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The interaction between protein and DNA plays an essential function in various critical natural processes, like DNA replication, transcription, splicing, and repair. Studying the binding affinity of proteins to DNA helps to understand the recognition mechanism of protein-DNA complexes. Since there are still many limitations on the protein-DNA binding affinity data measured by experiments, accurate and reliable calculation methods are necessarily required. So we put forward a computational approach in this paper, called PreDBA, that can forecast protein-DNA binding affinity effectively by using heterogeneous ensemble models. One hundred protein-DNA complexes are manually collected from the related literature as a data set for protein-DNA binding affinity. Then, 52 sequence and structural features are obtained. Based on this, the correlation between these 52 characteristics and protein-DNA binding affinity is calculated. Furthermore, we found that the protein-DNA binding affinity is affected by the DNA molecule structure of the compound. We classify all protein-DNA compounds into five classifications based on the DNA structure related to the proteins that make up the protein-DNA complexes. In each group, a stacked heterogeneous ensemble model is constructed based on the obtained features. In the end, based on the binding affinity data set, we used the leave-one-out cross-validation to evaluate the proposed method comprehensively. In the five categories, the Pearson correlation coefficient values of our recommended method range from 0.735 to 0.926. We have demonstrated the advantages of the proposed method compared to other machine learning methods and currently existing protein-DNA binding affinity prediction approach.

Plasmonic metamaterial absorbers are particularly important in different applications such as photodetectors, microbolometers and solar cells. In this paper, we propose a tungsten boride (WB, a refractory ceramic) based broadband metamaterial absorber whose optical properties is numerically analyzed and experimentally characterized. We have also analyzed the damage characteristics of this absorber using a femtosecond laser and compared with an ordinary Au metamaterial absorber. We observe that WB has almost the double absorption bandwidth with absorption more than 90% over the spectral range of 950 to 1400 nm when compared with the Au counterpart. Furthermore, we show that Au metamaterial is damaged at the power of around 36.4 mW whereas WB metamaterial is not damaged at that power (WB has high Tammann temperature than Au)-however the atom of WB material was knocked off by the bombardment of a femtosecond laser.

Celiac disease (CeD) is a multifactorial disease influenced by both genetic and environmental risk factors. CeD genetic components are mainly due to HLA class II genes, which account for approximately 40% of the disease heritability. The environmental factor is linked to gliadin ingestion. Despite genetic and epigenetic studies, the pathological molecular mechanism remains unclarified. The strong genetic component does not explain more than half of the hereditability; we identified several epigenetic features that contribute to the understanding of the missing hereditability. The lipid profile of infants has been proposed as a potential biomarker of CeD metabolism that can be measured before they exhibit developmental disorders and clinical symptoms. We suggest that the state of the host is a main factor for the abnormal immune response to gluten. Long before any exposure to the offending agent or any production of specific antibodies, several molecular mechanisms are differentially expressed in infants who will develop CeD compared to their peers matched for the same genetic profile. The present study explored the serum phospholipid profile of a group of infants at risk for celiac disease, followed up to 8 years to monitor the onset of CeD. We compared 30 patients who developed the disease with 20 age- and sex-matched peers with similar genetic profiles who did not develop the disease within 8 years. Serum phospholipids were analysed at 4 months, before exposure to gluten, and at 12 months of age, when none showed any marker of disease. In the 30 CeD patients, we also analysed the serum at the time of diagnosis (>24 months). The serum phospholipid profile was fairly constant across 4 and 12 months of age and, in CeD, up to 24–36 months. The phospholipid signature was dramatically different in infants who developed CeD when compared to that of control NY-CeD (Not Yet developing Celiac Disease) peers. We identified a specific serum phospholipid signature that predicts the onset of celiac disease in HLA at-risk infants years before the appearance of antibodies specific for CeD in the serum and before any clinical symptoms, even before gluten introduction into the diet at 4 months. Specifically, lysophosphatidylcholine, phosphatidylcholine, alkylacyl-phosphatidylcholine, phosphoethanolamines, phosphatidylserines, phosphatidylglycerol and phosphatidylinositol were found to be differentially represented in CeD versus NY-CeD. A set constituted by a limited number of alkylacyl-phosphatidylcholine and lyso-phosphatidylcholine, together with the duration of breast-feeding, allows the discrimination of infants who develop celiac disease before 8 years of age from those at a similar genetic risk who do not develop the disease. In addition to recent discovery, our paper unveiled a specifc phopholipid profile, able to discriminate infants who eventually develop celiac disease years before antibodies or clinical symptoms ensue.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Control chart methods have been received much attentions in biosurvillance studies. The correlation between charting statistics or regions could be considerably important in monitoring the states of multiple outcomes or regions. In addition, the process variable distribution is unknown in most situations. In this paper, we propose a new nonparametric strategy for multivariate process monitoring when the distribution of a process variable is unknown. We discuss the EWMA control chart based on rank methods for a multivariate process, and the approach is completely nonparametric. A simulation study demonstrates that the proposed method is efficient in detecting shifts for multivariate processes. A real Japanese influenza data example is given to illustrate the performance of the proposed method.

