bluuebunny/crossref_metadata_2025_split huggingface dataset:
In-situ visualization of solute-driven phase coexistence within individual nanorods
Authors: Hayee Fariah , Narayan Tarun C. , Nadkarni Neel , Baldi Andrea , Koh Ai Leen , Bazant Martin Z. , Sinclair Robert , Dionne Jennifer A. 
Published: April 2018

AbstractNanorods are promising components of energy and information storage devices that rely on solute-driven phase transformations, due to their large surface-to-volume ratio and ability to accommodate strain. Here we investigate the hydrogen-induced phase transition in individual penta-twinned palladium nanorods of varying aspect ratios with ~3 nm spatial resolution to understand the correlation between nanorod structure and thermodynamics. We find that the hydrogenated phase preferentially nucleates at the rod tips, progressing along the length of the nanorods with increasing hydrogen pressure. While nucleation pressure is nearly constant for all lengths, the number of phase boundaries is length-dependent, with stable phase coexistence always occurring for rods longer than 55 nm. Moreover, such coexistence occurs within individual crystallites of the nanorods and is accompanied by defect formation, as supported by in situ electron microscopy and elastic energy calculations. These results highlight the effect of particle shape and dimension on thermodynamics, informing nanorod design for improved device cyclability.
Plasmepsin II–III copy number accounts for bimodal piperaquine resistance among Cambodian Plasmodium falciparum
Authors: Bopp Selina , Magistrado Pamela , Wong Wesley , Schaffner Stephen F. , Mukherjee Angana , Lim Pharath , Dhorda Mehul , Amaratunga Chanaki , Woodrow Charles J. , Ashley Elizabeth A. , White Nicholas J. , Dondorp Arjen M. , Fairhurst Rick M. , Ariey Frederic , Menard Didier , Wirth Dyann F. , Volkman Sarah K. 
Published: April 2018

AbstractMultidrug resistant Plasmodium falciparum in Southeast Asia endangers regional malaria elimination and threatens to spread to other malaria endemic areas. Understanding mechanisms of piperaquine (PPQ) resistance is crucial for tracking its emergence and spread, and to develop effective strategies for overcoming it. Here we analyze a mechanism of PPQ resistance in Cambodian parasites. Isolates exhibit a bimodal dose–response curve when exposed to PPQ, with the area under the curve quantifying their survival in vitro. Increased copy number for plasmepsin II and plasmepsin III appears to explain enhanced survival when exposed to PPQ in most, but not all cases. A panel of isogenic subclones reinforces the importance of plasmepsin II–III copy number to enhanced PPQ survival. We conjecture that factors producing increased parasite survival under PPQ exposure in vitro may drive clinical PPQ failures in the field.
Representation of multiple objects in macaque category-selective areas
Authors: Bao Pinglei , Tsao Doris Y. 
Published: April 2018

AbstractObject recognition in the natural world usually occurs in the presence of multiple surrounding objects, but responses of neurons in inferotemporal (IT) cortex, the large brain area responsible for object recognition, have mostly been studied only to isolated objects. We study rules governing responses to multiple objects by cells in two category-selective regions of macaque IT cortex, the middle lateral face patch (ML) and the middle body patch (MB). We find that responses of single ML and MB cells to pairs of objects can be explained by the widely accepted framework of normalization, with one added ingredient: homogeneous category selectivity of neighboring neurons forming the normalization pool. This rule leads to winner-take-all, contralateral-take-all, or weighted averaging behavior in single cells, depending on the category, spatial configuration, and relative contrast of the two objects. The winner-take-all behavior suggests a potential mechanism for clutter-invariant representation of face and bodies under certain conditions.
Structures of chaperone-substrate complexes docked onto the export gate in a type III secretion system
Authors: Xing Qiong , Shi Ke , Portaliou Athina , Rossi Paolo , Economou Anastassios , Kalodimos Charalampos G. 
Published: April 2018

