bluuebunny/crossref_metadata_2025_split huggingface dataset:
The microscopic structure of charge density waves in underdoped YBa2Cu3O6.54 revealed by X-ray diffraction
Authors: Forgan E. M. , Blackburn E. , Holmes A. T. , Briffa A. K. R. , Chang J. , Bouchenoire L. , Brown S. D. , Liang Ruixing , Bonn D. , Hardy W. N. , Christensen N. B. , Zimmermann M. V. , Hücker M. , Hayden S. M. 
Published: December 2015

AbstractCharge density wave (CDW) order appears throughout the underdoped high-temperature cuprate superconductors, but the underlying symmetry breaking and the origin of the CDW remain unclear. We use X-ray diffraction to determine the microscopic structure of the CDWs in an archetypical cuprate YBa2Cu3O6.54 at its superconducting transition temperature ∼60 K. We find that the CDWs in this material break the mirror symmetry of the CuO2 bilayers. The ionic displacements in the CDWs have two components, which are perpendicular and parallel to the CuO2 planes, and are out of phase with each other. The planar oxygen atoms have the largest displacements, perpendicular to the CuO2 planes. Our results allow many electronic properties of the underdoped cuprates to be understood. For instance, the CDWs will lead to local variations in the electronic structure, giving an explicit explanation of density-wave states with broken symmetry observed in scanning tunnelling microscopy and soft X-ray measurements.
Cold-sensing regulates Drosophila growth through insulin-producing cells
Authors: Li Qiaoran , Gong Zhefeng 
Published: December 2015

AbstractAcross phyla, body size is linked to climate. For example, rearing fruit flies at lower temperatures results in bigger body sizes than those observed at higher temperatures. The underlying molecular basis of this effect is poorly understood. Here we provide evidence that the temperature-dependent regulation of Drosophila body size depends on a group of cold-sensing neurons and insulin-producing cells (IPCs). Electrically silencing IPCs completely abolishes the body size increase induced by cold temperature. IPCs are directly innervated by cold-sensing neurons. Stimulation of these cold-sensing neurons activates IPCs, promotes synthesis and secretion of Drosophila insulin-like peptides and induces a larger body size, mimicking the effects of rearing the flies in cold temperature. Taken together, these findings reveal a neuronal circuit that mediates the effects of low temperature on fly growth.
Linker histone H1 and H3K56 acetylation are antagonistic regulators of nucleosome dynamics
Authors: Bernier Morgan , Luo Yi , Nwokelo Kingsley C. , Goodwin Michelle , Dreher Sarah J. , Zhang Pei , Parthun Mark R. , Fondufe-Mittendorf Yvonne , Ottesen Jennifer J. , Poirier Michael G. 
Published: December 2015

AbstractH1 linker histones are highly abundant proteins that compact nucleosomes and chromatin to regulate DNA accessibility and transcription. However, the mechanisms that target H1 regulation to specific regions of eukaryotic genomes are unknown. Here we report fluorescence measurements of human H1 regulation of nucleosome dynamics and transcription factor (TF) binding within nucleosomes. H1 does not block TF binding, instead it suppresses nucleosome unwrapping to reduce DNA accessibility within H1-bound nucleosomes. We then investigated H1 regulation by H3K56 and H3K122 acetylation, two transcriptional activating histone post translational modifications (PTMs). Only H3K56 acetylation, which increases nucleosome unwrapping, abolishes H1.0 reduction of TF binding. These findings show that nucleosomes remain dynamic, while H1 is bound and H1 dissociation is not required for TF binding within the nucleosome. Furthermore, our H3K56 acetylation measurements suggest that a single-histone PTM can define regions of the genome that are not regulated by H1.
Long-term neural and physiological phenotyping of a single human
Authors: Poldrack Russell A. , Laumann Timothy O. , Koyejo Oluwasanmi , Gregory Brenda , Hover Ashleigh , Chen Mei-Yen , Gorgolewski Krzysztof J. , Luci Jeffrey , Joo Sung Jun , Boyd Ryan L. , Hunicke-Smith Scott , Simpson Zack Booth , Caven Thomas , Sochat Vanessa , Shine James M. , Gordon Evan , Snyder Abraham Z. , Adeyemo Babatunde , Petersen Steven E. , Glahn David C. , Reese Mckay D. , Curran Joanne E. , Göring Harald H. H. , Carless Melanie A. , Blangero John , Dougherty Robert , Leemans Alexander , Handwerker Daniel A. , Frick Laurie , Marcotte Edward M. , Mumford Jeanette A. 
Published: December 2015

