bluuebunny/crossref_metadata_2025_split huggingface dataset:
The plant circadian clock influences rhizosphere community structure and function
Authors: Hubbard Charley J , Brock Marcus T , van Diepen Linda T A , Maignien Loïs , Ewers Brent E , Weinig Cynthia 
Published: October 2017

Abstract
Plants alter chemical and physical properties of soil, and thereby influence rhizosphere microbial community structure. The structure of microbial communities may in turn affect plant performance. Yet, outside of simple systems with pairwise interacting partners, the plant genetic pathways that influence microbial community structure remain largely unknown, as are the performance feedbacks of microbial communities selected by the host plant genotype. We investigated the role of the plant circadian clock in shaping rhizosphere community structure and function. We performed 16S ribosomal RNA gene sequencing to characterize rhizosphere bacterial communities of Arabidopsis thaliana between day and night time points, and tested for differences in community structure between wild-type (Ws) vs clock mutant (toc1-21, ztl-30) genotypes. We then characterized microbial community function, by growing wild-type plants in soils with an overstory history of Ws, toc1-21 or ztl-30 and measuring plant performance. We observed that rhizosphere community structure varied between day and night time points, and clock misfunction significantly altered rhizosphere communities. Finally, wild-type plants germinated earlier and were larger when inoculated with soils having an overstory history of wild-type in comparison with clock mutant genotypes. Our findings suggest the circadian clock of the plant host influences rhizosphere community structure and function.
Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations
Authors: Qin Wei , Amin Shady A , Lundeen Rachel A , Heal Katherine R , Martens-Habbena Willm , Turkarslan Serdar , Urakawa Hidetoshi , Costa Kyle C , Hendrickson Erik L , Wang Tony , Beck David A C , Tiquia-Arashiro Sonia M , Taub Fred , Holmes Andrew D , Vajrala Neeraja , Berube Paul M , Lowe Todd M , Moffett James W , Devol Allan H , Baliga Nitin S , Arp Daniel J , Sayavedra-Soto Luis A , Hackett Murray , Armbrust E Virginia , Ingalls Anitra E , Stahl David A 
Published: October 2017

Abstract
High representation by ammonia-oxidizing archaea (AOA) in marine systems is consistent with their high affinity for ammonia, efficient carbon fixation, and copper (Cu)-centric respiratory system. However, little is known about their response to nutrient stress. We therefore used global transcriptional and proteomic analyses to characterize the response of a model AOA, Nitrosopumilus maritimus SCM1, to ammonia starvation, Cu limitation and Cu excess. Most predicted protein-coding genes were transcribed in exponentially growing cells, and of ~74% detected in the proteome, ~6% were modified by N-terminal acetylation. The general response to ammonia starvation and Cu stress was downregulation of genes for energy generation and biosynthesis. Cells rapidly depleted transcripts for the A and B subunits of ammonia monooxygenase (AMO) in response to ammonia starvation, yet retained relatively high levels of transcripts for the C subunit. Thus, similar to ammonia-oxidizing bacteria, selective retention of amoC transcripts during starvation appears important for subsequent recovery, and also suggests that AMO subunit transcript ratios could be used to assess the physiological status of marine populations. Unexpectedly, cobalamin biosynthesis was upregulated in response to both ammonia starvation and Cu stress, indicating the importance of this cofactor in retaining functional integrity during times of stress.
Harnessing mechanical instabilities at the nanoscale to achieve ultra-low stiffness metals
Authors: Reeve Samuel Temple , Belessiotis-Richards Alexis , Strachan Alejandro 
Published: October 2017

AbstractAlloy and microstructure optimization have led to impressive improvements in the strength of engineering metals, while the range of Young’s moduli achievable has remained essentially unchanged. This is because stiffness is insensitive to microstructure and bounded by individual components in composites. Here we design ultra-low stiffness in fully dense, nanostructured metals via the stabilization of a mechanically unstable, negative stiffness state of a martensitic alloy by its coherent integration with a compatible, stable second component. Explicit large-scale molecular dynamics simulations of the metamaterials with state of the art potentials confirm the expected ultra-low stiffness while maintaining full strength. We find moduli as low as 2 GPa, a value typical of soft materials and over one order of magnitude lower than either constituent, defying long-standing composite bounds. Such properties are attractive for flexible electronics and implantable devices. Our concept is generally applicable and could significantly enhance materials science design space.
Characterization of histone acylations links chromatin modifications with metabolism
Authors: Simithy Johayra , Sidoli Simone , Yuan Zuo-Fei , Coradin Mariel , Bhanu Natarajan V. , Marchione Dylan M. , Klein Brianna J. , Bazilevsky Gleb A. , McCullough Cheryl E. , Magin Robert S. , Kutateladze Tatiana G. , Snyder Nathaniel W. , Marmorstein Ronen , Garcia Benjamin A. 
Published: October 2017