Microbial fuel cell (MFC) technology is a simple way to accelerate the treatment of the oily sludge which is a major problem affecting the quality of oil fields and surrounding environment while generating electricity. To investigate the oil removal and the characteristics of changes in the composition of bacteria, sediment microbial fuel cells (SMFCs) supplemented with oily sludge was constructed. The results showed that the degradation efficiency of total petroleum hydrocarbon (TPH) of SMFC treatment was 10.1 times higher than the common anaerobic degradation. In addition, the degradation rate of n-alkanes followed the order of high carbon number > low carbon number > medium carbon number. The odd–even alkane predominance (OEP) increased, indicating that a high contribution of even alkanes whose degradation predominates. The OUT number, Shannon index, AEC index, and Chao1 index of the sludge treated with SMFC (YN2) are greater than those of the original sludge (YN1), showing that the microbial diversity of sludge increased after SMFC treatment. After SMFC treatment the relative abundance of Chloroflexi, Bacteroidia and Pseudomonadales which are essential for the degradation of the organic matter and electricity production increased significantly in YN2. These results will play a crucial role in improving the performance of oily sludge MFC.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Rapid histopathological evaluation of fresh, unfixed human tissue using optical sectioning microscopy would have applications to intraoperative surgical margin assessment. Microscopy with ultraviolet surface excitation (MUSE) is a low-cost optical sectioning technique using ultraviolet illumination which limits fluorescence excitation to the specimen surface. In this paper, we characterize MUSE using high incident angle, water immersion illumination to improve sectioning. Propidium iodide is used as a nuclear stain and eosin yellow as a counterstain. Histologic features of specimens using MUSE, nonlinear microscopy (NLM) and conventional hematoxylin and eosin (H&E) histology were evaluated by pathologists to assess potential application in Mohs surgery for skin cancer and lumpectomy for breast cancer. MUSE images of basal cell carcinoma showed high correspondence with frozen section H&E histology, suggesting that MUSE may be applicable to Mohs surgery. However, correspondence in breast tissue between MUSE and paraffin embedded H&E histology was limited due to the thicker optical sectioning in MUSE, suggesting that further development is needed for breast surgical applications. We further demonstrate that the transverse image resolution of MUSE is limited by the optical sectioning thickness and use co-registered NLM to quantify the improvement in MUSE optical sectioning from high incident angle water immersion illumination.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The universal linguistic colour categorisation pattern as evident in the World Colour Survey (WCS) has been a principal focus of investigations on the relationship between language and cognition, yet most existing studies have failed to clarify whether this universality resulted primarily from individual perceptual constraints and/or socio-cultural transmissions. This paper designed an agent-based, unsupervised learning model to address the relative importance of these two aspects to linguistic colour categorisation. By directly comparing with the empirical data in the WCS, our study demonstrated that: the physical colour stimuli that reflect human perceptual constraints on colours trigger a categorisation pattern quantitatively resembling the WCS data, the randomised stimuli that distort such constraints lead to distinct categorisation patterns, and the processes of linguistic categorisation in both cases follow similar dynamics. These results reveal how perceptual and socio-cultural factors interact with each other to trigger linguistic universality, and serve as decisive evidence that human perceptual constraints induce the universality in linguistic categorisation, yet socio-cultural transmissions, though imperative, play an auxiliary role of transcribing perceptual constraints into common linguistic categories with slight variations.

Depressive disorder (DD) is a mental illness affecting more than 300 million people worldwide, whereas social stigma and subtle, variant symptoms impede diagnosis. Psychomotor retardation is a common component of DD with a negative impact on motor function, usually reflected on patients’ routine activities, including, nowadays, their interaction with mobile devices. Therefore, such interactions constitute an enticing source of information towards unsupervised screening for DD symptoms in daily life. In this vein, this paper proposes a machine learning-based method for discriminating between subjects with depressive tendency and healthy controls, as denoted by self-reported Patient Health Questionnaire-9 (PHQ-9) compound scores, based on typing patterns captured in-the-wild. The latter consisted of keystroke timing sequences and typing metadata, passively collected during natural typing on touchscreen smartphones by 11/14 subjects with/without depressive tendency. Statistical features were extracted and tested in univariate and multivariate classification pipelines to reach a decision on subjects’ status. The best-performing pipeline achieved an AUC = 0.89 (0.72–1.00; 95% Confidence Interval) and 0.82/0.86 sensitivity/specificity, with the outputted probabilities significantly correlating (>0.60) with the respective PHQ-9 scores. This work adds to the findings of previous research associating typing patterns with psycho-motor impairment and contributes to the development of an unobtrusive, high-frequency monitoring of depressive tendency in everyday living.

A correction to this article has been published and is linked from the HTML version of this paper. The error has not been fixed in the paper.

Extracellular vesicles (EV), including exosomes and microvesicles (MV), represent a rapidly expanding field of research with diagnostic and therapeutic applications. Although many aspects of EV function remain to be revealed and broad investigations are warranted, most published findings focus on only one vesicle category or a non-separated mix of EVs. In this paper, we investigated both MVs and exosomes from Ovalbumin (OVA)-pulsed dendritic cells for their immunostimulatory potential side-by-side in vivo. Only exosomes induced antigen-specific CD8+ T-cells, and were more efficient than MVs in eliciting antigen-specific IgG production. Further, mainly exosome-primed mouse splenocytes showed significant ex vivo interferon gamma production in response to antigen restimulation. Exosomes carried high levels of OVA, while OVA in MVs was barely detectable, which could explain the more potent antigen-specific response induced by exosomes. Moreover, exosomes induced increased germinal center B cell proportions, whereas MVs had no such effect. Immunisation with both vesicle types combined showed neither inhibitory nor synergistic effects. We conclude that DC-derived MVs and exosomes differ in their capacity to incorporate antigen and induce immune responses. The results are of importance for understanding the role of EVs in vivo, and for future design of vesicle-based immunotherapies and vaccines.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

There has been recent substantial interest in extracting sub-visual features from medical images for improved disease characterization compared to what might be achievable via visual inspection alone. Features such as Haralick and Gabor can provide a multi-scale representation of the original image by extracting measurements across differently sized neighborhoods. While these multi-scale features are effective, on large-scale digital pathological images, the process of extracting these features is computationally expensive. Moreover for different problems, different scales and neighborhood sizes may be more or less important and thus a large number of features extracted might end up being redundant. In this paper, we present a Discriminative Scale learning (DiScrn) approach that attempts to automatically identify the distinctive scales at which features are able to best separate cancerous from non-cancerous regions on both radiologic and digital pathology tissue images. To evaluate the efficacy of our approach, our approach was employed to detect presence and extent of prostate cancer on a total of 60 MRI and digitized histopathology images. Compared to a multi-scale feature analysis approach invoking features across all scales, DiScrn achieved 66% computational efficiency while also achieving comparable or even better classifier performance.