AbstractPsychiatric disorders are characterized by major fluctuations in psychological function over the course of weeks and months, but the dynamic characteristics of brain function over this timescale in healthy individuals are unknown. Here, as a proof of concept to address this question, we present the MyConnectome project. An intensive phenome-wide assessment of a single human was performed over a period of 18 months, including functional and structural brain connectivity using magnetic resonance imaging, psychological function and physical health, gene expression and metabolomics. A reproducible analysis workflow is provided, along with open access to the data and an online browser for results. We demonstrate dynamic changes in brain connectivity over the timescales of days to months, and relations between brain connectivity, gene expression and metabolites. This resource can serve as a testbed to study the joint dynamics of human brain and metabolic function over time, an approach that is critical for the development of precision medicine strategies for brain disorders.
Predicting cancerlectins by the optimal g-gap dipeptides
Authors: Lin Hao , Liu Wei-Xin , He Jiao , Liu Xin-Hui , Ding Hui , Chen Wei 
Published: December 2015

AbstractThe cancerlectin plays a key role in the process of tumor cell differentiation. Thus, to fully understand the function of cancerlectin is significant because it sheds light on the future direction for the cancer therapy. However, the traditional wet-experimental methods were money- and time-consuming. It is highly desirable to develop an effective and efficient computational tool to identify cancerlectins. In this study, we developed a sequence-based method to discriminate between cancerlectins and non-cancerlectins. The analysis of variance (ANOVA) was used to choose the optimal feature set derived from the g-gap dipeptide composition. The jackknife cross-validated results showed that the proposed method achieved the accuracy of 75.19%, which is superior to other published methods. For the convenience of other researchers, an online web-server CaLecPred was established and can be freely accessed from the website http://lin.uestc.edu.cn/server/CalecPred. We believe that the CaLecPred is a powerful tool to study cancerlectins and to guide the related experimental validations.
Long-lived Aqueous Rechargeable Lithium Batteries Using Mesoporous LiTi2(PO4)3@C Anode
Authors: Sun Dan , Tang Yougen , He Kejian , Ren Yu , Liu Suqin , Wang Haiyan 
Published: December 2015

AbstractThe instability of anode materials during cycling has been greatly limiting the lifetime of aqueous rechargeable lithium batteries (ARLBs). Here, to tackle this issue, mesoporous LiTi2(PO4)3@C composites with a pore size of 4 nm and a large BET surface area of 165 m2 g−1 have been synthesized by a novel two-step approach. The ARLB with this type of LiTi2(PO4)3@C anode, commercial LiMn2O4 cathode and 2 M Li2(SO4) aqueous solution (oxygen was removed) exhibited superior cycling stability (a capacity retention of 88.9% after 1200 cycles at 150 mA g−1 and 82.7% over 5500 cycles at 750 mA g−1) and excellent rate capability (discharge capacities of 121, 110, 90 and 80 mAh g−1 based on the mass of LiTi2(PO4)3 at 30, 150, 1500, and 3000 mA g−1, respectively). As verified, the mesoporous structure, large surface area and high-quality carbon coating layer of the LiTi2(PO4)3@C composite contribute to the breakthrough in achieving excellent electrochemical properties for ARLB.
A Petal-type Chiral NADH Model: Design, Synthesis and its Asymmetric Reduction
Authors: Bai Cui-Bing , Wang Nai-Xing , Wang Yan-Jing , Xing Yalan , Zhang Wei , Lan Xing-Wang 
Published: December 2015

AbstractA new type of NADH model compound has been synthesized by an efficient and convenient method. This model compound exhibits high reactivity and enantioselectivity in asymmetric reduction reactions. The results show that chiral NADH model S could be effectively combined with Mg2+ to form ternary complexes. This novel C3 symmetrical NADH model is capable of fluorescence emission at 460 nm when excited at 377 nm.
Quantifying replicative senescence as a tumor suppressor pathway and a target for cancer therapy
Authors: Rodriguez-Brenes Ignacio A. , Wodarz Dominik , Komarova Natalia L. 
Published: December 2015