AbstractThe flagellum and the injectisome enable bacterial locomotion and pathogenesis, respectively. These nanomachines assemble and function using a type III secretion system (T3SS). Exported proteins are delivered to the export apparatus by dedicated cytoplasmic chaperones for their transport through the membrane. The structural and mechanistic basis of this process is poorly understood. Here we report the structures of two ternary complexes among flagellar chaperones (FliT and FliS), protein substrates (the filament-capping FliD and flagellin FliC), and the export gate platform protein FlhA. The substrates do not interact directly with FlhA; however, they are required to induce a binding-competent conformation to the chaperone that exposes the recognition motif featuring a highly conserved sequence recognized by FlhA. The structural data reveal the recognition signal in a class of T3SS proteins and provide new insight into the assembly of key protein complexes at the export gate.
P53 and mTOR signalling determine fitness selection through cell competition during early mouse embryonic development
Authors: Bowling Sarah , Di Gregorio Aida , Sancho Margarida , Pozzi Sara , Aarts Marieke , Signore Massimo , D. Schneider Michael , Martinez-Barbera Juan Pedro , Gil Jesús , Rodríguez Tristan A. 
Published: April 2018

AbstractEnsuring the fitness of the pluripotent cells that will contribute to future development is important both for the integrity of the germline and for proper embryogenesis. Consequently, it is becoming increasingly apparent that pluripotent cells can compare their fitness levels and signal the elimination of those cells that are less fit than their neighbours. In mammals the nature of the pathways that communicate fitness remain largely unknown. Here we identify that in the early mouse embryo and upon exit from naive pluripotency, the confrontation of cells with different fitness levels leads to an inhibition of mTOR signalling in the less fit cell type, causing its elimination. We show that during this process, p53 acts upstream of mTOR and is required to repress its activity. Finally, we demonstrate that during normal development around 35% of cells are eliminated by this pathway, highlighting the importance of this mechanism for embryonic development.
CE-BLAST makes it possible to compute antigenic similarity for newly emerging pathogens
Authors: Qiu Tianyi , Yang Yiyan , Qiu Jingxuan , Huang Yang , Xu Tianlei , Xiao Han , Wu Dingfeng , Zhang Qingchen , Zhou Chen , Zhang Xiaoyan , Tang Kailin , Xu Jianqing , Cao Zhiwei 
Published: April 2018

AbstractMajor challenges in vaccine development include rapidly selecting or designing immunogens for raising cross-protective immunity against different intra- or inter-subtypic pathogens, especially for the newly emerging varieties. Here we propose a computational method, Conformational Epitope (CE)-BLAST, for calculating the antigenic similarity among different pathogens with stable and high performance, which is independent of the prior binding-assay information, unlike the currently available models that heavily rely on the historical experimental data. Tool validation incorporates influenza-related experimental data sufficient for stability and reliability determination. Application to dengue-related data demonstrates high harmonization between the computed clusters and the experimental serological data, undetectable by classical grouping. CE-BLAST identifies the potential cross-reactive epitope between the recent zika pathogen and the dengue virus, precisely corroborated by experimental data. The high performance of the pathogens without the experimental binding data suggests the potential utility of CE-BLAST to rapidly design cross-protective vaccines or promptly determine the efficacy of the currently marketed vaccine against emerging pathogens, which are the critical factors for containing emerging disease outbreaks.
Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants
Authors: Nagata Ryuhei , Fujihashi Masahiro , Sato Takaaki , Atomi Haruyuki , Miki Kunio 
Published: April 2018

AbstractAlmost all kinases utilize ATP as their phosphate donor, while a few kinases utilize pyrophosphate (PPi) instead. PPi-dependent kinases are often homologous to their ATP-dependent counterparts, but determinants of their different donor specificities remain unclear. We identify a PPi-dependent member of the ribokinase family, which differs from known PPi-dependent kinases, and elucidate its PPi-binding mode based on the crystal structures. Structural comparison and sequence alignment reveal five important residues: three basic residues specifically recognizing PPi and two large hydrophobic residues occluding a part of the ATP-binding pocket. Two of the three basic residues adapt a conserved motif of the ribokinase family for the PPi binding. Using these five key residues as a signature pattern, we discover additional PPi-specific members of the ribokinase family, and thus conclude that these residues are the determinants of PPi-specific binding. Introduction of these residues may enable transformation of ATP-dependent ribokinase family members into PPi-dependent enzymes.
Precisely timed inhibition facilitates action potential firing for spatial coding in the auditory brainstem
Authors: Beiderbeck Barbara , Myoga Michael H. , Müller Nicolas I. C. , Callan Alexander R. , Friauf Eckhard , Grothe Benedikt , Pecka Michael 
Published: April 2018

