bluuebunny/crossref_metadata_2025_split huggingface dataset:
A universal probe design for colorimetric detection of single-nucleotide variation with visible readout and high specificity
Authors: Chen Xueping , Zhou Dandan , Shen Huawei , Chen Hui , Feng Wenli , Xie Guoming 
Published: February 2016

AbstractSingle-nucleotide variation (SNV) is a crucial biomarker for drug resistance-related detection in cancer and bacterial infection. However, the unintended binding of DNA probes limits the specificity of SNV detection and the need for redesigned sequences compromise the universality of SNV assay. Herein, we demonstrated a universal and low-cost assay for the colorimetric discrimination of drug-resistance related point mutation. By the use of a universal DNA probe and a split G-quadruplex, the signal could be recognized by naked eye at room temperature. The DNA probe was used as a signal reporter which not only improved the universality, but also enabled high specificity of probe hybridization. This assay was successfully applied in the detection of cancer-related SNV in the epidermal growth factor receptor (EGFR) gene, kirsten rat sarcoma viral oncogene homologue (KRAS) and tuberculosis drug-resistance related point mutation in RNA polymerase beta subunit gene (rpoB) with high specificity and visible readout. This method was simple, rapid, high-throughput and effective, which was suitable for point-of-care applications.
Bacterial Muramyl Dipeptide (MDP) Restricts Human Cytomegalovirus Replication via an IFN-β-Dependent Pathway
Authors: Kapoor Arun , Fan Yi-Hsin , Arav-Boger Ravit 
Published: February 2016

AbstractWe recently reported that induction of NOD2 by human Cytomegalovirus (HCMV) resulted in virus inhibition and upregulation of antiviral and inflammatory cytokines. Here we investigated the effects of muramyl dipeptide (MDP), a bacterial cell wall component that activates NOD2, on HCMV replication and antiviral responses. HCMV infection of human foreskin fibroblasts induced NOD2, the downstream receptor-interacting serine/threonine-protein kinase 2 (RIPK2), resulting in phosphorylation of TANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3). MDP treatment following infection at low multiplicity (MOI = 0.1 PFU/cell) inhibited HCMV in a dose-dependent manner and further induced phosphorylation of TBK1, IRF3 and expression of IFN-β. None of these effects of MDP were observed following infection at multiplicity of 1. In infected NOD2 knocked-down cells MDP did not induce IFN-β, irrespective of MOI. Treatment with MDP before infection also inhibited HCMV, an effect augmented with treatment duration. Treatment with an IFN-β receptor blocking antibody or knockdown of IFN-β significantly attenuated the inhibitory effect of MDP on HCMV. MDP treatment before or after infection with herpesvirus 1 did not inhibit its replication. Summarized, NOD2 activation exerts anti-HCMV activities predominantly via IFN-β. Since MDP is a bacterial cell wall component, ongoing microbial exposure may influence HCMV replication.
An integrated multi-electrode-optrode array for in vitro optogenetics
Authors: Welkenhuysen Marleen , Hoffman Luis , Luo Zhengxiang , De Proft Anabel , Van den Haute Chris , Baekelandt Veerle , Debyser Zeger , Gielen Georges , Puers Robert , Braeken Dries 
Published: February 2016

AbstractModulation of a group of cells or tissue needs to be very precise in order to exercise effective control over the cell population under investigation. Optogenetic tools have already demonstrated to be of great value in the study of neuronal circuits and in neuromodulation. Ideally, they should permit very accurate resolution, preferably down to the single cell level. Further, to address a spatially distributed sample, independently addressable multiple optical outputs should be present. In current techniques, at least one of these requirements is not fulfilled. In addition to this, it is interesting to directly monitor feedback of the modulation by electrical registration of the activity of the stimulated cells. Here, we present the fabrication and characterization of a fully integrated silicon-based multi-electrode-optrode array (MEOA) for in vitro optogenetics. We demonstrate that this device allows for artifact-free electrical recording. Moreover, the MEOA was used to reliably elicit spiking activity from ChR2-transduced neurons. Thanks to the single cell resolution stimulation capability, we could determine spatial and temporal activation patterns and spike latencies of the neuronal network. This integrated approach to multi-site combined optical stimulation and electrical recording significantly advances today’s tool set for neuroscientists in their search to unravel neuronal network dynamics.
Comparison of Particle-Associated Bacteria from a Drinking Water Treatment Plant and Distribution Reservoirs with Different Water Sources
Authors: Liu G. , Ling F. Q. , van der Mark E. J. , Zhang X. D. , Knezev A. , Verberk J. Q. J. C. , van der Meer W. G. J. , Medema G. J. , Liu W. T. , van Dijk J. C. 
Published: February 2016