Liver X receptorβ (LXRβ) is a promising therapeutic target for lipid disorders, atherosclerosis, chronic inflammation, autoimmunity, cancer and neurodegenerative diseases. Druggable LXRβ agonists have been explored over the past decades. However, the pocket of LXRβ ligand-binding domain (LBD) is too large to predict LXRβ agonists with novel scaffolds based on either receptor or agonist structures. In this paper, we report a de novo algorithm which drives privileged LXRβ agonist fragments by starting with individual chemical bonds (de novo) from every molecule in a LXRβ agonist library, growing the bonds into substructures based on the agonist structures with isomorphic and homomorphic restrictions, and electing the privileged fragments from the substructures with a popularity threshold and background chemical and biological knowledge. Using these privileged fragments as queries, we were able to figure out the rules to reconstruct LXRβ agonist molecules from the fragments. The privileged fragments were validated by building regularized logistic regression (RLR) and supporting vector machine (SVM) models as descriptors to predict a LXRβ agonist activities.

A selective colon cancer cell therapy was effectively achieved with catalase-mediated intra-cellular heterogeneous Fenton reactions triggered by cellular uptake of SnFe2O4 nanocrystals. The treatment was proven effective for eradicating colon cancer cells, whereas was benign to normal colon cells, thus effectively realizing the selective colon cancer cell therapeutics. Cancer cells possess much higher innate hydrogen peroxide (H2O2) but much lower catalase levels than normal cells. Catalase, an effective H2O2 scavenger, prevented attacks on cells by reactive oxygen species induced from H2O2. The above intrinsic difference between cancer and normal cells was utilized to achieve selective colon cancer cell eradication through endocytosing efficient heterogeneous Fenton catalysts to trigger the formation of highly reactive oxygen species from H2O2. In this paper, SnFe2O4 nanocrystals, a newly noted outstanding paramagnetic heterogeneous Fenton catalyst, have been verified an effective selective colon cancerous cell treatment reagent of satisfactory blood compatibility.

In this paper, we demonstrate that the microstructure and the surface of a thin palladium (Pd) film can be intentionally altered by the presence of a subjacent niobium (Nb) film. Depending on the thickness of the Nb film and on the hydrogen gas pressure, defects in the Pd film can be healed or created. To demonstrate this effect, Pd/Nb/sapphire (Al2O3) stacks are studied during hydrogen gas exposure at room temperature by using scanning tunneling microscopy (STM), X-ray diffraction (XRD) and environmental transmission electron microscopy (ETEM). STM shows that hydrogen-induced topography changes in the Nb films depend on the film thickness which affects the height of the Nb surface corrugations, their lateral size and distribution. XRD measurements show that these changes in the Nb hydride film influence the microstructure of the overlaying Pd film. ETEM reveals that the modifications of the Pd film occur due to the precipitation and growth of the Nb hydride phase. The appearance of new defects, interface and surface roughening is observed in the Pd film above locally grown Nb hydride grains. These results can open a new route to design ‘smart’ catalysts or membranes, which may accommodate their microstructure depending on the gaseous environment.

Laser speckle imaging (LSI) has developed into a versatile tool to image dynamical processes in turbid media, such as subcutaneous blood perfusion and heterogeneous dynamics in soft materials. Spatially resolved information about local dynamics is obtained by measuring time-dependent correlation functions of multiply scattered light. Due to the diffusive nature of photons in highly scattering media, the measured signal is a convolution of the local dynamics in the material and the spatial distribution of photons. This spatial averaging inevitably leads to a loss of resolution, which must be taken into account for a correct interpretation of LSI measurements. In this paper we derive analytical expressions to quantify the effects of spatial blurring in backscatter LSI for materials with heterogeneous dynamics. Using the diffusion approximation, we calculate the photon density distribution for a semi-infinite material, and we predict the effect of dynamic heterogeneity on the measured correlation function. We verify our theoretical expressions using random walk simulations. Our results show that LSI measurements in dynamically heterogeneous materials should be interpreted with caution, especially when only a single wavelength and correlation time are used to obtain the dynamical map.

When individuals interact with each other and meaningfully contribute toward a common goal, it results in a collaboration, as can be seen in many walks of life such as scientific research, motion picture production, or team sports. The artifacts resulting from a collaboration (e.g. papers, movies) are best captured using a hypergraph model, whereas the relation of who has collaborated with whom is best captured via an abstract simplicial complex (SC). In this paper, we propose a generative algorithm GeneSCs for SCs modeling fundamental collaboration relations, primarily based on preferential attachment. The proposed network growth process favors attachment that is preferential not to an individual's degree, i.e., how many people has he/she collaborated with, but to his/her facet degree, i.e., how many maximal groups or facets has he/she collaborated within. Unlike graphs, in SCs, both facet degrees (of nodes) and facet sizes are important to capture connectivity properties. Based on our observation that several real-world facet size distributions have significant deviation from power law-mainly due to the fact that larger facets tend to subsume smaller ones-we adopt a data-driven approach. We seed GeneSCs with a facet size distribution informed by collaboration network data and randomly grow the SC facet-by-facet to generate a final SC whose facet degree distribution matches real data. We prove that the facet degree distribution yielded by GeneSCs is power law distributed for large SCs and show that it is in agreement with real world co-authorship data. Finally, based on our intuition of collaboration formation in domains such as collaborative scientific experiments and movie production, we propose two variants of GeneSCs based on clamped and hybrid preferential attachment schemes, and show that they perform well in these domains.

