re-expression of CDK6 in Cdk6
−/−
mature or precursor cells, or ablation of RUNX1 in K43M mature or precursor cells, reverses these phenotypes. Furthermore, RUNX1 positively regulates the expression of Ucp-1 and Pgc1α by binding to proximal promoter regions. Our findings indicate that CDK6 kinase activity negatively regulates the conversion of fat-storing cells into fat-burning cells by suppressing RUNX1, and suggest that CDK6 may be a therapeutic target for the treatment of obesity and related metabolic diseases.
Turning microplastics into nanoplastics through digestive fragmentation by Antarctic krill
Authors: Dawson Amanda L. , Kawaguchi So , King Catherine K. , Townsend Kathy A. , King Robert , Huston Wilhelmina M. , Bengtson Nash Susan M. 
Published: March 2018

AbstractMicroplastics (plastics <5 mm diameter) are at the forefront of current environmental pollution research, however, little is known about the degradation of microplastics through ingestion. Here, by exposing Antarctic krill (Euphausia superba) to microplastics under acute static renewal conditions, we present evidence of physical size alteration of microplastics ingested by a planktonic crustacean. Ingested microplastics (31.5 µm) are fragmented into pieces less than 1 µm in diameter. Previous feeding studies have shown spherical microplastics either; pass unaffected through an organism and are excreted, or are sufficiently small for translocation to occur. We identify a new pathway; microplastics are fragmented into sizes small enough to cross physical barriers, or are egested as a mixture of triturated particles. These findings suggest that current laboratory-based feeding studies may be oversimplifying interactions between zooplankton and microplastics but also introduces a new role of Antarctic krill, and potentially other species, in the biogeochemical cycling and fate of plastic.
Author Correction: Metabolic changes in Medaka fish induced by cyanobacterial exposures in mesocosms: an integrative approach combining proteomic and metabolomic analyses
Authors: Sotton Benoît , Paris Alain , Le Manach Séverine , Blond Alain , Lacroix Gérard , Millot Alexis , Duval Charlotte , Huet Hélène , Qiao Qin , Labrut Sophie , Chiappetta Giovanni , Vinh Joelle , Catherine Arnaud , Marie Benjamin 
Published: March 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Publisher Correction: TLR4-Mediated Placental Pathology and Pregnancy Outcome in Experimental Malaria
Authors: Barboza Renato , Lima Flávia Afonso , Reis Aramys Silva , Murillo Oscar Javier , Peixoto Erika Paula Machado , Bandeira Carla Letícia , Fotoran Wesley Luzetti , Sardinha Luis Roberto , Wunderlich Gerhard , Bevilacqua Estela , Lima Maria Regina D’Império , Alvarez José Maria , Costa Fabio Trindade Maranhão , Gonçalves Lígia Antunes , Epiphanio Sabrina , Marinho Claudio Romero Farias 
Published: March 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Small-RNA sequencing identifies dynamic microRNA deregulation during skeletal muscle lineage progression
Authors: Castel David , Baghdadi Meryem B. , Mella Sébastien , Gayraud-Morel Barbara , Marty Virginie , Cavaillé Jérôme , Antoniewski Christophe , Tajbakhsh Shahragim 
Published: March 2018

AbstractSkeletal muscle satellite cells are quiescent adult resident stem cells that activate, proliferate and differentiate to generate myofibres following injury. They harbour a robust proliferation potential and self-renewing capacity enabling lifelong muscle regeneration. Although several classes of microRNAs were shown to regulate adult myogenesis, systematic examination of stage-specific microRNAs during lineage progression from the quiescent state is lacking. Here we provide a genome-wide assessment of the expression of small RNAs during the quiescence/activation transition and differentiation by RNA-sequencing. We show that the majority of small RNAs present in quiescent, activated and differentiated muscle cells belong to the microRNA class. Furthermore, by comparing expression in distinct cell states, we report a massive and dynamic regulation of microRNAs, both in numbers and amplitude, highlighting their pivotal role in regulation of quiescence, activation and differentiation. We also identify a number of microRNAs with reliable and specific expression in quiescence including several maternally-expressed miRNAs generated at the imprinted Dlk1-Dio3 locus. Unexpectedly, the majority of class-switching miRNAs are associated with the quiescence/activation transition suggesting a poised program that is actively repressed. These data constitute a key resource for functional analyses of miRNAs in skeletal myogenesis, and more broadly, in the regulation of stem cell self-renewal and tissue homeostasis.
B49, a BST-2-based peptide, inhibits adhesion and growth of breast cancer cells
Authors: Mahauad-Fernandez Wadie D. , Okeoma Chioma M. 
Published: March 2018

