bluuebunny/crossref_metadata_2025_split huggingface dataset:
A non-classical view on calcium oxalate precipitation and the role of citrate
Authors: Ruiz-Agudo Encarnación , Burgos-Cara Alejandro , Ruiz-Agudo Cristina , Ibañez-Velasco Aurelia , Cölfen Helmut , Rodriguez-Navarro Carlos 
Published: September 2017

AbstractAlthough calcium oxalates are relevant biominerals, their formation mechanisms remain largely unresolved. Here, we investigate the early stages of calcium oxalate formation in pure and citrate-bearing solutions. Citrate is used as a well-known oxalate precipitation inhibitor; moreover, it resembles the functional domains of the biomolecules that modulate biomineralization. Our data suggest that calcium oxalate forms after Ca2+ and C2O42− association into polynuclear stable complexes that aggregate into larger assemblies, from which amorphous calcium oxalate nucleates. Previous work has explained citrate inhibitory effects according to classical theories. Here we show that citrate interacts with all early stage CaC2O4 species (polynuclear stable complexes and amorphous precursors), inhibiting calcium oxalate nucleation by colloidal stabilization of polynuclear stable complexes and amorphous calcium oxalate. The control that citrate exerts on calcium oxalate biomineralization may thus begin earlier than previously thought. These insights provide information regarding the mechanisms governing biomineralization, including pathological processes (e.g., kidney stone formation).
Enantioselective semireduction of allenes
Authors: Chen Zhiwei , Dong Vy M. 
Published: September 2017

AbstractRh-hydride catalysis solves a synthetic challenge by affording the enantioselective reduction of allenes, thereby yielding access to motifs commonly used in medicinal chemistry. A designer Josiphos ligand promotes the generation of chiral benzylic isomers, when combined with a Hantzsch ester as the reductant. This semireduction proceeds chemoselectively in the presence of other functional groups, which are typically reduced using conventional hydrogenations. Isotopic labelling studies support a mechanism where the hydride is delivered to the branched position of a Rh-allyl intermediate.
Interplay of hot electrons from localized and propagating plasmons
Authors: Hoang Chung V. , Hayashi Koki , Ito Yasuo , Gorai Naoki , Allison Giles , Shi Xu , Sun Quan , Cheng Zhenzhou , Ueno Kosei , Goda Keisuke , Misawa Hiroaki 
Published: September 2017

AbstractPlasmon-induced hot-electron generation has recently received considerable interest and has been studied to develop novel applications in optoelectronics, photovoltaics and green chemistry. Such hot electrons are typically generated from either localized plasmons in metal nanoparticles or propagating plasmons in patterned metal nanostructures. Here we simultaneously generate these heterogeneous plasmon-induced hot electrons and exploit their cooperative interplay in a single metal-semiconductor device to demonstrate, as an example, wavelength-controlled polarity-switchable photoconductivity. Specifically, the dual-plasmon device produces a net photocurrent whose polarity is determined by the balance in population and directionality between the hot electrons from localized and propagating plasmons. The current responsivity and polarity-switching wavelength of the device can be varied over the entire visible spectrum by tailoring the hot-electron interplay in various ways. This phenomenon may provide flexibility to manipulate the electrical output from light-matter interaction and offer opportunities for biosensors, long-distance communications, and photoconversion applications.
Crossing the threshold of ultrafast laser writing in bulk silicon
Authors: Chanal Margaux , Fedorov Vladimir Yu. , Chambonneau Maxime , Clady Raphaël , Tzortzakis Stelios , Grojo David 
Published: September 2017

AbstractAn important challenge in the field of three-dimensional ultrafast laser processing is to achieve permanent modifications in the bulk of silicon and narrow-gap materials. Recent attempts by increasing the energy of infrared ultrashort pulses have simply failed. Here, we establish that it is because focusing with a maximum numerical aperture of about 1.5 with conventional schemes does not allow overcoming strong nonlinear and plasma effects in the pre-focal region. We circumvent this limitation by exploiting solid-immersion focusing, in analogy to techniques applied in advanced microscopy and lithography. By creating the conditions for an interaction with an extreme numerical aperture near 3 in a perfect spherical sample, repeatable femtosecond optical breakdown and controllable refractive index modifications are achieved inside silicon. This opens the door to the direct writing of three-dimensional monolithic devices for silicon photonics. It also provides perspectives for new strong-field physics and warm-dense-matter plasma experiments.
Longitudinal outcomes of different asthma phenotypes in primary care, an observational study
Authors: Khusial Rishi J. , Sont Jacob K. , Loijmans Rik J. B. , Snoeck-Stroband Jiska B. , Assendelft Pim J. J. , Schermer Tjard R. J. , Honkoop Persijn J. ,   for the ACCURATE Study Group
Published: September 2017