Chitin is a major component of insect exoskeleton, tracheal system and gut where it is synthesized by chitin synthase (CHS) enzymes. In this paper, we report the isolation and RNAi of chitin synthase A (PhoCHSA) from the potato tuber moth Phthorimaea operculella. The full-length cDNA of PhoCHSA is 5,627 bp with 4,689 bp open reading frame coding for 1,563 amino acids. Structural analysis of conceptual amino acid translation showed three distinct regions found in all known insect CHS proteins; N-terminus region having 9 transmembrane helices, middle catalytic region containing several conserved domains identified in insect CHS enzymes, and C-terminus region containing seven transmembrane spans. Phylogenetic analysis showed that PhoCHSA protein clustered with CHSA enzymes identified from insects from different insect orders. RNAi targeting three different regions of the gene showed different efficacy against potato tuber moth larvae and dsRNA targeting the 5′ region has the highest efficacy. Results were verified by qRT-PCR which showed that dsRNA targeting the 5′ region caused the highest reduction in PhoCHSA mRNA level. Our results show the importance of selecting the RNAi target region and that chitin synthase A can be a suitable RNAi target for the potato tuber moth control.

Supplementary information accompanies this paper at doi:10.1038/s41598-017-10080-z.; International audience; In the nasal olfactory epithelium, olfactory metabolic enzymes ensure odorant clearance from the olfactory receptor environment. This biotransformation of odorants into deactivated polar metabolites is critical to maintaining peripheral sensitivity and perception. Olfactory stimuli consist of complex mixtures of odorants, so binding interactions likely occur at the enzyme level and may impact odor processing. Here, we used the well-described model of mammary pheromone-induced sucking-related behavior in rabbit neonates. It allowed to demonstrate how the presence of different aldehydic odorants efficiently affects the olfactory metabolism of this pheromone (an aldehyde too: 2-methylbut-2-enal). Indeed, according to in vitro and ex vivo measures, this metabolic interaction enhances the pheromone availability in the epithelium. Furthermore, in vivo presentation of the mammary pheromone at subthreshold concentrations efficiently triggers behavioral responsiveness in neonates when the pheromone is in mixture with a metabolic challenger odorant. These findings reveal that the periphery of the olfactory system is the place of metabolic interaction between odorants that may lead, in the context of odor mixture processing, to pertinent signal detection and corresponding behavioral effect. (15) Odorant-odorant metabolic interaction, a novel actor in olfactory perception and behavioral responsiveness. Available from: https://www.researchgate.net/publication/318725346_Odorant-odorant_metabolic_interaction_a_novel_actor_in_olfactory_perception_and_behavioral_responsiveness?citedPublicationUid=263745821 [accessed Sep 20, 2017].

Peaches are known for their palatable flavor and abundant nutrients. However, peaches are perishable, and the existing preservation techniques for peaches are still immature. To further extend the shelf life and prevent nutrient loss of perishable peaches under ambient temperature in summer (approximately 25–32 °C), we conducted experiments wrapping peaches (Prunus persica cv ‘Baihua’) in single- and composite-treated vegetal fibrous papers that contained calcium carbonate, phytic acid, Na-alginate and vitamin C. The pathogenic fungi that primarily caused peach decay during storage belonged to the genera of Penicillium, Botrytis, Aspergillus, Alternaria, and Rhizopus. After analyzing quality attributes, including weight loss, firmness, soluble sugar content, respiration rate, relative electric conductivity, malonaldehyde content, peroxidase activity and the decay index, we proved that vitamin C within the preservative paper greatly contributes to peach preservation. Combined with phytic acid and Na-alginate, the composite vitamin C preservative papers played significant roles in delaying fruit senescence, and 0.4% (w/v) vitamin C preservative paper with 1% Na-alginate could maintain quality and extend shelf life with the best effect. This preservation technique significantly postponed the respiration peak by 2–3 days and is a significant contribution to contemporary commercial production.

Plasmonic chirality represents significant potential for novel nanooptical devices due to its association with strong chiroptical responses. Previous reports on plasmonic chirality mechanism mainly focus on phase retardation and coupling. In this paper, we propose a model similar to the chiral molecules for explaining the intrinsic plasmonic chirality mechanism of varies 3D chiral structures quantitatively based on the interplay and mixing of electric and magnetic dipole modes (directly from electromagnetic field numerical simulations), which forms mixed electric and magnetic polarizability.

In this paper, we propose a strategy for the control of mobile chaotic oscillators by adaptively rewiring connections between nearby agents with local information. In contrast to the dominant adaptive control schemes where coupling strength is adjusted continuously according to the states of the oscillators, our method does not request adaption of coupling strength. As the resulting interaction structure generated by this proposed strategy is strongly related to unidirectional chains, by investigating synchronization property of unidirectional chains, we reveal that there exists a certain coupling range in which the agents could be controlled regardless of the length of the chain. This feature enables the adaptive strategy to control the mobile oscillators regardless of their moving speed. Compared with existing adaptive control strategies for networked mobile agents, our proposed strategy is simpler for implementation where the resulting interaction networks are kept unweighted at all time.

The sense of touch is a fundamental mechanism that nearly all organisms use to interact with their surroundings. However, the process of mechanotransduction whereby a mechanical stimulus gives rise to a neuronal response is not well understood. In this paper we present an investigation of the biomechanics of touch using the model organism C. elegans. By developing a custom micromanipulation and force sensing system around a high resolution optical microscope, we measured the spatial deformation of the organism’s cuticle and force response to controlled uniaxial indentations. We combined these experimental results with anatomical data to create a multilayer computational biomechanical model of the organism and accurately derive its material properties such as the elastic modulus and poisson’s ratio. We demonstrate the utility of this model by combining it with previously published electrophysiological data to provide quantitative insights into different biomechanical states for mechanotransduction, including the first estimate of the sensitivity of an individual mechanoreceptor to an applied stimulus (parameterised as strain energy density). We also interpret empirical behavioural data to estimate the minimum number of mechanoreceptors which must be activated to elicit a behavioural response.