AbstractTo study quantitatively replicative senescence as a tumor suppressor mechanism, we investigate the distribution of a growing clonal cell population restricted by Hayflick’s limit. We find that in the biologically relevant range of parameters, if the imbalance between cell division and death is moderate or low (high death-to-birth ratio), senescence offers significant protection against cancer by halting abnormal cell proliferation at early pre-diagnostic stages of tumor development. We also find that by the time tumors are typically detected, there is a high probability that telomerase is activated, even if the cell of origin was telomerase negative. Hence, the fact that most cancers are positive for telomerase is not necessarily an indication that cancer originated in a telomerase positive cell. Finally, we discuss how the population dynamics of cells can determine the outcomes of anti-telomerase cancer therapies and provide guidelines on how the model could potentially be applied to develop clinically useful tools to predict the response to treatment by telomerase inhibitors in individual patients.
Revealing text in a complexly rolled silver scroll from Jerash with computed tomography and advanced imaging software
Authors: Hoffmann Barfod Gry , Larsen John Møller , Lichtenberger Achim , Raja Rubina 
Published: December 2015

AbstractThroughout Antiquity magical amulets written on papyri, lead and silver were used for apotropaic reasons. While papyri often can be unrolled and deciphered, metal scrolls, usually very thin and tightly rolled up, cannot easily be unrolled without damaging the metal. This leaves us with unreadable results due to the damage done or with the decision not to unroll the scroll. The texts vary greatly and tell us about the cultural environment and local as well as individual practices at a variety of locations across the Mediterranean. Here we present the methodology and the results of the digital unfolding of a silver sheet from Jerash in Jordan from the mid-8th century CE. The scroll was inscribed with 17 lines in presumed pseudo-Arabic as well as some magical signs. The successful unfolding shows that it is possible to digitally unfold complexly folded scrolls, but that it requires a combination of the know-how of the software and linguistic knowledge.
Extreme decay of meteoric beryllium-10 as a proxy for persistent aridity
Authors: Valletta Rachel D. , Willenbring Jane K. , Lewis Adam R. , Ashworth Allan C. , Caffee Marc 
Published: December 2015

AbstractThe modern Antarctic Dry Valleys are locked in a hyper-arid, polar climate that enables the East Antarctic Ice Sheet (EAIS) to remain stable, frozen to underlying bedrock. The duration of these dry, cold conditions is a critical prerequisite when modeling the long-term mass balance of the EAIS during past warm climates and is best examined using terrestrial paleoclimatic proxies. Unfortunately, deposits containing such proxies are extremely rare and often difficult to date. Here, we apply a unique dating approach to tundra deposits using concentrations of meteoric beryllium-10 (10Be) adhered to paleolake sediments from the Friis Hills, central Dry Valleys. We show that lake sediments were emplaced between 14–17.5 My and have remained untouched by meteoric waters since that time. Our results support the notion that the onset of Dry Valleys aridification occurred ~14 My, precluding the possibility of EAIS collapse during Pliocene warming events. Lake fossils indicate that >14 My ago the Dry Valleys hosted a moist tundra that flourished in elevated atmospheric CO2 (>400 ppm). Thus, Dry Valleys tundra deposits record regional climatic transitions that affect EAIS mass balance, and, in a global paleoclimatic context, these deposits demonstrate how warming induced by 400 ppm CO2 manifests at high latitudes.
Vasculogenic dynamics in 3D engineered tissue constructs
Authors: Blinder Yaron J. , Freiman Alina , Raindel Noa , Mooney David J. , Levenberg Shulamit 
Published: December 2015

AbstractImplantable 3D engineered vascular tissue constructs can be formed by co-culturing endothelial and fibroblast cells on macroporous scaffolds. Here we show that these constructs can be used for studying the dynamics of neovascular formation in-vitro by a combination of live confocal imaging and an array of image processing and analysis tools, revealing multiple distinct stages of morphogenesis. We show that this process involves both vasculogenic and angiogenic elements, including an initial endothelial multicellular cluster formation followed by rapid extensive sprouting, ultimately resulting in a stable interconnected endothelial network morphology. This vascular morphogenesis is time-correlated with the deposition and formation of an extensive extra-cellular matrix environment. We further show that endothelial network junctions are formed by two separate morphogenic mechanisms of anastomosis and cluster thinning.
Mapping the genetic diversity of HLA haplotypes in the Japanese populations
Authors: Saw Woei-Yuh , Liu Xuanyao , Khor Chiea-Chuen , Takeuchi Fumihiko , Katsuya Tomohiro , Kimura Ryosuke , Nabika Toru , Ohkubo Takayoshi , Tabara Yasuharu , Yamamoto Ken , Yokota Mitsuhiro ,   Japanese Genome Variation Consortium, Akiyama Koichi , Asano Hiroyuki , Asayama Kei , Haga Toshikazu , Hara Azusa , Hirose Takuo , Hosaka Miki , Ichihara Sahoko , Imai Yutaka , Inoue Ryusuke , Ishiguro Aya , Isomura Minoru , Isono Masato , Kamide Kei , Kato Norihiro , Katsuya Tomohiro , Kikuya Masahiro , Kohara Katsuhiko , Matsubara Tatsuaki , Matsuda Ayako , Metoki Hirohito , Miki Tetsuro , Murakami Keiko , Nabika Toru , Nakatochi Masahiro , Ogihara Toshio , Ohnaka Keizo , Ohkubo Takayoshi , Rakugi Hiromi , Satoh Michihiro , Shiwaku Kunihiro , Sugimoto Ken , Tabara Yasuharu , Takami Yoichi , Takayanagi Ryoichi , Takeuchi Fumihiko , Tsubota-Utsugi Megumi , Yamamoto Ken , Yamamoto Koichi , Yamasaki Masayuki , Yasui Daisaku , Yokota Mitsuhiro , Teo Yik-Ying , Kato Norihiro 
Published: December 2015