AbstractWhile asthma presentation is heterogeneous, current asthma management guidelines in primary care are quite homogeneous. In this study we aim to cluster patients together into different phenotypes, that may aid the general practitioner in individualised asthma management. We analysed data from the ACCURATE trial, containing 611 adult asthmatics, 18–50 year-old, treated in primary care, with one year follow-up. Variables obtained at baseline (n = 14), were assessed by cluster analysis. Subsequently, established phenotypes were assessed separately on important asthma outcomes after one year follow-up: asthma control (Asthma Control Questionnaire (ACQ)), quality of life (Asthma Quality of Life Questionnaire (AQLQ)), exacerbation-rate and medication-usage. Five distinct phenotypes were identified. The first phenotype was predominantly defined by their early onset atopic form of asthma. The second phenotype mainly consisted of female patients with a late onset asthma. The third phenotype were patients with high reversibility rates after bronchodilator usage. The fourth phenotype were smokers and the final phenotype were frequent exacerbators. The exacerbators phenotype had the worst outcomes for asthma control and quality of life and experienced the highest exacerbation-rate, despite using the most medication. The early onset phenotype patients were relatively well controlled and their medication dosage was low.
Cognitive control during audiovisual working memory engages frontotemporal theta-band interactions
Authors: Daume Jonathan , Graetz Sebastian , Gruber Thomas , Engel Andreas K. , Friese Uwe 
Published: September 2017

AbstractWorking memory (WM) maintenance of sensory information has been associated with enhanced cross-frequency coupling between the phase of low frequencies and the amplitude of high frequencies, particularly in medial temporal lobe (MTL) regions. It has been suggested that these WM maintenance processes are controlled by areas of the prefrontal cortex (PFC) via frontotemporal phase synchronisation in low frequency bands. Here, we investigated whether enhanced cognitive control during audiovisual WM as compared to visual WM alone is associated with increased low-frequency phase synchronisation between sensory areas maintaining WM content and areas from PFC. Using magnetoencephalography, we recorded neural oscillatory activity from healthy human participants engaged in an audiovisual delayed-match-to-sample task. We observed that regions from MTL, which showed enhanced theta-beta phase-amplitude coupling (PAC) during the WM delay window, exhibited stronger phase synchronisation within the theta-band (4–7 Hz) to areas from lateral PFC during audiovisual WM as compared to visual WM alone. Moreover, MTL areas also showed enhanced phase synchronisation to temporooccipital areas in the beta-band (20–32 Hz). Our results provide further evidence that a combination of long-range phase synchronisation and local PAC might constitute a mechanism for neuronal communication between distant brain regions and across frequencies during WM maintenance.
Isotope-coded protein label based quantitative proteomic analysis reveals significant up-regulation of apolipoprotein A1 and ovotransferrin in the myopic chick vitreous
Authors: Yu Feng-juan , Lam Thomas chuen , Liu Long-qian , Chun Rachel Ka-man , Cheung Jimmy Ka-wai , Li King-kit , To Chi-ho 
Published: September 2017