AbstractThe integration of excitatory and inhibitory synaptic inputs is fundamental to neuronal processing. In the mammalian auditory brainstem, neurons compare excitatory and inhibitory inputs from the ipsilateral and contralateral ear, respectively, for sound localization. However, the temporal precision and functional roles of inhibition in this integration process are unclear. Here, we demonstrate by in vivo recordings from the lateral superior olive (LSO) that inhibition controls spiking with microsecond precision throughout high frequency click trains. Depending on the relative timing of excitation and inhibition, neuronal spike probability is either suppressed or—unexpectedly—facilitated. In vitro conductance-clamp LSO recordings establish that a reduction in the voltage threshold for spike initiation due to a prior hyperpolarization results in post-inhibitory facilitation of otherwise sub-threshold synaptic events. Thus, microsecond-precise differences in the arrival of inhibition relative to excitation can facilitate spiking in the LSO, thereby promoting spatial sensitivity during the processing of faint sounds.
Exceptional point engineered glass slide for microscopic thermal mapping
Authors: Zhao Han , Chen Zhaowei , Zhao Ruogang , Feng Liang 
Published: April 2018

AbstractThermal sensing with fine spatial resolution is important to the study of many scientific areas. While modern microscopy systems allow optical detection at high spatial resolution, their intrinsic functions are mainly focused on imaging but limited in detecting other physical parameters, for example, mapping thermal variations. Here, with a coating of an optical exceptional point structure, we demonstrate a low-cost but efficient multifunctional microscope slide, supporting real-time monitoring and mapping of temperature distribution and heat transport in addition to conventional microscopic imaging. The square-root dependency associated with an exceptional point leads to enhanced thermal sensitivity for precise temperature measurement. With a microscale resolution, real-time thermal mapping is conducted, showing dynamic temperature variation in a spatially defined area. Our strategy of integrating low-cost and efficient optical sensing technologies on a conventional glass slide enables simultaneous detection of multiple environmental parameters, producing improved experimental control at the microscale in various scientific disciplines.
Incorporating epilepsy genetics into clinical practice: a 360°evaluation
Authors: Oates Stephanie , Tang Shan , Rosch Richard , Lear Rosalie , Hughes Elaine F. , Williams Ruth E. , Larsen Line H. G. , Hao Qin , Dahl Hans Atli , Møller Rikke S. , Pal Deb K. 
Published: April 2018

AbstractWe evaluated a new epilepsy genetic diagnostic and counseling service covering a UK population of 3.5 million. We calculated diagnostic yield, estimated clinical impact, and surveyed referring clinicians and families. We costed alternative investigational pathways for neonatal onset epilepsy. Patients with epilepsy of unknown aetiology onset < 2 years; treatment resistant epilepsy; or familial epilepsy were referred for counseling and testing. We developed NGS panels, performing clinical interpretation with a multidisciplinary team. We held an educational workshop for paediatricians and nurses. We sent questionnaires to referring paediatricians and families. We analysed investigation costs for 16 neonatal epilepsy patients. Of 96 patients, a genetic diagnosis was made in 34% of patients with seizure onset < 2 years, and 4% > 2 years, with turnaround time of 21 days. Pathogenic variants were seen in SCN8A, SCN2A, SCN1A, KCNQ2, HNRNPU, GRIN2A, SYNGAP1, STXBP1, STX1B, CDKL5, CHRNA4, PCDH19 and PIGT. Clinician prediction was poor. Clinicians and families rated the service highly. In neonates, the cost of investigations could be reduced from £9362 to £2838 by performing gene panel earlier and the median diagnostic delay of 3.43 years reduced to 21 days. Panel testing for epilepsy has a high yield among children with onset < 2 years, and an appreciable clinical and financial impact. Parallel gene testing supersedes single gene testing in most early onset cases that do not show a clear genotype-phenotype correlation. Clinical interpretation of laboratory results, and in-depth discussion of implications for patients and their families, necessitate multidisciplinary input and skilled genetic counseling.
Printed microelectrode arrays on soft materials: from PDMS to hydrogels
Authors: Adly Nouran , Weidlich Sabrina , Seyock Silke , Brings Fabian , Yakushenko Alexey , Offenhäusser Andreas , Wolfrum Bernhard 
Published: April 2018