AbstractBone marrow stromal antigen 2 (BST-2) also known as Tetherin has been implicated in the growth and progression of many cancers. BST-2 employs its pro-tumor effects through the formation of BST-2:BST-2 dimers which ultimately promotes cell to cell and cell to matrix adhesion, cell motility, survival, and growth. The aim of this study was to evaluate the effect of a novel BST-2-based peptide—B49 on adhesion and growth of breast cancer cells. Homotypic/heterotypic adhesion, three-dimensional spheroid formation, and anchorage-independent growth were used to assess the effect of B49 on cell adhesion and growth. Additionally, we provide evidence of the anti-tumor effect of B49 in a preclinical mouse model of breast cancer. Results show that breast cancer cell adhesion to other cancer cells or components of the tumor microenvironment were inhibited by B49. Most well-known evaluation indexes of cancer cell growth, including spheroid formation, anchorage-independent, and primary tumor growth were significantly inhibited by B49. These data affirm that i) BST-2 plays a key role in mediating breast cancer cell adhesion and growth, and ii) B49 and its analog B49Mod1 significantly inhibits BST-2-mediated cancer cell adhesion and growth. Therefore, B49 and its analogs offer a promising anti-adhesion and therapeutic lead for BST-2-dependent cancers.
Glyco-engineered Long Acting FGF21 Variant with Optimal Pharmaceutical and Pharmacokinetic Properties to Enable Weekly to Twice Monthly Subcutaneous Dosing
Authors: Weng Yan , Ishino Tetsuya , Sievers Annette , Talukdar Saswata , Chabot Jeffrey R. , Tam Amy , Duan Weili , Kerns Kelvin , Sousa Eric , He Tao , Logan Alison , Lee Darwin , Li Dongmei , Zhou Yingjiang , Bernardo Barbara , Joyce Alison , Kavosi Mania , O’Hara Denise M. , Clark Tracey , Guo Jie , Giragossian Craig , Stahl Mark , Calle Roberto A. , Kriz Ron , Somers Will , Lin Laura 
Published: March 2018

AbstractPharmacological administration of FGF21 analogues has shown robust body weight reduction and lipid profile improvement in both dysmetabolic animal models and metabolic disease patients. Here we report the design, optimization, and characterization of a long acting glyco-variant of FGF21. Using a combination of N-glycan engineering for enhanced protease resistance and improved solubility, Fc fusion for further half-life extension, and a single point mutation for improving manufacturability in Chinese Hamster Ovary cells, we created a novel FGF21 analogue, Fc-FGF21[R19V][N171] or PF-06645849, with substantially improved solubility and stability profile that is compatible with subcutaneous (SC) administration. In particular, it showed a low systemic clearance (0.243 mL/hr/kg) and long terminal half-life (~200 hours for intact protein) in cynomolgus monkeys that approaches those of monoclonal antibodies. Furthermore, the superior PK properties translated into robust improvement in glucose tolerance and the effects lasted 14 days post single SC dose in ob/ob mice. PF-06645849 also caused greater body weight loss in DIO mice at lower and less frequent SC doses, compared to previous FGF21 analogue PF-05231023. In summary, the overall PK/PD and pharmaceutical profile of PF-06645849 offers great potential for development as weekly to twice-monthly SC administered therapeutic for chronic treatment of metabolic diseases.
A simple and robust real-time qPCR method for the detection of PIK3CA mutations
Authors: Alvarez-Garcia Virginia , Bartos Clare , Keraite Ieva , Trivedi Urmi , Brennan Paul M. , Kersaudy-Kerhoas Maïwenn , Gharbi Karim , Oikonomidou Olga , Leslie Nicholas R. 
Published: March 2018

AbstractPIK3CA mutations are seemingly the most common driver mutations in breast cancer with H1047R and E545K being the most common of these, accounting together for around 60% of all PIK3CA mutations and have promising therapeutic implications. Given the low sensitivity and the high cost of current genotyping methods we sought to develop fast, simple and inexpensive assays for PIK3CA H1047R and E545K mutation screening in clinical material. The methods we describe are based on a real-time PCR including a mutation specific primer combined with a non-productive oligonucleotide which inhibits wild-type amplification and a parallel internal control reaction. We demonstrate consistent detection of PIK3CA H1047R mutant DNA in genomic DNA extracted from frozen breast cancer biopsies, FFPE material or cancer cell lines with a detection sensitivity of approximately 5% mutant allele fraction and validate these results using both Sanger sequencing and deep next generation sequencing methods. The detection sensitivity for PIK3CA E545K mutation was approximately 10%. We propose these methods as simple, fast and inexpensive diagnostic tools to determine PIK3CA mutation status.
Intensified summer monsoon and the urbanization of Indus Civilization in northwest India
Authors: Dixit Yama , Hodell David A. , Giesche Alena , Tandon Sampat K. , Gázquez Fernando , Saini Hari S. , Skinner Luke C. , Mujtaba Syed A. I. , Pawar Vikas , Singh Ravindra N. , Petrie Cameron A. 
Published: March 2018