AbstractThis study used isotope-coded protein label (ICPL) quantitative proteomics and bioinformatics analysis to examine changes in vitreous protein content and associated pathways during lens-induced eye growth. First, the vitreous protein profile of normal 7-day old chicks was characterized by nano-liquid chromatography electrospray ionization tandem mass spectrometry. A total of 341 unique proteins were identified. Next, myopia and hyperopia were induced in the same chick by attaching −10D lenses to the right eye and +10D lenses to the left eye, for 3 and 7 days. Protein expression in lens-induced ametropic eyes was analyzed using the ICPL approach coupled to LCMS. Four proteins (cystatin, apolipoprotein A1, ovotransferrin, and purpurin) were significantly up-regulated in the vitreous after 3 days of wearing −10D lenses relative to +10D lens contralateral eyes. The differences in protein expression were less pronounced after 7 days when the eyes approached full compensation. In a different group of chicks, western blot confirmed the up-regulation of apolipoprotein A1 and ovotransferrin in the myopic vitreous relative to both contralateral lens-free eyes and hyperopic eyes in separate animals wearing +10D lenses. Bioinformatics analysis suggested oxidative stress and lipid metabolism as pathways involved in compensated ocular elongation.
Discrete Modeling of Amoeboid Locomotion and Chemotaxis in Dictyostelium discoideum by Tracking Pseudopodium Growth Direction
Authors: Eidi Zahra 
Published: September 2017

AbstractDictyostelium discoideum amoeba is a well-established model organism for studying the crawling locomotion of eukaryotic cells. These amoebae extend pseudopodium - a temporary actin-based protrusion of their body membrane to probe the medium and crawl through it. Experiments show highly-ordered patterns in the growth direction of these pseudopodia, which results in persistence cell motility. Here, we propose a discrete model for studying and investigating the cell locomotion based on the experimental evidences. According to our model, Dictyostelium selects its pseudopodium growth direction based on a second-order Markov chain process, in the absence of external cues. Consequently, compared to a random walk process, our model indicates stronger growth in the mean-square displacement of cells, which is consistent with empirical findings. In the presence of external chemical stimulants, cells tend to align with the gradient of chemoattractant molecules. To quantify this tendency, we define a coupling coefficient between the pseudopodium extension direction and the gradient of an external stimulant, which depends on the local stimulant concentration and its gradient. Additionally, we generalize the model to weak-coupling regime by utilizing perturbation methods.
The free-energy cost of interaction between DNA loops
Authors: Huang Lifang , Liu Peijiang , Yuan Zhanjiang , Zhou Tianshou , Yu Jianshe 
Published: September 2017

AbstractFrom the viewpoint of thermodynamics, the formation of DNA loops and the interaction between them, which are all non-equilibrium processes, result in the change of free energy, affecting gene expression and further cell-to-cell variability as observed experimentally. However, how these processes dissipate free energy remains largely unclear. Here, by analyzing a mechanic model that maps three fundamental topologies of two interacting DNA loops into a 4-state model of gene transcription, we first show that a longer DNA loop needs more mean free energy consumption. Then, independent of the type of interacting two DNA loops (nested, side-by-side or alternating), the promotion between them always consumes less mean free energy whereas the suppression dissipates more mean free energy. More interestingly, we find that in contrast to the mechanism of direct looping between promoter and enhancer, the facilitated-tracking mechanism dissipates less mean free energy but enhances the mean mRNA expression, justifying the facilitated-tracking hypothesis, a long-standing debate in biology. Based on minimal energy principle, we thus speculate that organisms would utilize the mechanisms of loop-loop promotion and facilitated tracking to survive in complex environments. Our studies provide insights into the understanding of gene expression regulation mechanism from the view of energy consumption.
Variations of parathyroid hormone and bone biomarkers are concordant only after a long term follow-up in hemodialyzed patients
Authors: Delanaye Pierre , Warling Xavier , Moonen Martial , Smelten Nicole , Jouret François , Krzesinski Jean-Marie , Maillard Nicolas , Pottel Hans , Cavalier Etienne 
Published: September 2017