AbstractJapan has often been viewed as an Asian country that possesses a genetically homogenous community. The basis for partitioning the country into prefectures has largely been geographical, although cultural and linguistic differences still exist between some of the districts/prefectures, especially between Okinawa and the mainland prefectures. The Major Histocompatibility Complex (MHC) region has consistently emerged as the most polymorphic region in the human genome, harbouring numerous biologically important variants; nevertheless the presence of population-specific long haplotypes hinders the imputation of SNPs and classical HLA alleles. Here, we examined the extent of genetic variation at the MHC between eight Japanese populations sampled from Okinawa and six other prefectures located in or close to the mainland of Japan, specifically focusing at the haplotypes observed within each population and what the impact of any variation has on imputation. Our results indicated that Okinawa was genetically farther to the mainland Japanese than were Gujarati Indians from Tamil Indians, while the mainland Japanese from six prefectures were more homogeneous than between northern and southern Han Chinese. The distribution of haplotypes across Japan was similar, although imputation was most accurate for Okinawa and several mainland prefectures when population-specific panels were used as reference.
Contrasting levels of absorption of intense femtosecond laser pulses by solids
Authors: Singh Prashant Kumar , Cui Y. Q. , Adak Amitava , Lad Amit D. , Chatterjee Gourab , Brijesh P. , Sheng Z. M. , Kumar G. Ravindra 
Published: December 2015

AbstractThe absorption of ultraintense, femtosecond laser pulses by a solid unleashes relativistic electrons, thereby creating a regime of relativistic optics. This has enabled exciting applications of relativistic particle beams and coherent X-ray radiation and fundamental leaps in high energy density science and laboratory astrophysics. Obviously, central to these possibilities lies the basic problem of understanding and if possible, manipulating laser absorption. Surprisingly, the absorption of intense light largely remains an open question, despite the extensive variations in target and laser pulse structures. Moreover, there are only few experimental measurements of laser absorption carried out under very limited parameter ranges. Here we present an extensive investigation of absorption of intense 30 femtosecond laser pulses by solid metal targets. The study, performed under varying laser intensity and contrast ratio over four orders of magnitude, reveals a significant and non-intuitive dependence on these parameters. For contrast ratio of 10−9 and intensity of 2 × 1019 W cm−2, three observations are revealed: preferential acceleration of electrons along the laser axis, a ponderomotive scaling of electron temperature and red shifting of emitted second-harmonic. These point towards the role of J × B absorption mechanism at relativistic intensity. The experimental results are supported by particle-in-cell simulations.
Ca-α1T, a fly T-type Ca2+ channel, negatively modulates sleep
Authors: Jeong Kyunghwa , Lee Soyoung , Seo Haengsoo , Oh Yangkyun , Jang Donghoon , Choe Joonho , Kim Daesoo , Lee Jung-Ha , Jones Walton D. 
Published: December 2015

AbstractMammalian T-type Ca2+ channels are encoded by three separate genes (Cav3.1, 3.2, 3.3). These channels are reported to be sleep stabilizers important in the generation of the delta rhythms of deep sleep, but controversy remains. The identification of precise physiological functions for the T-type channels has been hindered, at least in part, by the potential for compensation between the products of these three genes and a lack of specific pharmacological inhibitors. Invertebrates have only one T-type channel gene, but its functions are even less well-studied. We cloned Ca-α1T, the only Cav3 channel gene in Drosophila melanogaster, expressed it in Xenopus oocytes and HEK-293 cells and confirmed it passes typical T-type currents. Voltage-clamp analysis revealed the biophysical properties of Ca-α1T show mixed similarity, sometimes falling closer to Cav3.1, sometimes to Cav3.2 and sometimes to Cav3.3. We found Ca-α1T is broadly expressed across the adult fly brain in a pattern vaguely reminiscent of mammalian T-type channels. In addition, flies lacking Ca-α1T show an abnormal increase in sleep duration most pronounced during subjective day under continuous dark conditions despite normal oscillations of the circadian clock. Thus, our study suggests invertebrate T-type Ca2+ channels promote wakefulness rather than stabilizing sleep.
Sensitive detection of vortex-core resonance using amplitude-modulated magnetic field
Authors: Cui Xiaomin , Hu Shaojie , Hidegara Makoto , Yakata Satoshi , Kimura Takashi 
Published: December 2015