Imaging flow cytometry (IFC) is an emerging technology that acquires single-cell images at high-throughput for analysis of a cell population. Rich information that comes from high sensitivity and spatial resolution of a single-cell microscopic image is beneficial for single-cell analysis in various biological applications. In this paper, we present a fast image-processing pipeline (R-MOD: Real-time Moving Object Detector) based on deep learning for high-throughput microscopy-based label-free IFC in a microfluidic chip. The R-MOD pipeline acquires all single-cell images of cells in flow, and identifies the acquired images as a real-time process with minimum hardware that consists of a microscope and a high-speed camera. Experiments show that R-MOD has the fast and reliable accuracy (500 fps and 93.3% mAP), and is expected to be used as a powerful tool for biomedical and clinical applications.

Our study focusses on investigating a modern modelling paradigm, a bivariate stochastic process, that allows us to link individual tree variables with growth and yield stand attributes. In this paper, our aim is to introduce the mathematics of mixed effect parameters in a bivariate stochastic differential equation and to describe how such a model can be used to aid our understanding of the bivariate height and diameter distribution in a stand using a large dataset provided by the Lithuanian National Forest Inventory (LNFI). We examine tree height and diameter evolution with a Vasicek-type bivariate stochastic differential equation and mixed effect parameters. It is focused on demonstrating how new developed bivariate conditional probability density functions allowed us to calculate the evolution, in the forward and backward directions, of the mean diameter, height, dominant height, assortments, stem volume of a stand and uncertainties in these attributes for a given stand age. We estimate the parameters by considering discrete samples of the diameter and height at a given age and by using an approximated maximum likelihood procedure. The model performance criteria for the height and diameter growth models include statistical indexes and an analysis of residuals.

The assessment of executive functions poses researchers with several challenges related to both the complexity of the construct of executive functions itself and/or the methodological difficulties related to its evaluation. The main objective of the current study was to evaluate a 360° version of an ecologically valid assessment called the Picture Interpretation Test (PIT). Participants included 19 patients with Parkinson’s disease (PD) and 19 healthy controls. All participants endorsed globally positive experiences of the PIT 360°. Furthermore, findings indicated that patients with PD took longer to correctly interpret the PIT 360° scene and tended to significantly focus on details of the 360° scene instead of the most informative elements. The time needed for a correct interpretation of the presented scene also correlated significantly with performance in conventional paper and pencil tests of executive functions for patients with PD. Classification analysis indicated the potential of the PIT 360° for distinguishing between patients with PD and healthy controls. Overall, these data provide preliminary evidence in support of the PIT 360° for evaluating executive functions.

Graphene oxide (GO) has shown a high potential to adsorb and store water molecules due to the oxygen-containing functional groups on its hydrophilic surface. In this study, we characterized the water absorbing properties of graphene oxide in the form of papers. We fabricated three kinds of graphene oxide papers, two with rich oxygen functional groups and one with partial chemical reduction, to vary the oxygen/carbon ratio and found that the paper with high oxygen content has higher moisture adsorption capability. For the GO paper with reduction, the overall moisture absorbance was reduced. However, the absorbance at high humidity was significantly improved due to direct formation of multilayer water vapor in the system, which derived from the weak interaction between the adsorbent and the adsorbate. To demonstrate one application of GO papers as a desiccant, we tested grape fruits with and without GO paper. The fruits with a GO paper exhibited longer-term preservation with delayed mold gathering because of desiccation effect from the paper. Our results suggest that GO will find numerous practical applications as a desiccant and is a promising material for moisture desiccation and food preservation.

Hepatocellular carcinoma with bile duct tumor thrombus (BDTT) is a malignant disease. The most commonly used diagnosis methods for BDTT are MRCP/ERCP, ultrasonic diagnosis or CT scan. However, BDTT is often misdiagnosed as other bile duct diseases, such as extrahepatic cholangiocarcinoma (EHCC), choledochal cyst (Cyst) and common bile duct stone (Stone). Diagnostic methods, which are more accurate and less destructive, are urgently needed. In this paper, we analyzed the small molecule metabolites in the serum of BDTT, Stone, Cyst and EHCC patients and normal people using untargeted GC-MS, and identified 21 metabolites that show different levels among different samples. Using targeted UHPLC-QQQ-MS analysis, we found that several metabolites are significantly changed. ROC curve analysis revealed two metabolites, L-citrulline and D-aspartic acid, as potential biomarkers that can distinguish BDTT from other bile duct diseases.

Reliability issues associated with driving metal-oxide semiconductor thin film transistors (TFTs), which may arise from various sequential drain/gate pulse voltage stresses and/or certain environmental parameters, have not received much attention due to the competing desire to characterise the shift in the transistor characteristics caused by gate charging. In this paper, we report on the reliability of these devices under AC bias stress conditions because this is one of the major sources of failure. In our analysis, we investigate the effects of the driving frequency, pulse shape, strength of the applied electric field, and channel current, and the results are compared with those from a general reliability test in which the devices were subjected to negative/positive bias, temperature, and illumination stresses, which are known to cause the most stress to oxide semiconductor TFTs. We also report on the key factors that affect the sub-gap defect states, and suggest a possible origin of the current degradation observed with an AC drive. Circuit designers should apply a similar discovery and analysis method to ensure the reliable design of integrated circuits with oxide semiconductor devices, such as the gate driver circuits used in display devices.