AbstractOver the last decade, numerous histone acyl post-translational modifications (acyl-PTMs) have been discovered, of which the functional significance is still under intense study. Here, we use high-resolution mass spectrometry to accurately quantify eight acyl-PTMs in vivo and after in vitro enzymatic assays. We assess the ability of seven histone acetyltransferases (HATs) to catalyze acylations on histones in vitro using short-chain acyl-CoA donors, proving that they are less efficient towards larger acyl-CoAs. We also observe that acyl-CoAs can acylate histones through non-enzymatic mechanisms. Using integrated metabolomic and proteomic approaches, we achieve high correlation (R2 > 0.99) between the abundance of acyl-CoAs and their corresponding acyl-PTMs. Moreover, we observe a dose-dependent increase in histone acyl-PTM abundances in response to acyl-CoA supplementation in in nucleo reactions. This study represents a comprehensive profiling of scarcely investigated low-abundance histone marks, revealing that concentrations of acyl-CoAs affect histone acyl-PTM abundances by both enzymatic and non-enzymatic mechanisms.
Functional Activation of Osteoclast Commitment in Chronic Lymphocytic Leukaemia: a Possible Role for RANK/RANKL Pathway
Authors: Marini Cecilia , Bruno Silvia , Fiz Francesco , Campi Cristina , Piva Roberta , Cutrona Giovanna , Matis Serena , Nieri Alberto , Miglino Maurizio , Ibatici Adalberto , Maria Orengo Anna , Maria Massone Anna , Neumaier Carlo Emanuele , Totero Daniela de , Giannoni Paolo , Bauckneht Matteo , Pennone Michele , Tenca Claudya , Gugiatti Elena , Bellini Alessandro , Borra Anna , Tedone Elisabetta , Efetürk Hülya , Rosa Francesca , Emionite Laura , Cilli Michele , Bagnara Davide , Brucato Valerio , Bruzzi Paolo , Piana Michele , Fais Franco , Sambuceti Gianmario 
Published: October 2017

AbstractSkeletal erosion has been found to represent an independent prognostic indicator in patients with advanced stages of chronic lymphocytic leukaemia (CLL). Whether this phenomenon also occurs in early CLL phases and its underlying mechanisms have yet to be fully elucidated. In this study, we prospectively enrolled 36 consecutive treatment-naïve patients to analyse skeletal structure and bone marrow distribution using a computational approach to PET/CT images. This evaluation was combined with the analysis of RANK/RANKL loop activation in the leukemic clone, given recent reports on its role in CLL progression. Bone erosion was particularly evident in long bone shafts, progressively increased from Binet stage A to Binet stage C, and was correlated with both local expansion of metabolically active bone marrow documented by FDG uptake and with the number of RANKL + cells present in the circulating blood. In immune-deficient NOD/Shi-scid, γcnull (NSG) mice, administration of CLL cells caused an appreciable compact bone erosion that was prevented by Denosumab. CLL cell proliferation in vitro correlated with RANK expression and was impaired by Denosumab-mediated disruption of the RANK/RANKL loop. This study suggests an interaction between CLL cells and stromal elements able to simultaneously impair bone structure and increase proliferating potential of leukemic clone.
A method for the unbiased and efficient segmental labelling of RNA-binding proteins for structure and biophysics
Authors: Gallagher Christopher , Burlina Fabienne , Offer John , Ramos Andres 
Published: October 2017