AbstractEnd-stage renal disease is associated with mineral and bone disorders. Guidelines recommending therapies should be based on serial assessments of biomarkers, and thus on variations (Δ), rather than scattered values. We analyzed the correlations between ΔPTH and Δbone biomarkers such as bone-specific alkaline phosphatase (b-ALP), Beta-CrossLaps (CTX), osteocalcin, intact serum procollagen type-1 N-propeptide (P1NP), and tartrate-resistant acid phosphatase 5B (TRAP-5B) at different time-points. In this prospective observational analysis, variations of biomarkers were followed after 6-week (n = 129), 6-month (n = 108) and one-year (n = 93) period. Associations between variations were studied by univariate linear regression. Patients followed for one-year period were classified (increaser or decliner) according to variations reaching the critical difference. Over the 6-week period, only ΔCTX was correlated with ΔPTH (r = 0.38, p < 0.0001). Over the one-year period, correlations between ΔPTH and Δbone biomarkers became significant (r from 0.23 to 0.47, p < 0.01), except with ΔTRAP-5b. Correlations between Δbone biomarkers were all significant after one-year period (r from 0.31 to 0.68, p < 0.01), except between Δb-ALP and ΔTRAP-5b. In the head-to-head classifications (decliners/increasers), the percentage of concordant patients was significantly higher over the one-year than the 6-week period. A concordance between ΔPTH and Δbone biomarkers is observed in dialysis patients, but only after a long follow-up.
Neural activity in macaque medial frontal cortex represents others’ choices
Authors: Falcone Rossella , Cirillo Rossella , Ferraina Stefano , Genovesio Aldo 
Published: September 2017

AbstractPredicting the behavior of others is a fundamental skill in primate social life. We tested the role of medial frontal cortex in the prediction of other agents’ behavior in two male macaques, using a monkey-human interactive task in which their actor-observer roles were intermixed. In every trial, the observer monitored the actor’s choice to reject it for a different one when he became the actor on the subsequent trial. In the delay period preceding the action, we identified neurons modulated by the agent’s identity, as well as a group of neurons encoding the agent’s future choice, some of which were neurons that showed differential patterns of activity between agents. The ability of these neurons to flexibly move from ‘self-oriented’ to ‘other-oriented’ representations could correspond to the “other side of the coin” of the simulative mirroring activity. Neurons that changed coding scheme, together with neurons exclusively involved in the prediction of the other agent’s choice, show a neural substrate for predicting or anticipating others’ choices beyond simulation.
Optical Control of Young’s Type Double-slit Interferometer for Laser-induced Electron Emission from a Nano-tip
Authors: Yanagisawa Hirofumi , Ciappina Marcelo , Hafner Christian , Schötz Johannes , Osterwalder Jürg , Kling Matthias F. 
Published: September 2017

AbstractInterference experiments with electrons in a vacuum can illuminate both the quantum and the nanoscale nature of the underlying physics. An interference experiment requires two coherent waves, which can be generated by splitting a single coherent wave using a double slit. If the slit-edge separation is larger than the coherence width at the slit, no interference appears. Here we employed variations in surface barrier at the apex of a tungsten nano-tip as slits and achieved an optically controlled double slit, where the separation and opening-and-closing of the two slits can be controlled by respectively adjusting the intensity and polarization of ultrashort laser pulses. Using this technique, we have demonstrated interference between two electron waves emitted from the tip apex, where interference has never been observed prior to this technique because of the large slit-edge separation. Our findings pave the way towards simple time-resolved electron holography on e.g. molecular adsorbates employing just a nano-tip and a screen.
Immunological tumor status may predict response to neoadjuvant chemotherapy and outcome after radical cystectomy in bladder cancer
Authors: Tervahartiala Minna , Taimen Pekka , Mirtti Tuomas , Koskinen Ilmari , Ecke Thorsten , Jalkanen Sirpa , Boström Peter J. 
Published: September 2017

AbstractBladder cancer (BC) is the ninth most common cancer worldwide. Radical cystectomy (RC) with neoadjuvant chemotherapy (NAC) is recommended for muscle-invasive BC. The challenge of the neoadjuvant approach relates to challenges in selection of patients to chemotherapy that are likely to respond to the treatment. To date, there are no validated molecular markers or baseline clinical characteristics to identify these patients. Different inflammatory markers, including tumor associated macrophages with their plastic pro-tumorigenic and anti-tumorigenic functions, have extensively been under interests as potential prognostic and predictive biomarkers in different cancer types. In this immunohistochemical study we evaluated the predictive roles of three immunological markers, CD68, MAC387, and CLEVER-1, in response to NAC and outcome of BC. 41% of the patients had a complete response (pT0N0) to NAC. Basic clinicopathological variables did not predict response to NAC. In contrast, MAC387+ cells and CLEVER-1+ macrophages associated with poor NAC response, while CLEVER-1+ vessels associated with more favourable response to NAC. Higher counts of CLEVER-1+ macrophages associated with poorer overall survival and CD68+ macrophages seem to have an independent prognostic value in BC patients treated with NAC. Our findings point out that CD68, MAC387, and CLEVER-1 may be useful prognostic and predictive markers in BC.
Revisiting the impact of age and molecular subtype on overall survival after radiotherapy in breast cancer patients
Authors: Mao Jian-Hua , Diest Paul J. van , Perez-Losada Jesus , Snijders Antoine M. 
Published: September 2017