Optical phased arrays have been demonstrated to enable a variety of applications ranging from high-speed on-chip communications to vertical surface emitting lasers. Despite the prosperities of the researches on optical phased arrays, presently, the reported designs of optical phased arrays are based on silicon photonics while plasmonic-based optical phased arrays have not been demonstrated yet. In this paper, a passive plasmonic optical phased array is proposed and experimentally demonstrated. The beam of the proposed plasmonic optical phased array is steerable in the far-field area and a high directivity can be achieved. In addition, radio frequency phased array theory is demonstrated to be applicable to the description of the coupling conditions of the delocalized surface plasmons in optical phased arrays and thus the gap between the phased arrays at two distinctly different wavelengths can be bridged. The potential applications of the proposed plasmonic phased arrays include on-chip optical wireless nanolinks, optical interconnections and integrated plasmonic lasers.

Taraditionally, the water-soluble contaminants of biodiesel are treated by water wash method. However, water wash method ends up in an aqueous effluent, which might then cause a harmful environmental impact. As a consequence, waterless purification of biodiesel has triggered primary interest in biodiesel manufacturing process. To address this issue, an endeavour has been made in this work to investigate the waterless purification of biodiesel from waste cooking oil using cow dung ash at different concentration of 1, 2, 3 and 4 wt/wt %. The optimum concentration of cow dung ash for biodiesel purification was found through chemometric analysis by comparing the Fourier transform infrared transmission (FTIR) spectral characteristics of cow dung ash with the water treated FTIR. It was observed from the experimental study that 1 wt/wt % of cow dung ash exhibited similar structural characteristics as that of traditional water treated method of biodiesel purification. Therefore, bio-waste cow dung ash is an effective adsorbent in purifying biodiesel analogous to traditional water washing technology.

There is a perceived gap between dietary advice given by health practitioners and adherence to the advice by patients. We investigated whether a behaviour change technique (implementation-planning) was more effective than standard-of-care diet advice at reducing dietary acid intake using quantitative erosive tooth wear progression as an objective clinical outcome. This study was a randomised controlled, double-blind, single-centre clinical trial in the UK. Participants (n = 60) with high dietary acid intake (≥2 daily), were recruited and randomly assigned (1:1) to receive either implementation-planning or standard-of-care diet advice in a single clinical session. Questionnaires and impressions were taken at baseline and 6 months later. Dental casts were scanned using laser profilometry and superimposed using surface-matching software. Data were analysed per protocol and intention-to-treat using independent t-tests and Mann-Whitney tests. The intervention group reduced their dietary acid intake between meals to 1 intake per day compared to 2 intakes per day for the controls and demonstrated reduced dental hard tissue volume loss (−0.00 mm3 (SD = 0.01)) compared to controls (−0.07 mm3 (SD 0.17)), p = 0.049. This paper supports the use of implementation planning in clinical practice and presents a non-invasive method of intervention assessment in behaviour change. Larger trials are needed to confirm the generalisability of results.

In this paper, we propose a simple design with an excellent performance to obtain high contrast in transmission asymmetry based on dielectric microspheres. Initially, we scrutinize the impact of the sphere radius on forward and backward transmissions. Afterward, by introducing a capping layer on top of the sphere, transmission response for the backward illuminated light will be blocked. In the next step, in order to replace the reflecting metal cap with a metal free absorbing design, we adopt a modeling approach based on the transfer matrix method (TMM) to explore an ideal material to achieve metal free perfect absorption in a multilayer configuration of material-insulator-material-insulator (MIMI). As a result of our investigations, it is found that Titanium Nitride (TiN) is an excellent alternative to replace metal in a MIMI multilayer stack. Setting this stack as the top capping coating, we obtain a high contrast between forward and backward light transmission where in an ultra-broadband range of 400 nm–1000 nm, forward transmission is above 0.85 while its backward response stays below 0.2. Moreover, due to the existence of multilayer stack, a high asymmetry is also observed for absorption profiles. This design has a relatively simple and large scale compatible fabrication route.

Brain imaging genetics intends to uncover associations between genetic markers and neuroimaging quantitative traits. Sparse canonical correlation analysis (SCCA) can discover bi-multivariate associations and select relevant features, and is becoming popular in imaging genetic studies. The L1-norm function is not only convex, but also singular at the origin, which is a necessary condition for sparsity. Thus most SCCA methods impose $${\ell }_{{\bf{1}}}$$ ℓ 1 -norm onto the individual feature or the structure level of features to pursuit corresponding sparsity. However, the $${\ell }_{{\bf{1}}}$$ ℓ 1 -norm penalty over-penalizes large coefficients and may incurs estimation bias. A number of non-convex penalties are proposed to reduce the estimation bias in regression tasks. But using them in SCCA remains largely unexplored. In this paper, we design a unified non-convex SCCA model, based on seven non-convex functions, for unbiased estimation and stable feature selection simultaneously. We also propose an efficient optimization algorithm. The proposed method obtains both higher correlation coefficients and better canonical loading patterns. Specifically, these SCCA methods with non-convex penalties discover a strong association between the APOE e4 rs429358 SNP and the hippocampus region of the brain. They both are Alzheimer’s disease related biomarkers, indicating the potential and power of the non-convex methods in brain imaging genetics.

