bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the possible cause of distinct El Niño types in the recent decades
Authors: Jadhav Jyoti , Panickal Swapna , Marathe Shamal , Ashok K. 
Published: November 2015

AbstractDistinct El Niño types have been observed in the recent decades with warm anomalies in the eastern Pacific (Canonical El Niño, EL) and central Pacific (El Niño Modoki, EM). Among these, a basinwide tropical Pacific (TP) warming is seen during 2009 and recently during 2014. We carried out data analysis and numerical simulation experiments to understand the possible cause for different El Niño flavours. The results reveal that the co-evolution of ocean-atmospheric conditions are critically important. Stronger boreal spring (Mar-May) through summer (June-September) westerly wind anomalies (WWA), with relatively stronger ocean pre-conditioning can lead to EL, weaker ocean pre-conditioning and weaker WWA can generate EM, while stronger ocean preconditioning and weaker WWA can lead to basinwide warming pattern. The strength of the WWA is crucial in determining the strength of the ocean dynamic response and the thermocline displacements in the Pacific. The study has important implications for understanding the nature of El Niño in advance.
First Structural View of a Peptide Interacting with the Nucleotide Binding Domain of Heat Shock Protein 90
Authors: Raman Swetha , Singh Meetali , Tatu Utpal , Suguna Kaza 
Published: November 2015

AbstractThe involvement of Hsp90 in progression of diseases like cancer, neurological disorders and several pathogen related conditions is well established. Hsp90, therefore, has emerged as an attractive drug target for many of these diseases. Several small molecule inhibitors of Hsp90, such as geldanamycin derivatives, that display antitumor activity, have been developed and are under clinical trials. However, none of these tested inhibitors or drugs are peptide-based compounds. Here we report the first crystal structure of a peptide bound at the ATP binding site of the N-terminal domain of Hsp90. The peptide makes several specific interactions with the binding site residues, which are comparable to those made by the nucleotide and geldanamycin. A modified peptide was designed based on these interactions. Inhibition of ATPase activity of Hsp90 was observed in the presence of the modified peptide. This study provides an alternative approach and a lead peptide molecule for the rational design of effective inhibitors of Hsp90 function.
Spin splitting in 2D monochalcogenide semiconductors
Authors: Do Dat T. , Mahanti Subhendra D. , Lai Chih Wei 
Published: November 2015

AbstractWe report ab initio calculations of the spin splitting of the uppermost valence band (UVB) and the lowermost conduction band (LCB) in bulk and atomically thin GaS, GaSe, GaTe and InSe. These layered monochalcogenides appear in four major polytypes depending on the stacking order, except for the monoclinic GaTe. Bulk and few-layer ε-and γ -type and odd-number β-type GaS, GaSe and InSe crystals are noncentrosymmetric. The spin splittings of the UVB and the LCB near the Γ-point in the Brillouin zone are finite, but still smaller than those in a zinc-blende semiconductor such as GaAs. On the other hand, the spin splitting is zero in centrosymmetric bulk and even-number few-layer β-type GaS, GaSe and InSe, owing to the constraint of spatial inversion symmetry. By contrast, GaTe exhibits zero spin splitting because it is centrosymmetric down to a single layer. In these monochalcogenide semiconductors, the separation of the non-degenerate conduction and valence bands from adjacent bands results in the suppression of Elliot-Yafet spin relaxation mechanism. Therefore, the electron- and hole-spin relaxation times in these systems with zero or minimal spin splittings are expected to exceed those in GaAs when the D’yakonov-Perel’ spin relaxation mechanism is also suppressed.
True navigation in migrating gulls requires intact olfactory nerves
Authors: Wikelski Martin , Arriero Elena , Gagliardo Anna , Holland Richard A. , Huttunen Markku J. , Juvaste Risto , Mueller Inge , Tertitski Grigori , Thorup Kasper , Wild Martin , Alanko Markku , Bairlein Franz , Cherenkov Alexander , Cameron Alison , Flatz Reinhard , Hannila Juhani , Hüppop Ommo , Kangasniemi Markku , Kranstauber Bart , Penttinen Maija-Liisa , Safi Kamran , Semashko Vladimir , Schmid Heidi , Wistbacka Ralf 
Published: November 2015