AbstractMicroelectrode arrays (MEAs) provide promising opportunities to study electrical signals in neuronal and cardiac cell networks, restore sensory function, or treat disorders of the nervous system. Nevertheless, most of the currently investigated devices rely on silicon or polymer materials, which neither physically mimic nor mechanically match the structure of living tissue, causing inflammatory response or loss of functionality. Here, we present a new method for developing soft MEAs as bioelectronic interfaces. The functional structures are directly deposited on PDMS-, agarose-, and gelatin-based substrates using ink-jet printing as a patterning tool. We demonstrate the versatility of this approach by printing high-resolution carbon MEAs on PDMS and hydrogels. The soft MEAs are used for in vitro extracellular recording of action potentials from cardiomyocyte-like HL-1 cells. Our results represent an important step toward the design of next-generation bioelectronic interfaces in a rapid prototyping approach.
Meteorological Controls on Local and Regional Volcanic Ash Dispersal
Authors: Poulidis Alexandros P. , Phillips Jeremy C. , Renfrew Ian A. , Barclay Jenni , Hogg Andrew , Jenkins Susanna F. , Robertson Richard , Pyle David M. 
Published: April 2018

AbstractVolcanic ash has the capacity to impact human health, livestock, crops and infrastructure, including international air traffic. For recent major eruptions, information on the volcanic ash plume has been combined with relatively coarse-resolution meteorological model output to provide simulations of regional ash dispersal, with reasonable success on the scale of hundreds of kilometres. However, to predict and mitigate these impacts locally, significant improvements in modelling capability are required. Here, we present results from a dynamic meteorological-ash-dispersion model configured with sufficient resolution to represent local topographic and convectively-forced flows. We focus on an archetypal volcanic setting, Soufrière, St Vincent, and use the exceptional historical records of the 1902 and 1979 eruptions to challenge our simulations. We find that the evolution and characteristics of ash deposition on St Vincent and nearby islands can be accurately simulated when the wind shear associated with the trade wind inversion and topographically-forced flows are represented. The wind shear plays a primary role and topographic flows a secondary role on ash distribution on local to regional scales. We propose a new explanation for the downwind ash deposition maxima, commonly observed in volcanic eruptions, as resulting from the detailed forcing of mesoscale meteorology on the ash plume.
A new phylogeny-based tribal classification of subfamily Detarioideae, an early branching clade of florally diverse tropical arborescent legumes
Authors: de la Estrella Manuel , Forest Félix , Klitgård Bente , Lewis Gwilym P. , Mackinder Barbara A. , de Queiroz Luciano P. , Wieringa Jan J. , Bruneau Anne 
Published: April 2018

AbstractDetarioideae (81 genera, c. 760 species) is one of the six Leguminosae subfamilies recently reinstated by the Legume Phylogeny Working Group. This subfamily displays high morphological variability and is one of the early branching clades in the evolution of legumes. Using previously published and newly generated sequences from four loci (matK-trnK, rpL16, trnG-trnG2G and ITS), we develop a new densely sampled phylogeny to assess generic relationships and tribal delimitations within Detarioideae. The ITS phylogenetic trees are poorly resolved, but the plastid data recover several strongly supported clades, which also are supported in a concatenated plastid + ITS sequence analysis. We propose a new phylogeny-based tribal classification for Detarioideae that includes six tribes: re-circumscribed Detarieae and Amherstieae, and the four new tribes Afzelieae, Barnebydendreae, Saraceae and Schotieae. An identification key and descriptions for each of the tribes are also provided.
Relationship between body mass index and renal function deterioration among the Taiwanese chronic kidney disease population
Authors: Chang Tian-Jong , Zheng Cai-Mei , Wu Mei-Yi , Chen Tzu-Ting , Wu Yun-Chun , Wu Yi-Lien , Lin Hsin-Ting , Zheng Jing-Quan , Chu Nain-Feng , Lin Yu-Me , Su Sui-Lung , Lu Kuo-Cheng , Chen Jin-Shuen , Sung Fung-Chang , Lee Chien-Te , Yang Yu , Hwang Shang-Jyh , Wang Ming-Cheng , Hsu Yung-Ho , Chiou Hung-Yi , Kao Senyeong , Lin Yuh-Feng 
Published: April 2018