AbstractMost eukaryotic RNA regulators recognise their RNA and protein partners by the combinatorial use of several RNA binding domains. Inter-domain dynamics and interactions play a key role in recognition and can be analysed by techniques such as NMR or FRET, provided that the information relative to the individual interactions can be de-convoluted. Segmentally labelling the proteins by ligating labelled and unlabelled peptide chains allows one to filter out unwanted information and observe the labelled moieties only. Several strategies have been implemented to ligate two protein fragments, but multiple ligations, which are necessary to segmentally label proteins of more than two domains, are more challenging and often dependent on the structure and solubility of the domains. Here we report a method to ligate multiple protein segments that allows the fast, high yield labelling of both internal and end domains, depending on the requirements. We use TCEP and mercaptophenylacetic acid (MPAA) in an optimised reaction environment to achieve an efficient ligation of protein domains independently from their structure or solubility. We expect the method will provide a useful tool for the molecular study of combinatorial protein–RNA recognition in RNA regulation.
Between-days intra-rater reliability with a hand held myotonometer to quantify muscle tone in the acute stroke population
Authors: Lo Wai Leung Ambrose , Zhao Jiang Li , Chen Ling , Lei Di , Huang Dong Feng , Tong Kin Fai 
Published: October 2017

AbstractA myotonometer can objectively quantify changes in muscle tone. The between-days intra-rater reliability in a ward setting for the acute stroke population remains unknown. This study aimed to investigate the device’s between-days intra-rater reliability when used in a ward setting for acute stroke participants. Muscle tone of biceps brachii, brachioradialis, rectus femoris, and tibialis anterior was recorded in the ward at bedside by one physiotherapist on two consecutive days. This study included participants who were within 1 month of their first stroke occurrence. Participants who were medically unstable or who suffered from brain stem injury were excluded. Reliability was assessed by the intraclass correlation coefficient (ICC), standard error of measurement (SEM), smallest real difference (SRD), and the Bland-Altman limits of agreement. The results indicated excellent between-days intra-rater reliability (ICC > 0.75). SEM and SRD show small differences between measurements. The Bland-Altman analysis indicated a tendency of overestimation of the rectus femoris. MyotonPRO demonstrated acceptable reliability when used in a ward setting in those patients with acute stroke. However, results should be interpreted with caution, due to the limitations of the study and the varying level of consistency observed between different muscles.
The characteristics of adjacent anatomy of mandibular third molar germs: a CBCT study to assess the risk of extraction
Authors: Sun Rui , Cai Yu , Yuan Yi , Zhao Ji-Hong 
Published: October 2017

AbstractThis study aims to investigate the characteristics of adjacent anatomy of mandibular third molar germs (MTMGs). Three hundred Chinese patients aged 12 to 17 years old who received cone-beam computed tomography (CBCT) were enrolled. The continuity of cortical outline of inferior alveolar canals (IACs) in the region of MTMGs, the integrity of lingual bone cortex and the relationship between hard tissue part of MTMGs and IACs were investigated by observing CBCT data via the NNT viewer software. The age, degree of dental development, gender and location were recorded as variables. The associations between different variables and the observed data were analysed. The possibilities of disrupted cortical outline of IACs or the hard tissue part of MTMGs contacting IACs were significantly lower in 12 or 13 age groups, lower in Nolla stage ≤ 6. Males were significantly less than females in the incidence of disrupted cortical outline of IACs. As to the perforation of lingual bone cortex, no significant differences were observed in gender, ages, location or development stages. According to the CBCT images, anatomical factors contributed the lest to the risk of inferior alveolar nerve and lingual nerve injury in the 12 to 13 age group during removing the MTMG removal.
Positive impact of the participation in the ENCHANTED trial in reducing Door-to-Needle Time
Authors: Yang Jie , Wang Xia , Yu Jian ping , Hang Jing , Lavados Pablo , Robinson Thompson , Arima Hisatomi , Lindley Richard I. , Anderson Craig S. , Chalmers John 
Published: October 2017

AbstractDoor-to-needle time (DNT) is a key performance indicator for efficient use of intravenous thrombolysis in acute ischemic stroke (AIS). We aimed to determine whether DNT improved over time in the Enhanced Control of Hypertension and Acute Stroke Study (ENCHANTED) and the clinical predictors of DNT. Temporal trends in DNT were assessed across fourths of time since activation of study centers using generalized linear model. Predictors of long DNT (>60 min) were determined in logistic regression models. Overall mean DNT (min) was 71.8 (95% confidence interval [CI] 70.4–73.2), but decreased significantly over time (fourths): 77.9 (74.9–80.9), 69.3 (66.7–72.0), 69.1 (66.5–71.8) and 71.4 (68.7–74.2) (P for trend, 0.003). The reduction in DNT was particularly marked in China (P for trend, 0.001), but was not significant across the other participating countries (P for trend, 0.065). Independent predictors of long DNT were recruitment from China, short onset-to-door time, lower numbers of patients treated per center, higher diastolic blood pressure, off-hour admission, and absence of proximal clot occlusion. DNT in ENCHANTED declined progressively during the trial, especially in China. However, DNT in China is still longer than the key performance parameter of ≤60 minutes recommended in guidelines. Effective national programs are needed to improve DNT in China.
Nonlinear magnetoelectric effect in paraelectric state of Co4Nb2O9 single crystal
Authors: Cao Yiming , Deng Guochu , Beran Přemysl , Feng Zhenjie , Kang Baojuan , Zhang Jincang , Guiblin Nicolas , Dkhil Brahim , Ren Wei , Cao Shixun 
Published: October 2017