AbstractDuring migratory journeys, birds may become displaced from their normal migratory route. Experimental evidence has shown that adult birds can correct for such displacements and return to their goal. However, the nature of the cues used by migratory birds to perform long distance navigation is still debated. In this experiment we subjected adult lesser black-backed gulls migrating from their Finnish/Russian breeding grounds (from >60°N) to Africa (to < 5°N) to sensory manipulation, to determine the sensory systems required for navigation. We translocated birds westward (1080 km) or eastward (885 km) to simulate natural navigational challenges. When translocated westwards and outside their migratory corridor birds with olfactory nerve section kept a clear directional preference (southerly) but were unable to compensate for the displacement, while intact birds and gulls with the ophthalmic branch of the trigeminal nerve sectioned oriented towards their population-specific migratory corridor. Thus, air-borne olfactory information seems to be important for migrating gulls to navigate successfully in some circumstances.
Wearable Fall Detector using Integrated Sensors and Energy Devices
Authors: Jung Sungmook , Hong Seungki , Kim Jaemin , Lee Sangkyu , Hyeon Taeghwan , Lee Minbaek , Kim Dae-Hyeong 
Published: November 2015

AbstractWearable devices have attracted great attentions as next-generation electronic devices. For the comfortable, portable and easy-to-use system platform in wearable electronics, a key requirement is to replace conventional bulky and rigid energy devices into thin and deformable ones accompanying the capability of long-term energy supply. Here, we demonstrate a wearable fall detection system composed of a wristband-type deformable triboelectric generator and lithium ion battery in conjunction with integrated sensors, controllers and wireless units. A stretchable conductive nylon is used as electrodes of the triboelectric generator and the interconnection between battery cells. Ethoxylated polyethylenimine, coated on the surface of the conductive nylon electrode, tunes the work function of a triboelectric generator and maximizes its performance. The electrical energy harvested from the triboelectric generator through human body motions continuously recharges the stretchable battery and prolongs hours of its use. The integrated energy supply system runs the 3-axis accelerometer and related electronics that record human body motions and send the data wirelessly. Upon the unexpected fall occurring, a custom-made software discriminates the fall signal and an emergency alert is immediately sent to an external mobile device. This wearable fall detection system would provide new opportunities in the mobile electronics and wearable healthcare.
Ediacaran Marine Redox Heterogeneity and Early Animal Ecosystems
Authors: Li Chao , Planavsky Noah J. , Shi Wei , Zhang Zihu , Zhou Chuanming , Cheng Meng , Tarhan Lidya G. , Luo Genming , Xie Shucheng 
Published: November 2015

AbstractOxygenation has widely been viewed as a major factor driving the emergence and diversification of animals. However, links between early animal evolution and shifts in surface oxygen levels have largely been limited to extrapolation of paleoredox conditions reconstructed from unfossiliferous strata to settings in which contemporaneous fossils were preserved. Herein, we present a multi-proxy paleoredox study of late Ediacaran (ca. 560-551 Ma) shales hosting the Miaohe Konservat-Lagerstätte of South China and, for comparison, equivalent non-fossil-bearing shales at adjacent sections. For the fossiliferous strata at Miaohe there is geochemical evidence for anoxic conditions, but paleontological evidence for at least episodically oxic conditions. An oxygen-stressed environment is consistent with the low diversity and simple morphology of Miaohe Biota macrofossils. However, there is no evidence for euxinic (anoxic and sulphidic) conditions for the fossiliferous strata at Miaohe, in contrast to adjacent unfossiliferous sections. Our results indicate that Ediacaran marine redox chemistry was highly heterogeneous, even at the kilometre-scale. Therefore, our study provides direct—rather than inferred—evidence that anoxia played a role in shaping a landmark Ediacaran ecosystem. If the anoxic conditions characteristic of the studied sections were widespread in the late Neoproterozoic, environmental stress would have hindered the development of complex ecosystems.
Selective distillation phenomenon in two-species Bose-Einstein condensates in open boundary optical lattices
Authors: Bai Xiao-Dong , Zhang Mei , Xiong Jun , Yang Guo-Jian , Deng Fu-Guo 
Published: November 2015