Platinum regimens still play a key role in chemotherapy for incurable non-small cell lung cancer (NSCLC). Although guidelines list many platina regimens, the best regimens have not yet clarified. Electronic searches were carried out during November 26th-28th, 2016. We included individually randomized trials comparing two or more platinum regimes for incurable chemo-naive NSCLC published in English full papers. The platinum doublets should be either Cisplatin (CDDP), Carboplatin (CBDCA), or Nedaplatin (CDGP) plus one of the third-generation agents. The platinum triplet should be the doublet plus bevacizumab (BEV). The data were independently extracted and cross-checked by two investigators. We did not observed heterogeneity (whole network level Q = 28.9, df = 34, P = 0.717) among 59 pairwise comparisons from 45 studies with 16141 cases for the primary outcome, hazard ratio for overall survival (HRos). Using CBDCA + Paclitaxel (PTX) + BEV as a common comparator, CDGP + Docetaxel (DTX) (HRos = 0.98, 95%CI: 0.75–1.29, P = 0.884), CDDP + Tegafur gimeracil oteracil (S1) (HRos = 1.23, 95%CI: 0.96–1.57, P = 0.099), CBDCA + S1 (HRos = 1.23, 95%CI: 0.99–1.53, P = 0.062), and CDGP + Gemcitabine (GEM) (HRos = 1.24, 95%CI: 0.71–2.17, P = 0.45) did not have significantly poorer HRos. We suggest that these regimens as acceptable first-choice regimens.

Storing biologically equivalent indels as distinct entries in databases causes data redundancy, and misleads downstream analysis. It is thus desirable to have a unified system for identifying and representing equivalent indels. Moreover, a unified system is also desirable to compare the indel calling results produced by different tools. This paper describes UPS-indel, a utility tool that creates a universal positioning system for indels so that equivalent indels can be uniquely determined by their coordinates in the new system, which also can be used to compare different indel calling results. UPS-indel identifies 15% redundant indels in dbSNP, 29% in COSMIC coding, and 13% in COSMIC noncoding datasets across all human chromosomes, higher than previously reported. Comparing the performance of UPS-indel with existing variant normalization tools vt normalize, BCFtools, and GATK LeftAlignAndTrimVariants shows that UPS-indel is able to identify 456,352 more redundant indels in dbSNP; 2,118 more in COSMIC coding, and 553 more in COSMIC noncoding indel dataset in addition to the ones reported jointly by these tools. Moreover, comparing UPS-indel to state-of-the-art approaches for indel call set comparison demonstrates its clear superiority in finding common indels among call sets. UPS-indel is theoretically proven to find all equivalent indels, and thus exhaustive.

Liquid marble is a liquid droplet coated with hydrophobic powder that can be used as a bioreactor. This paper reports the three-dimensional self-assembly and culture of a cell toroid in a slow-releasing, non-adhesive and evaporation-reducing bioreactor platform based on a liquid marble. The bioreactor is constructed by embedding a hydrogel sphere containing growth factor into a liquid marble filled with a suspension of dissociated cells. The hydrogel maintains the water content and concurrently acts as a slow-release carrier. The concentration gradient of growth factor induces cell migration and assembly into toroidal aggregates. An optimum cell concentration resulted in the toroidal (doughnut-like) tissue after 12 hours. The harvested cell toroids showed rapid closure of the inner opening when treated with the growth factor. We also present a geometric growth model to describe the shape of the toroidal tissue over time. In analogy to the classical two-dimensional scratch assay, we propose that the cell toroids reported here open up new possibilities to screen drugs affecting cell migration in three dimensions.

This paper presents a method to generate a multi-segmented optical needle with a strong longitudinally polarized field, uniform intensity along the optical axis, and a transverse size (~0.36λ). The length of each segment in the optical needle and the spacing between adjacent segments are controllable by reversing and focusing the radiation pattern from a sectional-uniform line source antenna to the focal volume of a 4Pi focusing system. By solving the inverse problem, we can obtain the required incident field distribution at the pupil plane to create the multi-segmented optical needle. Numerical examples demonstrate that a multi-segmented optical needle with variable focal depth, adjustable interval, narrow lateral width, homogeneous intensity, and high longitudinal polarization purity can be formed using the proposed approach. The length of each needle segment is approximately equal to the length of the corresponding sectional uniform line source. The multi-segmented optical needle may be employed in applications such as multi-particle acceleration, multi-particle trapping and manipulation, laser machining, and laser material processing.

Although HNgCCX (Ng = Kr and Xe; X = F and Cl) have been identified in cryogenic matrices, similar Br and I analogues have not been prepared so far. In this paper, the nature of HNgCCX (Ng = Kr and Xe; X = F, Cl, Br and I) have been investigated by ab initio methods. The main characteristic absorption peak of HNgCCX is the vH-Ng, which decreases as X varies from F to I. Moreover, the H-Xe bond is stronger than the H-Kr bond. The vC≡C and vC-X exhibit red- and blue-shift characters, respectively, especially the C-X bond is abnormal blue-shift halogen bond. AIM results show that the H-Ng bond is essentially covalent bond and the covalent character of H-Xe bond is underestimated, and the trend of the covalent character is C-Cl > C-Br > C-F > C-I. Although HNgCCX is instable thermodynamically with respect to Ng + HCCX, it is kinetically stable with respect to the two-/three-body channels due to the relatively larger energy barriers. The three-body channels of HNgCCX is the main decomposition channel, and the kinetically stability of HXeCCX is more than its Kr analogues. This study is helpful for the preparation of new HNgCCX in cryogenic matrices.

For the first time, a paper-based fluorescence resonance energy transfer (FRET) determination with cyclic AMP (cAMP)-specific phosphodiesterase 4B (PDE4B) inhibitory assay using an inkjet-printing technique is proposed. Non-fabricated parchment paper is found to constitute a unique substrate to measure fluorescent energy transfer, due to its insignificant self-absorption, and enables efficient sample interaction. Here, we report the responsive FRET signals generated on paper, upon sequentially printing reaction components on parchment paper using a conventional inkjet printer equipped with four cartridges. After printing, the energy emitted by Eu chelate was transferred by FRET to ULight molecule on paper, detected at 665 nm. In the absence of free cAMP, a maximum FRET signal was achieved on paper, while a decrease in FRET signals was recorded when free cAMP produced by PDE4B inhibitors compete with Eu-cAMP, binding with ULight-mAb. The IM50 value was determined as 2.46 × 10−13 mole for roliparm and 1.86 × 10−13 mole for roflumilast, to effectively inhibit PDE4B activity. Inkjet printing-based FRET signal determination utilizes components that are less than the femtomole range, which was four-orders less than the standard assay method. The methodology reported here constitutes an innovative approach towards the determination of FRET signals generated on paper.