AbstractToday the desert margins of northwest India are dry and unable to support large populations, but were densely occupied by the populations of the Indus Civilization during the middle to late Holocene. The hydroclimatic conditions under which Indus urbanization took place, which was marked by a period of expanded settlement into the Thar Desert margins, remains poorly understood. We measured the isotopic values (δ18O and δD) of gypsum hydration water in paleolake Karsandi sediments in northern Rajasthan to infer past changes in lake hydrology, which is sensitive to changing amounts of precipitation and evaporation. Our record reveals that relatively wet conditions prevailed at the northern edge of Rajasthan from ~5.1 ± 0.2 ka BP, during the beginning of the agricultural-based Early Harappan phase of the Indus Civilization. Monsoon rainfall intensified further between 5.0 and 4.4 ka BP, during the period when Indus urban centres developed in the western Thar Desert margin and on the plains of Haryana to its north. Drier conditions set in sometime after 4.4 ka BP, and by ~3.9 ka BP an eastward shift of populations had occurred. Our findings provide evidence that climate change was associated with both the expansion and contraction of Indus urbanism along the desert margin in northwest India.
Automated high throughput animal CO1 metabarcode classification
Authors: Porter Teresita M. , Hajibabaei Mehrdad 
Published: March 2018

AbstractWe introduce a method for assigning names to CO1 metabarcode sequences with confidence scores in a rapid, high-throughput manner. We compiled nearly 1 million CO1 barcode sequences appropriate for classifying arthropods and chordates. Compared to our previous Insecta classifier, the current classifier has more than three times the taxonomic coverage, including outgroups, and is based on almost five times as many reference sequences. Unlike other popular rDNA metabarcoding markers, we show that classification performance is similar across the length of the CO1 barcoding region. We show that the RDP classifier can make taxonomic assignments about 19 times faster than the popular top BLAST hit method and reduce the false positive rate from nearly 100% to 34%. This is especially important in large-scale biodiversity and biomonitoring studies where datasets can become very large and the taxonomic assignment problem is not trivial. We also show that reference databases are becoming more representative of current species diversity but that gaps still exist. We suggest that it would benefit the field as a whole if all investigators involved in metabarocoding studies, through collaborations with taxonomic experts, also planned to barcode representatives of their local biota as a part of their projects.
Evaluation of the therapeutic effects of QuickOpt optimization in Chinese patients with chronic heart failure treated by cardiac resynchronization
Authors: Yan Ji , Zhang Shu , Huang Dejia , Xue Xiaolin , Xu Jing , Tao Qianmin , Zhang Weize , Zhang Zheng , Hua Wei , Liang Yanchun , Tang Baopeng , Xu Wei , Xu Geng , Ren Xuejun , Wang Jingfeng , Guo Tao , Jia Shaobin , Dong Yugang , Jiang Hong , Fu Guosheng , Zhu Liguang , Chen Lin , Tian Fuli , Ling Feng , Li Jianmei , Qi Xiaoyong , Hao Yinglu , Wang Yutang , Zheng Liangrong , Pu Xiaoqun , Shen Farong , Li Guangping , Li Hui , Peng Fang 
Published: March 2018

AbstractIn this trial, long-term therapeutic effects and clinical improvements in Chinese chronic heart failure patients optimized by QuickOpt or echocardiography were compared for atrioventricular (AV) and interventricular (VV) delay optimizations after cardiac resynchronization therapy (CRT) with pacing (CRT-P) or with pacing and defibrillator (CRT-D) therapy. One hundred and ninety-six subjects (50%) had dilated cardiomyopathy, 108 (27.6%) had ischemic heart disease and 112 (28.6%) were hypertensive and were randomized into QuickOpt (198) or echocardiographic optimization (control) (194) groups at ≤2-weeks post-implantation. Programmed AV/VV delay was optimized at baseline and at 3 and 6 months. Left ventricular end-systolic volume (LVESV), New York Heart Association (NYHA) class, specific activity scale (SAS), and the six-minute walk tests (6MWT) were evaluated by blinded researchers at 12 months. Of the QuickOpt group, LVESV decreased significantly by 24.7% ± 33.9% compared with baseline, while LVESV of Controls decreased by 25.1% ± 36.1% (P = 0.924). NYHA class, SAS and 6MWT also improved similarly in both groups at 12 months. Mortality in both groups was not significantly different (11.0% vs 7.6%, P = 0.289). However, there was a significant difference in the time required for optimization by QuickOpt compared with echocardiography (3.33 ± 3.11 vs 58.79 ± 27.03 minutes, P < 0.000).
Greenhouse gas released from the deep permafrost in the northern Qinghai-Tibetan Plateau
Authors: Mu Cuicui , Li Lili , Wu Xiaodong , Zhang Feng , Jia Lin , Zhao Qian , Zhang Tingjun 
Published: March 2018