AbstractWe investigate the formation of discrete breathers (DBs) and the dynamics of the mixture of two-species Bose-Einstein condensates (BECs) in open boundary optical lattices using the discrete nonlinear Schrödinger equations. The results show that the coupling of intra- and interspecies interaction can lead to the existence of pure single-species DBs and symbiotic DBs (i.e., two-species DBs). Furthermore, we find that there is a selective distillation phenomenon in the dynamics of the mixture of two-species BECs. One can selectively distil one species from the mixture of two-species BECs and can even control dominant species fraction by adjusting the intra- and interspecies interaction in optical lattices. Our selective distillation mechanism may find potential application in quantum information storage and quantum information processing based on multi-species atoms.
Modeling gene flow distribution within conventional fields and development of a simplified sampling method to quantify adventitious GM contents in maize
Authors: Melé Enric , Nadal Anna , Messeguer Joaquima , Melé-Messeguer Marina , Palaudelmàs Montserrat , Peñas Gisela , Piferrer Xavier , Capellades Gemma , Serra Joan , Pla Maria 
Published: November 2015

AbstractGenetically modified (GM) crops have been commercially grown for two decades. GM maize is one of 3 species with the highest acreage and specific events. Many countries established a mandatory labeling of products containing GM material, with thresholds for adventitious presence, to support consumers’ freedom of choice. In consequence, coexistence systems need to be introduced to facilitate commercial culture of GM and non-GM crops in the same agricultural area. On modeling adventitious GM cross-pollination distribution within maize fields, we deduced a simple equation to estimate overall GM contents (%GM) of conventional fields, irrespective of its shape and size and with no previous information on possible GM pollen donor fields. A sampling strategy was designed and experimentally validated in 19 agricultural fields. With 9 samples, %GM quantification requires just one analytical GM determination while identification of the pollen source needs 9 additional analyses. A decision support tool is provided.
p53 dynamics upon response element recognition explored by molecular simulations
Authors: Terakawa Tsuyoshi , Takada Shoji 
Published: November 2015

Abstractp53 is a representative transcription factor that activates multiple target genes. To realize stimulus-dependent specificities, p53 has to recognize targets with structural variety, of which molecular mechanisms are largely unknown. Here, we conducted a series of long-time scale (totally more than 100-ms) coarse-grained molecular dynamics simulations, uncovering structure and dynamics of full-length p53 tetramer that recognizes its response element (RE). We obtained structures of a full-length p53 tetramer that binds to the RE, which is strikingly different from the structure of p53 at search. These structures are not only consistent with previous low-resolution or partial structural information, but also give access to previously unreachable detail, such as the preferential distribution of intrinsically disordered regions, the contacts between core domains, the DNA bending and the connectivity of linker regions. We also explored how the RE variation affects the structure of the p53-RE complex. Further analysis of simulation trajectories revealed how p53 finds out the RE and how post-translational modifications affect the search mechanism.
Chikungunya nsP2 protease is not a papain-like cysteine protease and the catalytic dyad cysteine is interchangeable with a proximal serine
Authors: Saisawang Chonticha , Saitornuang Sawanan , Sillapee Pornpan , Ubol Sukathida , Smith Duncan R. , Ketterman Albert J. 
Published: November 2015