AbstractAdjuvant radiotherapy (RT) in breast cancer (BC) is often used to eradicate remaining tumor cells following surgery with the goal of maximizing local control and increasing overall survival. The current study investigated the impact of age and BC molecular subtype on overall survival after RT using a meta-analysis of the METABRIC and TCGA BC patient cohorts. We found that RT significantly prolonged survival across the whole BC patient population. The survival benefit of RT was predominantly observed in stage II BC patients treated with breast conserving surgery. Patients were then stratified by age and molecular subtype to investigate survival rate associated with RT. An increase in survival for the luminal-A and basal BC molecular subtypes was observed after RT. Stratifying patients based on age revealed that increased survival was restricted to younger patients (≤60 years of age at diagnosis). There was a significant survival benefit of radiotherapy for younger patients with tumors of the luminal A and basal molecular subtypes. Patients with other breast tumor subtypes or older breast cancer patients did not seem to benefit effects of RT. Therefore, alternate local treatment strategies should be considered for older, luminal B, and HER2 driven BC patients.
Machine Learning Improves Risk Stratification After Acute Coronary Syndrome
Authors: Myers Paul D. , Scirica Benjamin M. , Stultz Collin M. 
Published: September 2017

AbstractThe accurate assessment of a patient’s risk of adverse events remains a mainstay of clinical care. Commonly used risk metrics have been based on logistic regression models that incorporate aspects of the medical history, presenting signs and symptoms, and lab values. More sophisticated methods, such as Artificial Neural Networks (ANN), form an attractive platform to build risk metrics because they can easily incorporate disparate pieces of data, yielding classifiers with improved performance. Using two cohorts consisting of patients admitted with a non-ST-segment elevation acute coronary syndrome, we constructed an ANN that identifies patients at high risk of cardiovascular death (CVD). The ANN was trained and tested using patient subsets derived from a cohort containing 4395 patients (Area Under the Curve (AUC) 0.743) and validated on an independent holdout set containing 861 patients (AUC 0.767). The ANN 1-year Hazard Ratio for CVD was 3.72 (95% confidence interval 1.04–14.3) after adjusting for the TIMI Risk Score, left ventricular ejection fraction, and B-type natriuretic peptide. A unique feature of our approach is that it captures small changes in the ST segment over time that cannot be detected by visual inspection. These findings highlight the important role that ANNs can play in risk stratification.
The effect of feature image on sensitivity of the statistical analysis in the pipeline of a tractography atlas-based analysis
Authors: Mu Junya , Xu Qing , Tian Jie , Liu Jixin 
Published: September 2017

AbstractTractography atlas-based analysis (TABS) is a new diffusion tensor image (DTI) statistical analysis method for detecting and understanding voxel-wise white matter properties along a fiber tract. An important requisite for accurate and sensitive TABS is the availability of a deformation field that is able to register DTI in native space to standard space. Here, three different feature images including the fractional anisotropy (FA) image, T1 weighted image, and the maximum eigenvalue of the Hessian of the FA (hFA) image were used to calculate the deformation fields between individual space and population space. Our results showed that when the FA image was a feature image, the tensor template had the highest consistency with each subject for scalar and vector information. Additionally, to demonstrate the sensitivity and specificity of the TABS method with different feature images, we detected a gender difference along the corpus callosum. A significant difference between the male and female group in diffusion measurement appeared predominantly in the right corpus callosum only when FA was the feature image. Our results demonstrated that the FA image as a feature image was more accurate with respect to the underlying tensor information and had more accurate analysis results with the TABS method.