AbstractThis study assessed the characteristics of and changes in the suspended particles and the associated bacteria in an unchlorinated drinking water distribution system and its reservoirs with different water sources. The results show that particle-associated bacteria (PAB) were present at a level of 0.8–4.5 × 103 cells ml−1 with a biological activity of 0.01–0.04 ng l−1 ATP. Different PAB communities in the waters produced from different sources were revealed by a 16S rRNA-based pyrosequencing analysis. The quantified biomass underestimation due to the multiple cells attached per particle was ≥ 85%. The distribution of the biologically stable water increased the number of cells per particle (from 48 to 90) but had minor effects on the PAB community. Significant changes were observed at the mixing reservoir. Our results show the characteristics of and changes in suspended PAB during distribution and highlight the significance of suspended PAB in the distribution system, because suspended PAB can lead to a considerable underestimation of biomass and because they exist as biofilm, which has a greater mobility than pipe-wall biofilm and therefore presents a greater risk, given the higher probability that it will reach the customers’ taps and be ingested.
Sorting of Single Biomolecules based on Fourier Polar Representation of Surface Enhanced Raman Spectra
Authors: Leray Aymeric , Brulé Thibault , Buret Mickael , Colas des Francs Gérard , Bouhelier Alexandre , Dereux Alain , Finot Eric 
Published: February 2016

AbstractSurface enhanced Raman scattering (SERS) spectroscopy becomes increasingly used in biosensors for its capacity to detect and identify single molecules. In practice, a large number of SERS spectra are acquired and reliable ranking methods are thus essential for analysing all these data. Supervised classification strategies, which are the most effective methods, are usually applied but they require pre-determined models or classes. In this work, we propose to sort SERS spectra in unknown groups with an alternative strategy called Fourier polar representation. This non-fitting method based on simple Fourier sine and cosine transforms produces a fast and graphical representation for sorting SERS spectra with quantitative information. The reliability of this method was first investigated theoretically and numerically. Then, its performances were tested on two concrete biological examples: first with single amino-acid molecule (cysteine) and then with a mixture of three distinct odorous molecules. The benefits of this Fourier polar representation were highlighted and compared to the well-established statistical principal component analysis method.
Partitioned airs at microscale and nanoscale: thermal diffusivity in ultrahigh porosity solids of nanocellulose
Authors: Sakai Koh , Kobayashi Yuri , Saito Tsuguyuki , Isogai Akira 
Published: February 2016

AbstractHigh porosity solids, such as plastic foams and aerogels, are thermally insulating. Their insulation performance strongly depends on their pore structure, which dictates the heat transfer process in the material. Understanding such a relationship is essential to realizing highly efficient thermal insulators. Herein, we compare the heat transfer properties of foams and aerogels that have very high porosities (97.3–99.7%) and an identical composition (nanocellulose). The foams feature rather closed, microscale pores formed with a thin film-like solid phase, whereas the aerogels feature nanoscale open pores formed with a nanofibrous network-like solid skeleton. Unlike the aerogel samples, the thermal diffusivity of the foam decreases considerably with a slight increase in the solid fraction. The results indicate that for suppressing the thermal diffusion of air within high porosity solids, creating microscale spaces with distinct partitions is more effective than directly blocking the free path of air molecules at the nanoscale.
Detecting O2 binding sites in protein cavities
Authors: Kitahara Ryo , Yoshimura Yuichi , Xue Mengjun , Kameda Tomoshi , Mulder Frans A. A. 
Published: February 2016