AbstractWe report the structural, magnetoelectric (ME), magnetic and electric control of magnetic properties in Co4Nb2O9 (CNO) single crystal. A detailed ME measurement reveals a nonlinear ME effect instead of a linear ME effect in CNO single crystal. By fitting the magnetization-electric field (M-E) curve, it can be found that the linear ($${\alpha }_{e}$$

α

e

) and quadratic (γ) coefficients equal to ~8.27 ps/m and ~−6.46 ps/MV for upper branch, as well as ~8.38 ps/m and ~6.75 ps/MV for the lower branch. More importantly, a pronounced response was observed under a small cooling magnetic field, which cannot even cause the spin flop. This suggests a magnetoelectric effect can occur at paraelectric state for CNO single crystal. Furthermore, we also found that the magnetization of every axis responds to electric field applied along a-axis, but fails to do so when the electric field is applied c-axis. Such findings supply a direct evidence to the magnetic structure and ME coupling mechanism indirectly reflected by our neutron experiment.
Neurofilament light protein in CSF and blood is associated with neurodegeneration and disease severity in Huntington’s disease R6/2 mice
Authors: Soylu-Kucharz Rana , Sandelius Åsa , Sjögren Marie , Blennow Kaj , Wild Edward J. , Zetterberg Henrik , Björkqvist Maria 
Published: October 2017

AbstractThere is an unmet need to reliably and non-invasively monitor disease progression in preclinical Huntington’s disease (HD) models. As a marker of axonal damage, neurofilament light chain (NfL) has been suggested a marker for neurodegeneration. NfL concentrations in blood and CSF were recently shown to have prognostic value for clinical HD progression and brain atrophy. We therefore hypothesized that CSF and blood NfL concentrations could be useful preclinical HD markers, reflecting underlying pathology. To test our hypothesis we utilized the R6/2 mouse model of HD and measured NfL concentrations in CSF and serum using the ultrasensitive Single molecule array (Simoa) platform. In addition, we assessed HD mouse disease characteristics. We found robust increases of NfL in CSF and serum in R6/2 mice compared to wild-type littermates. CSF and serum concentrations of NfL were significantly correlated, suggesting similar marker potential of serum NfL. CSF and serum concentrations of NfL correlated with disease severity, as assessed by striatal volume and body weight loss. We here provide evidence that CSF and blood NfL concentrations can be used as accessible and reliable pre-clinical HD markers. This will be of potential use for monitoring HD mouse model disease progression and evaluating preclinical disease-modifying treatment response.
Mutation-Specific Mechanisms of Hyperactivation of Noonan Syndrome SOS Molecules Detected with Single-molecule Imaging in Living Cells
Authors: Nakamura Yuki , Umeki Nobuhisa , Abe Mitsuhiro , Sako Yasushi 
Published: October 2017

AbstractNoonan syndrome (NS) is a congenital hereditary disorder associated with developmental and cardiac defects. Some patients with NS carry mutations in SOS, a guanine nucleotide exchange factor (GEF) for the small GTPase RAS. NS mutations have been identified not only in the GEF domain, but also in various domains of SOS, suggesting that multiple mechanisms disrupt SOS function. In this study, we examined three NS mutations in different domains of SOS to clarify the abnormality in its translocation to the plasma membrane, where SOS activates RAS. The association and dissociation kinetics between SOS tagged with a fluorescent protein and the living cell surface were observed in single molecules. All three mutants showed increased affinity for the plasma membrane, inducing excessive RAS signalling. However, the mechanisms by which their affinity was increased were specific to each mutant. Conformational disorder in the resting state, increased probability of a conformational change on the plasma membrane, and an increased association rate constant with the membrane receptor are the suggested mechanisms. These different properties cause the specific phenotypes of the mutants, which should be rescuable with different therapeutic strategies. Therefore, single-molecule kinetic analyses of living cells are useful for the pathological analysis of genetic diseases.
Impact of Wide-Ranging Nanoscale Chemistry on Band Structure at Cu(In, Ga)Se2 Grain Boundaries
Authors: Stokes Adam , Al-Jassim Mowafak , Diercks David , Clarke Amy , Gorman Brian 
Published: October 2017