AbstractDeep carbon pool in permafrost regions is an important component of the global terrestrial carbon cycle. However, the greenhouse gas production from deep permafrost soils is not well understood. Here, using soils collected from 5-m deep permafrost cores from meadow and wet meadow on the northern Qinghai-Tibetan Plateau (QTP), we investigated the effects of temperature on CO2and N2O production under aerobic incubations and CH4production under anaerobic incubations. After a 35-day incubation, the CO2,N2O and CH4production at −2 °C to 10 °C were 0.44~2.12 mg C-CO2/g soil C, 0.0027~0.097 mg N-N2O/g soil N, and 0.14~5.88 μg C-CH4/g soil C, respectively. Greenhouse gas production in deep permafrost is related to the C:N ratio and stable isotopes of soil organic carbon (SOC), whereas depth plays a less important role. The temperature sensitivity (Q10) values of the CO2,N2O and CH4production were 1.67–4.15, 3.26–5.60 and 5.22–10.85, without significant differences among different depths. These results indicated that climate warming likely has similar effects on gas production in deep permafrost and surface soils. Our results suggest that greenhouse gas emissions from both the deep permafrost and surface soils to the air will increase under future climate change.
Identification of new abscisic acid receptor agonists using a wheat cell-free based drug screening system
Authors: Nemoto Keiichirou , Kagawa Makiko , Nozawa Akira , Hasegawa Yoshinori , Hayashi Minoru , Imai Kenichiro , Tomii Kentaro , Sawasaki Tatsuya 
Published: March 2018

AbstractAbscisic acid (ABA) is the main phytohormone involved in abiotic stress response and its adaptation, and is a candidate agrichemical. Consequently, several agonists of ABA have been developed using the yeast two-hybrid system. Here, we describe a novel cell-free-based drug screening approach for the development and validation of ABA receptor agonists. Biochemical validation of this approach between 14 ABA receptors (PYR/PYL/RCARs) and 7 type 2C-A protein phosphatases (PP2CAs) revealed the same interactions as those of previous proteome data, except for nine new interactions. By chemical screening using this approach, we identified two novel ABA receptor agonists, JFA1 (julolidine and fluorine containing ABA receptor activator 1) and JFA2 as its analog. The results of biochemical validation for this approach and biological analysis suggested that JFA1 and JFA2 inhibit seed germination and cotyledon greening of seedlings by activating PYR1 and PYL1, and that JFA2 enhanced drought tolerance without inhibiting root growth by activating not only PYR1 and PYL1 but also PYL5. Thus, our approach was useful for the development of ABA receptor agonists and their validation.
Vector species-specific association between natural Wolbachia infections and avian malaria in black fly populations
Authors: Woodford Luke , Bianco Giovanni , Ivanova Yoana , Dale Maeve , Elmer Kathryn , Rae Fiona , Larcombe Stephen D. , Helm Barbara , Ferguson Heather M. , Baldini Francesco 
Published: March 2018

AbstractArtificial infection of mosquitoes with the endosymbiont bacteriaWolbachiacan interfere with malaria parasite development. Therefore, the release ofWolbachia-infected mosquitoes has been proposed as a malaria control strategy. However,Wolbachiaeffects on vector competence are only partly understood, as indicated by inconsistent effects on malaria infection reported under laboratory conditions. Studies of naturally-occurringWolbachiainfections in wild vector populations could be useful to identify the ecological and evolutionary conditions under which these endosymbionts can block malaria transmission. Here we demonstrate the occurrence of naturalWolbachiainfections in three species of black fly (genusSimulium), which is a main vector of the avian malaria parasiteLeucocytozoon. Prevalence ofLeucocytozoonwas high (25%), but the nature and magnitude of its association withWolbachiadiffered between black fly species.Wolbachiainfection was positively associated with avian malaria infection inS. cryophilum, negatively associated inS. aureum, and unrelated inS. vernum. These differences suggest thatWolbachiainteracts with the parasite in a vector host species-specific manner. This provides a useful model system for further study of howWolbachiainfluences vector competence. Such knowledge, including the possibility of undesirable positive association, is required to guide endosymbiont based control methods.