AbstractInternal cavities are important elements in protein structure, dynamics, stability and function. Here we use NMR spectroscopy to investigate the binding of molecular oxygen (O2) to cavities in a well-studied model for ligand binding, the L99A mutant of T4 lysozyme. On increasing the O2 concentration to 8.9 mM, changes in 1H, 15N and 13C chemical shifts and signal broadening were observed specifically for backbone amide and side chain methyl groups located around the two hydrophobic cavities of the protein. O2-induced longitudinal relaxation enhancements for amide and methyl protons could be adequately accounted for by paramagnetic dipolar relaxation. These data provide the first experimental demonstration that O2 binds specifically to the hydrophobic and not the hydrophilic cavities, in a protein. Molecular dynamics simulations visualized the rotational and translational motions of O2 in the cavities, as well as the binding and egress of O2, suggesting that the channel consisting of helices D, E, G, H and J could be the potential gateway for ligand binding to the protein. Due to strong paramagnetic relaxation effects, O2 gas-pressure NMR measurements can detect hydrophobic cavities when populated to as little as 1% and thereby provide a general and highly sensitive method for detecting oxygen binding in proteins.
Resistance switching behavior of atomic layer deposited SrTiO3 film through possible formation of Sr2Ti6O13 or Sr1Ti11O20 phases
Authors: Lee Woongkyu , Yoo Sijung , Yoon Kyung Jean , Yeu In Won , Chang Hye Jung , Choi Jung-Hae , Hoffmann-Eifert Susanne , Waser Rainer , Hwang Cheol Seong 
Published: February 2016

AbstractIdentification of microstructural evolution of nanoscale conducting phase, such as conducting filament (CF), in many resistance switching (RS) devices is a crucial factor to unambiguously understand the electrical behaviours of the RS-based electronic devices. Among the diverse RS material systems, oxide-based redox system comprises the major category of these intriguing electronic devices, where the local, along both lateral and vertical directions of thin films, changes in oxygen chemistry has been suggested to be the main RS mechanism. However, there are systems which involve distinctive crystallographic phases as CF; the Magnéli phase in TiO2 is one of the very well-known examples. The current research reports the possible presence of distinctive local conducting phase in atomic layer deposited SrTiO3 RS thin film. The conducting phase was identified through extensive transmission electron microscopy studies, which indicated that oxygen-deficient Sr2Ti6O13 or Sr1Ti11O20 phase was presumably present mainly along the grain boundaries of SrTiO3 after the unipolar set switching in Pt/TiN/SrTiO3/Pt structure. A detailed electrical characterization revealed that the samples showed typical bipolar and complementary RS after the memory cell was unipolar reset.
Short environmental enrichment in adulthood reverses anxiety and basolateral amygdala hypertrophy induced by maternal separation
Authors: Koe A S , Ashokan A , Mitra R 
Published: February 2016

AbstractMaternal separation during early childhood results in greater sensitivity to stressors later in adult life. This is reflected as greater propensity to develop stress-related disorders in humans and animal models, including anxiety and depression. Environmental enrichment (EE) reverses some of the damaging effects of maternal separation in rodent models when provided during peripubescent life, temporally proximal to the separation. It is presently unknown if EE provided outside this critical window can still rescue separation-induced anxiety and neural plasticity. In this report we use a rat model to demonstrate that a single short episode of EE in adulthood reduced anxiety-like behaviour in maternally separated rats. We further show that maternal separation resulted in hypertrophy of dendrites and increase in spine density of basolateral amygdala neurons in adulthood, long after initial stress treatment. This is congruent with prior observations showing centrality of basolateral amygdala hypertrophy in anxiety induced by stress during adulthood. In line with the ability of the adult enrichment to rescue stress-induced anxiety, we show that enrichment renormalized stress-induced structural expansion of the amygdala neurons. These observations argue that behavioural plasticity induced by early adversity can be rescued by environmental interventions much later in life, likely mediated by ameliorating effects of enrichment on basolateral amygdala plasticity.
Neuroplasticity in response to cognitive behavior therapy for social anxiety disorder
Authors: Månsson K N T , Salami A , Frick A , Carlbring P , Andersson G , Furmark T , Boraxbekk C-J 
Published: February 2016