AbstractThis study investigated the characteristics of patients with different chronic kidney disease (CKD) stages according to various body mass index (BMI) categories and determined the influence of BMI in renal function deterioration. We conducted a multicenter, longitudinal cohort study based on the Epidemiology and Risk Factors Surveillance of CKD project (2008–2013) and National Health Insurance Research Database (2001–2013). A total of 7357 patients with CKD aged 20–85 years from 14 hospitals were included in the study. A higher male sex, diabetes mellitus (DM) and hypertension were noted among overweight and obese CKD patients, while more cancer prevalence was noted among underweight CKD patients. Charlson comorbidity index was significantly higher and correlated with BMI among late CKD patients. Patients with BMI < 18.5 kg/m2 exhibited non-significantly higher events of eGFR decline events in both early and late CKD stages than other BMI groups. BMI alone is not a determinant of CKD progression among our Taiwanese CKD patients. Obesity should be re-defined and body weight manipulation should be individualized in CKD patients.
Satiety behavior is regulated by ASI/ASH reciprocal antagonism
Authors: Davis Kristen C. , Choi Young-In , Kim Jeongho , You Young-Jai 
Published: April 2018

AbstractAppropriate decision-making is essential for ensuring survival; one such decision is whether to eat. Overall metabolic state and the safety of food are the two factors we examined using C. elegans to ask whether the metabolic state regulates neuronal activities and corresponding feeding behavior. We monitored the activity of sensory neurons that are activated by nutritious (or appetitive) stimuli (ASI) and aversive stimuli (ASH) in starved vs. well-fed worms during stimuli presentation. Starvation reduces ASH activity to aversive stimuli while increasing ASI activity to nutritious stimuli, showing the responsiveness of each neuron is modulated by overall metabolic state. When we monitored satiety quiescence behavior that reflects the overall metabolic state, ablation of ASI and ASH produce the opposite behavior, showing the two neurons interact to control the decision to eat or not. This circuit provides a simple approach to how neurons handle sensory conflict and reach a decision that is translated to behavior.
Interfacial magnetic-phase transition mediated large perpendicular magnetic anisotropy in FeRh/MgO by a heavy transition-metal capping
Authors: Odkhuu Dorj 
Published: April 2018

AbstractStacking a magnetic memory junction in spintronic devices necessarily involves making contacts with a transitional-metal capping electrode. Herein, by means of first-principles calculations, we reveal the importance of heavy transition-metal capping on magnetic-phase transition from antiferromagnetic (AFM) to ferromagnetic (FM) order and the large perpendicular magnetic anisotropy (PMA) found in Ta-capped FeRh films on MgO substrate. While magnetization of FeRh films reorients from in-plane to PMA when in contact with MgO, the presence of Ta capping further enhances the magnitude of the PMA energy by at least five times. This large PMA is associated with the AFM-FM transition at the interface, which in turn modifies the out-of-plane Fe 3d orbital states through the hybridization with the strong spin-orbit coupled Ta 5d orbitals. Furthermore, the magnetic-phase transition at the interface is the result of the mutual mechanisms of the capping-induced volume/tetragonal expansion in the interfacial FeRh layers and the competition between the direct and indirect exchange interactions. These findings suggest that Ta/FeRh/MgO multilayers may represent highly favourable memory materials with net interfacial ferromagnetism and large PMA in antiferromagnet spintronics.
Spectroscopic features of ultrahigh-pressure impact glasses of the Kara astrobleme
Authors: Shumilova T. G. , Lutoev V. P. , Isaenko S. I. , Kovalchuk N. S. , Makeev B. A. , Lysiuk A. Yu. , Zubov A. A. , Ernstson K. 
Published: April 2018

AbstractThe state of substances under ultrahigh pressures and temperatures (UHPHT) now raises a special interest as a matter existing under extreme conditions and as potential new material. Under laboratory conditions only small amounts of micrometer-sized matter are produced at a pressure up to 100 GPa and at room temperature. Simultaneous combination of ultrahigh pressures and temperatures in a lab still requires serious technological effort. Here we describe the composition and structure of the UHPHT vein-like impact glass discovered by us in 2015 on the territory of the Kara astrobleme (Russia) and compare its properties with impact glass from the Ries crater (Germany). A complex of structural and spectroscopic methods presents unusual high pressure marks of structural elements in 8-fold co-ordination that had been described earlier neither in synthetic nor natural glasses. The Kara natural UHPHT glasses being about 70 Ma old have well preserved initial structure, presenting some heterogeneity as a result of partial liquation and crystallization differentiation where an amorphous component is proposed to originate from low level polymerization. Homogeneous parts of the UHPHT glasses can be used to deepened fundamental investigation of a substance under extreme PT conditions and to technological studies for novel material creations.