AbstractUnderstanding and manipulating the dynamic properties of the magnetic vortices stabilized in patterned ferromagnetic structures are of great interest owing to the superior resonant features with the high thermal stability and their flexible tunability. So far, numerous methods for investigating the dynamic properties of the magnetic vortex have been proposed and demonstrated. However, those techniques have some regulations such as spatial resolution, experimental facility and sensitivity. Here, we develop a simple and sensitive method for investigating the vortex-core dynamics by using the electrically separated excitation and detection circuits. We demonstrate that the resonant oscillation of the magnetic vortex induced by the amplitude- modulated alternating-sign magnetic field is efficiently picked up by the lock-in detection with the modulated frequency. By extending this method, we also investigate the size dependence and the influence of the magneto-static interaction in the resonant property of the magnetic vortex.
Unexpected diversity of Anopheles species in Eastern Zambia: implications for evaluating vector behavior and interventions using molecular tools
Authors: Lobo Neil F. , Laurent Brandyce St. , Sikaala Chadwick H. , Hamainza Busiku , Chanda Javan , Chinula Dingani , Krishnankutty Sindhu M. , Mueller Jonathan D. , Deason Nicholas A. , Hoang Quynh T. , Boldt Heather L. , Thumloup Julie , Stevenson Jennifer , Seyoum Aklilu , Collins Frank H. 
Published: December 2015

AbstractThe understanding of malaria vector species in association with their bionomic traits is vital for targeting malaria interventions and measuring effectiveness. Many entomological studies rely on morphological identification of mosquitoes, limiting recognition to visually distinct species/species groups. Anopheles species assignments based on ribosomal DNA ITS2 and mitochondrial DNA COI were compared to morphological identifications from Luangwa and Nyimba districts in Zambia. The comparison of morphological and molecular identifications determined that interpretations of species compositions, insecticide resistance assays, host preference studies, trap efficacy and Plasmodium infections were incorrect when using morphological identification alone. Morphological identifications recognized eight Anopheles species while 18 distinct sequence groups or species were identified from molecular analyses. Of these 18, seven could not be identified through comparison to published sequences. Twelve of 18 molecularly identified species (including unidentifiable species and species not thought to be vectors) were found by PCR to carry Plasmodium sporozoites - compared to four of eight morphological species. Up to 15% of morphologically identified Anopheles funestus mosquitoes in insecticide resistance tests were found to be other species molecularly. The comprehension of primary and secondary malaria vectors and bionomic characteristics that impact malaria transmission and intervention effectiveness are fundamental in achieving malaria elimination.
An optical biosensor assay for rapid dual detection of Botulinum neurotoxins A and E
Authors: Lévêque Christian , Ferracci Géraldine , Maulet Yves , Mazuet Christelle , Popoff Michel R. , Blanchard Marie-Pierre , Seagar Michael , El Far Oussama 
Published: December 2015

AbstractThe enzymatic activity of the pathogenic botulinum neurotoxins type A and E (BoNT/A and E) leads to potentially lethal paralytic symptoms in humans and their prompt detection is of crucial importance. A chip assay based on Surface Plasmon Resonance monitoring of the cleavage products is a simple method that we have previously established to detect BoNT/A activity. We have now developed a similar format assay to measure BoNT/E activity. A monoclonal antibody specifically recognizing SNAP25 cleaved by BoNT/E was generated and used to measure the appearance of the neo-epitope following injection of BoNT/E over SNAP-25 immobilized on a chip. This assay detects BoNT/E activity at 1 LD50/ml within minutes and linear dose-responses curves were obtained using a multiplexed biosensor. A threshold of 0.01 LD50/ml was achieved after 5 h of cleavage. This assay is 10-fold more sensitive than the in vivo assay for direct detection of BoNT/E in serum samples. The SNAP25 chip assay is able to discriminate in an automated manner the presence of BoNT/E, BoNT/A or a combination of both toxins.