AbstractPatients with anxiety disorders exhibit excessive neural reactivity in the amygdala, which can be normalized by effective treatment like cognitive behavior therapy (CBT). Mechanisms underlying the brain’s adaptation to anxiolytic treatments are likely related both to structural plasticity and functional response alterations, but multimodal neuroimaging studies addressing structure–function interactions are currently missing. Here, we examined treatment-related changes in brain structure (gray matter (GM) volume) and function (blood–oxygen level dependent, BOLD response to self-referential criticism) in 26 participants with social anxiety disorder randomly assigned either to CBT or an attention bias modification control treatment. Also, 26 matched healthy controls were included. Significant time × treatment interactions were found in the amygdala with decreases both in GM volume (family-wise error (FWE) corrected PFWE=0.02) and BOLD responsivity (PFWE=0.01) after successful CBT. Before treatment, amygdala GM volume correlated positively with anticipatory speech anxiety (PFWE=0.04), and CBT-induced reduction of amygdala GM volume (pre–post) correlated positively with reduced anticipatory anxiety after treatment (PFWE⩽0.05). In addition, we observed greater amygdala neural responsivity to self-referential criticism in socially anxious participants, as compared with controls (PFWE=0.029), before but not after CBT. Further analysis indicated that diminished amygdala GM volume mediated the relationship between decreased neural responsivity and reduced social anxiety after treatment (P=0.007). Thus, our results suggest that improvement-related structural plasticity impacts neural responsiveness within the amygdala, which could be essential for achieving anxiety reduction with CBT.
MAP training: combining meditation and aerobic exercise reduces depression and rumination while enhancing synchronized brain activity
Authors: Alderman B L , Olson R L , Brush C J , Shors T J 
Published: February 2016

AbstractMental and physical (MAP) training is a novel clinical intervention that combines mental training through meditation and physical training through aerobic exercise. The intervention was translated from neuroscientific studies indicating that MAP training increases neurogenesis in the adult brain. Each session consisted of 30 min of focused-attention (FA) meditation and 30 min of moderate-intensity aerobic exercise. Fifty-two participants completed the 8-week intervention, which consisted of two sessions per week. Following the intervention, individuals with major depressive disorder (MDD;n=22) reported significantly less depressive symptoms and ruminative thoughts. Typical healthy individuals (n=30) also reported less depressive symptoms at follow-up. Behavioral and event-related potential indices of cognitive control were collected at baseline and follow-up during a modified flanker task. Following MAP training, N2 and P3 component amplitudes increased relative to baseline, especially among individuals with MDD. These data indicate enhanced neural responses during the detection and resolution of conflicting stimuli. Although previous research has supported the individual beneficial effects of aerobic exercise and meditation for depression, these findings indicate that a combination of the two may be particularly effective in increasing cognitive control processes and decreasing ruminative thought patterns.
Comment on “Promising blood-derived biomarkers for estimation of the postmortem interval” by I. Costa, F. Carvalho, T. Magalhães, P. G. de Pinho, R. Silvestre & R. J. Dinis-Oliveira. (Toxicol. Res., 2015, 4, 1443–1452)
Authors: Meurs Joris , Szykuła Katarzyna M. 
Published: February 2016

Abstract
Recently, Costa et al. published an article about promising biomarkers for estimating the postmortem interval. Instead of postmortem blood, antemortem blood was putrefied in vitro by exposing the blood to a temperature gradient. However, in this way several other influencing factors were excluded, hence, the accuracy of the proposed model is doubtful. Therefore, the aim of this comment is to discuss the methodology, results and shortcomings of the study of Costa et al.
How much can we trust life tables? Sensitivity of mortality measures to right-censoring treatment
Authors: Missov Trifon I , Németh László , Dańko Maciej J 
Published: February 2016