AbstractChikungunya virus is the pathogenic alphavirus that causes chikungunya fever in humans. In the last decade millions of cases have been reported around the world from Africa to Asia to the Americas. The alphavirus nsP2 protein is multifunctional and is considered to be pivotal to viral replication, as the nsP2 protease activity is critical for proteolytic processing of the viral polyprotein during replication. Classically the alphavirus nsP2 protease is thought to be papain-like with the enzyme reaction proceeding through a cysteine/histidine catalytic dyad. We performed structure-function studies on the chikungunya nsP2 protease and show that the enzyme is not papain-like. Characterization of the catalytic dyad cysteine residue enabled us to identify a nearby serine that is catalytically interchangeable with the dyad cysteine residue. The enzyme retains activity upon alanine replacement of either residue but a replacement of both cysteine and serine residues results in no detectable activity. Protein dynamics appears to allow the use of either the cysteine or the serine residue in catalysis. This switchable dyad residue has not been previously reported for alphavirus nsP2 proteases and would have a major impact on the nsP2 protease as an anti-viral target.
Stimulation of autophagy promotes functional recovery in diabetic rats with spinal cord injury
Authors: Zhou Kai-liang , Zhou Yi-fei , Wu Kai , Tian Nai-feng , Wu Yao-sen , Wang Yong-li , Chen De-heng , Zhou Bin , Wang Xiang-yang , Xu Hua-zi , Zhang Xiao-lei 
Published: November 2015

AbstractIn this study we examined the relationship between autophagy and apoptosis in diabetic rats after spinal cord injury (SCI), also we determined the role of autophagy in diabetes-aggravated neurological injury in vivo and in vitro. Our results showed that diabetes decreased the survival of neurons, promoted astrocytes proliferation, increased inflammatory cells infiltration and inhibited functional recovery after SCI. Diabetes was shown to confer increased activation of apoptotic pathways, along with an increase in autophagy; similar effects were also observed in vitro in neuronal PC12 cells. Treatment with rapamycin, an autophagy activator, partially abolished the adverse effect of diabetes, suggesting that diabetes may enhance neurological damage and suppress locomotor recovery after SCI, in addition to its effects on apoptosis and autophagy. In contrast, further stimulation of autophagy improved neurological function via inhibition of apoptosis. These results explained how diabetes exacerbates SCI in cellular level and suggested autophagy stimulation to be a new therapeutic strategy for diabetic SCI.
A model for chromosome organization during the cell cycle in live E. coli
Authors: Liu Yuru , Xie Ping , Wang Pengye , Li Ming , Li Hui , Li Wei , Dou Shuoxing 
Published: November 2015

AbstractBacterial chromosomal DNA is a highly compact nucleoid. The organization of this nucleoid is poorly understood due to limitations in the methods used to monitor the complexities of DNA organization in live bacteria. Here, we report that circular plasmid DNA is auto-packaged into a uniform dual-toroidal-spool conformation in response to mechanical stress stemming from sharp bending and un-winding by atomic force microscopic analysis. The mechanism underlying this phenomenon was deduced with basic physical principles to explain the auto-packaging behaviour of circular DNA. Based on our observations and previous studies, we propose a dynamic model of how chromosomal DNA in E. coli may be organized during a cell division cycle. Next, we test the model by monitoring the development of HNS clusters in live E. coli during a cell cycle. The results were in close agreement with the model. Furthermore, the model accommodates a majority of the thus-far-discovered remarkable features of nucleoids in vivo.
Preterm gut microbiota and metabolome following discharge from intensive care
Authors: Stewart Christopher J. , Skeath Tom , Nelson Andrew , Fernstad Sara J. , Marrs Emma C. L. , Perry John D. , Cummings Stephen P. , Berrington Janet E. , Embleton Nicholas D. 
Published: November 2015

AbstractThe development of the preterm gut microbiome is important for immediate and longer-term health following birth. We aimed to determine if modifications to the preterm gut on the neonatal intensive care unit (NICU) impacted the gut microbiota and metabolome long-term. Stool samples were collected from 29 infants ages 1–3 years post discharge (PD) from a single NICU. Additional NICU samples were included from 14/29 infants. Being diagnosed with disease or receiving increased antibiotics while on the NICU did not significantly impact the microbiome PD. Significant decreases in common NICU organisms including K. oxytoca and E. faecalis and increases in common adult organisms including Akkermansia sp., Blautia sp. and Bacteroides sp. and significantly different Shannon diversity was shown between NICU and PD samples. The metabolome increased in complexity, but while PD samples had unique bacterial profiles we observed comparable metabolomic profiles. The preterm gut microbiome is able to develop complexity comparable to healthy term infants despite limited environmental exposures, high levels of antibiotic administration and of the presence of serious disease. Further work is needed to establish the direct effect of weaning as a key event in promoting future gut health.
Shape recognition: convexities, concavities and things in between
Authors: Schmidtmann Gunnar , Jennings Ben J. , Kingdom Frederick A. A. 
Published: November 2015