AbstractThe relative chemistry from grain interiors to grain boundaries help explain why grain boundaries may be beneficial, detrimental or benign towards device performance. 3D Nanoscale chemical analysis extracted from atom probe tomography (APT) (10’s of parts-per-million chemical sensitivity and sub-nanometer spatial resolution) of twenty grain boundaries in a high-efficiency Cu(In, Ga)Se2solar cell shows the matrix and alkali concentrations are wide-ranging. The concentration profiles are then related to band structure which provide a unique insight into grain boundary electrical performance. Fluctuating Cu, In and Ga concentrations result in a wide distribution of potential barriers at the valence band maximum (VBM) (−10 to −160 meV) and the conduction band minimum (CBM) (−20 to −70 meV). Furthermore, Na and K segregation is not correlated to hampering donors, (In, Ga)Cuand VSe, contrary to what has been previously reported. In addition, Na and K are predicted to be n-type dopants at grain boundaries. An overall band structure at grain boundaries is presented.
Crystal Orientation Dependence of Gallium Nitride Wear
Authors: Zeng Guosong , Sun Wei , Song Renbo , Tansu Nelson , Krick Brandon A. 
Published: October 2017

AbstractWe explore how crystallographic order and orientation affect the tribological (friction and wear) performance of gallium nitride (GaN), through experiments and theory. Friction and wear were measured in every direction on the c-plane of GaN through rotary wear experiment. This revealed a strong crystallographic orientation dependence of the sliding properties of GaN; a 60° periodicity of wear rate and friction coefficient was observed. The origin of this periodicity is rooted in the symmetry presented in wurtzite hexagonal lattice structure of III-nitrides. The lowest wear rate was found as 0.6 × 10−7 mm3/Nm with <1$$\bar{1}$$

1
¯

00>, while the wear rate associated with <1$$\bar{2}$$

2
¯

10> had the highest wear rate of 1.4 × 10−7 mm3/Nm. On the contrary, higher friction coefficient can be observed along <1$$\bar{1}$$

1
¯

00> while lower friction coefficient always appeared along <1$$\bar{2}$$

2
¯

10>. We developed a simple molecular statics approach to understand energy barriers associated with sliding and material removal; this calculated change of free energy associated with sliding revealed that there were smaller energy barriers sliding along <1$$\bar{2}$$

2
¯

10> as compared to the <1$$\bar{1}$$

1
¯

00> direction.
From receptor binding kinetics to signal transduction; a missing link in predicting in vivo drug-action
Authors: Nederpelt Indira , Kuzikov Maria , de Witte Wilbert E. A. , Schnider Patrick , Tuijt Bruno , Gul Sheraz , IJzerman Adriaan P. , de Lange Elizabeth C. M. , Heitman Laura H. 
Published: October 2017

AbstractAn important question in drug discovery is how to overcome the significant challenge of high drug attrition rates due to lack of efficacy and safety. A missing link in the understanding of determinants for drug efficacy is the relation between drug-target binding kinetics and signal transduction, particularly in the physiological context of (multiple) endogenous ligands. We hypothesized that the kinetic binding parameters of both drug and endogenous ligand play a crucial role in determining cellular responses, using the NK1 receptor as a model system. We demonstrated that the binding kinetics of both antagonists (DFA and aprepitant) and endogenous agonists (NKA and SP) have significantly different effects on signal transduction profiles, i.e. potency values, in vitro efficacy values and onset rate of signal transduction. The antagonistic effects were most efficacious with slowly dissociating aprepitant and slowly associating NKA while the combination of rapidly dissociating DFA and rapidly associating SP had less significant effects on the signal transduction profiles. These results were consistent throughout different kinetic assays and cellular backgrounds. We conclude that knowledge of the relationship between in vitro drug-target binding kinetics and cellular responses is important to ultimately improve the understanding of drug efficacy in vivo.