AbstractInternational organizations, research institutions, insurance companies, pension funds and health policymakers calculate human mortality measures from life tables. Life-table data, though, are usually right-censored; that is, the last open-end age group does not contain information about the exact ages at death of individuals there, and mortality measures are sensitive to the way censoring is addressed. The standard way of “closing” the life table assumes a constant hazard of death for the last age group. This might lead to erroneous conclusions about mortality measures, especially when the open-end age interval contains a large proportion of the study population. In this article, we propose, instead, fitting a parametric model that well describes human mortality patterns, the gamma-Gompertz-Makeham, accounting for censoring, and constructing model-based equivalents of five mortality measures: life expectancy, the modal age at death, life disparity, entropy and the Gini coefficient. We show that, in comparison to conventional life-table measures, model-based measures are less sensitive to the age at censoring or, equivalently, to the proportion of censored individuals, and can be only slightly distorted even if the age at censoring is low. This study also compares life-table and model-based mortality measures for a non-human population with an underlying Gompertz mortality schedule in which a fixed proportion of the population is censored. Using model-based mortality measures is essential when studying the mortality of populations subjected to substantial censoring; for instance, many life tables for developing countries contain an open-end interval that contains more than 10% of the population. In this study, we show that life expectancy at birth for Brazilian females in 2007, calculated by standard life-table algebra, exceeds by almost 3 years the gamma-Gompertz-Makeham model-based life expectancy. This article might serve as a basis for recalculation of mortality measures for all populations subjected to substantial censoring.
Policy impacts of ecosystem services knowledge
Authors: Posner Stephen M. , McKenzie Emily , Ricketts Taylor H. 
Published: February 2016

Significance
Our study introduces a conceptual framework and empirical approach to explore how knowledge impacts decision-making. We illustrate this approach with knowledge about ecosystem services (ES), but the approach itself can be applied broadly. Our results indicate that the legitimacy of knowledge (i.e., perceived as unbiased and representative of multiple points of view) is of paramount importance for impact. More surprisingly, we found that credibility of knowledge is not a significant predictor of impact. To enhance legitimacy, ES researchers must engage meaningfully with decision-makers and stakeholders in processes of knowledge coproduction that incorporate diverse perspectives transparently. Our results indicate how research can be designed and carried out to maximize the potential impact on real-world decisions.
Regional specialization within the human striatum for diverse psychological functions
Authors: Pauli Wolfgang M. , O’Reilly Randall C. , Yarkoni Tal , Wager Tor D. 
Published: February 2016

Significance
The subcortical striatum is critical for the planning and execution of motor behavior, and its dysfunction is associated with disorders such as Parkinson’s disease. More recently, the human striatum has also been reported to be involved in heterogeneous nonmotor psychological functions. However, detailed functional mappings of human psychological processes to striatal regions have been bound by theoretical and methodological limitations, including a strong focus on experimental paradigms derived from animal research, and the tendency to infer function from anatomical connectivity, rather than task-related activation. To overcome these limitations, we used a large-scale, unbiased, data-driven approach, and generated a precise, comprehensive functional map, directly associating striatal zones with the broadest range of psychological processes to date.
Brain responses in humans reveal ideal observer-like sensitivity to complex acoustic patterns
Authors: Barascud Nicolas , Pearce Marcus T. , Griffiths Timothy D. , Friston Karl J. , Chait Maria 
Published: February 2016

Significance
We reveal the temporal dynamics and underlying neural sources of the process by which the brain discovers complex temporal patterns in rapidly unfolding sound sequences. We demonstrate that the auditory system, supported by a network of auditory cortical, hippocampal, and frontal sources, continually scans the environment, efficiently represents complex stimulus statistics, and rapidly (close to the bounds implied by an ideal observer model) responds to emergence of regular patterns, even when these are not behaviorally relevant. Neuronal activity correlated with the predictability of ongoing auditory input, both in terms of deterministic structure and the entropy of random sequences, providing clear neurophysiological evidence of the brain's capacity to automatically encode high-order statistics in sensory input.