AbstractVisual objects are effortlessly recognized from their outlines, largely irrespective of viewpoint. Previous studies have drawn different conclusions regarding the importance to shape recognition of specific shape features such as convexities and concavities. However, most studies employed familiar objects, or shapes without curves and did not measure shape recognition across changes in scale and position. We present a novel set of random shapes with well-defined convexities, concavities and inflections (intermediate points), segmented to isolate each feature type. Observers matched the segmented reference shapes to one of two subsequently presented whole-contour shapes (target or distractor) that were re-scaled and re-positioned. For very short segment lengths, performance was significantly higher for convexities than for concavities or intermediate points and for convexities remained constant with increasing segment length. For concavities and intermediate points, performance improved with increasing segment length, reaching convexity performance only for long segments. No significant differences between concavities and intermediates were found. These results show for the first time that closed curvilinear shapes are encoded using the positions of convexities, rather than concavities or intermediate regions. A shape-template model with no free parameters gave an excellent account of the data.
Berry phase mechanism of the anomalous Hall effect in a disordered two-dimensional magnetic semiconductor structure
Authors: Oveshnikov L. N. , Kulbachinskii V. A. , Davydov A. B. , Aronzon B. A. , Rozhansky I. V. , Averkiev N. S. , Kugel K. I. , Tripathi V. 
Published: November 2015

AbstractThe anomalous Hall effect (AHE) arises from the interplay of spin-orbit interactions and ferromagnetic order and is a potentially useful probe of electron spin polarization, especially in nanoscale systems where direct measurement is not feasible. While AHE is rather well-understood in metallic ferromagnets, much less is known about the relevance of different physical mechanisms governing AHE in insulators. As ferromagnetic insulators, but not metals, lend themselves to gate-control of electron spin polarization, understanding AHE in the insulating state is valuable from the point of view of spintronic applications. Among the mechanisms proposed in the literature for AHE in insulators, the one related to a geometric (Berry) phase effect has been elusive in past studies. The recent discovery of quantized AHE in magnetically doped topological insulators - essentially a Berry phase effect - provides strong additional motivation to undertake more careful search for geometric phase effects in AHE in the magnetic semiconductors. Here we report our experiments on the temperature and magnetic field dependences of AHE in insulating, strongly-disordered two-dimensional Mn delta-doped semiconductor heterostructures in the hopping regime. In particular, it is shown that at sufficiently low temperatures, the mechanism of AHE related to the Berry phase is favoured.
Identification of novel autophagic Radix Polygalae fraction by cell membrane chromatography and UHPLC-(Q)TOF-MS for degradation of neurodegenerative disease proteins
Authors: Wu An-Guo , Kam-Wai Wong Vincent , Zeng Wu , Liu Liang , Yuen-Kwan Law Betty 
Published: November 2015

AbstractWith its traditional use in relieving insomnia and anxiety, our previous study has identified onjisaponin B from Radix Polygalae (RP), as a novel autophagic enhancer with potential neuroprotective effects. In current study, we have further identified a novel active fraction from RP, contains 17 major triterpenoid saponins including the onjisaponin B, by the combinational use of cell membrane chromatography (CMC) and ultra-performance liquid chromatography coupled to (quadrupole) time-of-flight mass spectrometry {UHPLC-(Q)TOF-MS}. By exhibiting more potent autophagic effect in cells, the active fraction enhances the clearance of mutant huntingtin and reduces protein level and aggregation of α-synuclein in a higher extent when compared with onjisaponin B. Here, we have reported for the first time the new application of cell-based CMC and UHPLC-(Q)TOF-MS analysis in identifying new autophagy inducers with neuroprotective effects from Chinese medicinal herb. This result has provided novel insights into the possible pharmacological actions of the active components present in the newly identified active fraction of RP, which may help to improve the efficacy of the traditional way of prescribing RP and also provide new standard for the quality control of decoction of RP or its medicinal products in the future.