Subunit viral vaccines are typically not as efficient as live attenuated or inactivated vaccines at inducing protective immune responses. This paper describes an alternative ‘biomimetic’ technology; whereby viral antigens were formulated around a polymeric shell in a rationally arranged fashion with a surface glycoprotein coated on to the surface and non-structural antigen and adjuvant encapsulated. We evaluated this model using BVDV E2 and NS3 proteins formulated in poly-(D, L-lactic-co-glycolic acid) (PLGA) nanoparticles adjuvanted with polyinosinic:polycytidylic acid (poly(I:C) as an adjuvant (Vaccine-NP). This Vaccine-NP was compared to ovalbumin and poly(I:C) formulated in a similar manner (Control-NP) and a commercial adjuvanted inactivated BVDV vaccine (IAV), all inoculated subcutaneously and boosted prior to BVDV-1 challenge. Significant virus-neutralizing activity, and E2 and NS3 specific antibodies were observed in both Vaccine-NP and IAV groups following the booster immunisation. IFN-γ responses were observed in ex vivo PBMC stimulated with E2 and NS3 proteins in both vaccinated groups. We observed that the protection afforded by the particulate vaccine was comparable to the licenced IAV formulation. In conclusion, the biomimetic particulates showed a promising immunogenicity and efficacy profile that may be improved by virtue of being a customisable mode of delivery.

Assessment of burn scars is an important study in both medical research and clinical settings because it can help determine response to burn treatment and plan optimal surgical procedures. Scar rating has been performed using both subjective observations and objective measuring devices. However, there is still a lack of consensus with respect to the accuracy, reproducibility, and feasibility of the current methods. Computerized scar assessment appears to have potential for meeting such requirements but has been rarely found in literature. In this paper an image analysis and pattern classification approach for automating burn scar rating based on the Vancouver Scar Scale (VSS) was developed. Using the image data of pediatric patients, a rating accuracy of 85% was obtained, while 92% and 98% were achieved for the tolerances of one VSS score and two VSS scores, respectively. The experimental results suggest that the proposed approach is very promising as a tool for clinical burn scar assessment that is reproducible and cost-effective.

We report a disposable point-of-care sensing platform specific to salivary cortisol detection. The sensor is inkjet printed on a paper substrate with a metalloporphyrin based macrocyclic catalyst ink that can electrochemically reduce cortisol, captured by aptamer functionalized magnetic nanoparticles. The sensor consists of a thin magnet disc, aligned at the back of the electrode, in order to populate the magnetic nanoparticle bound cortisol at the sensing electrode area. Proof of concept studies were performed to detect salivary cortisol levels in human subjects with high and low risks for obstructive sleep apnea (OSA). High selectivity was observed to salivary cortisol against a background of closely related steroids.

This paper presents short wavelength operation of tunable thulium-doped mode-locked lasers with sweep ranges of 1702 to 1764 nm and 1788 to 1831 nm. This operation is realized by a combination of the partial amplified spontaneous emission suppression method, the bidirectional pumping mechanism and the nonlinear polarization rotation (NPR) technique. Lasing at emission bands lower than the 1800 nm wavelength in thulium-doped fiber lasers is achieved using mode confinement loss in a specially designed photonic crystal fiber (PCF). The enlargement of the first outer ring air holes around the core region of the PCF attenuates emissions above the cut-off wavelength and dominates the active region. This amplified spontaneous emission (ASE) suppression using our presented PCF is applied to a mode-locked laser cavity and is demonstrated to be a simple and compact solution to widely tunable all-fiber lasers.

Carbon material containing nickel, nitrogen and sulfur (Ni-NSC) has been synthesized using metal-organic frameworks (MOFs) as precursor by annealing treatment with a size from 200 to 300 nm. Pd nanoparticles supported on the Ni-NSC (Pd/Ni-NSC) are used as electrocatalysts for ethanol oxidation in alkaline media. Due to the synergistic effect between Pd and Ni, S, N, free OH radicals can form on the surface of Ni, N and S atoms at lower potentials, which react with CH3CO intermediate species on the Pd surface to produce CH3COO− and release the active sites. On the other hand, the stronger binding force between Pd and co-doped N and S is responsible for enhancing dispersion and preventing agglomeration of the Pd nanoparticles. The Pd(20 wt%)/Ni-NSC shows better electrochemical performance of ethanol oxidation than the traditional commercial Pd(20 wt%)/C catalyst. Onset potential on the Pd(20 wt%)/Ni-NSC electrode is 36 mV more negative compared with that on the commercial Pd(20 wt%)/C electrode. The Pd(20 wt%)/Ni-NSC in this paper demonstrates to have excellent electrocatalytic properties and is considered as a promising catalyst in alkaline direct ethanol fuel cells.

A high extinction ratio (ER) electromagnetically induced transparency (EIT) analogue based on single-layer metamaterial is designed and experimentally demonstrated in this paper. This design involves four mirror-like symmetrically coupled split ring resonators (SRRs) that exhibit a bright-dark-dark-bright mode configuration. The EIT-like effect is realized by coupling between the bright resonators and dark resonators. The high ER feature is achieved from the suppression of radiative losses, due to opposite directions of electric and magnetic dipoles of two dark modes in the unit cell. Classical coupled resonator model is used to theoretically analyze the device transmission performances and to characterize parameter influence of the ER. Both numerical simulation and experiment results demonstrate that the ER of this device can reach more than 21 dB, which is 11 dB higher than that of conventional bright-dark coupling SRR arrangement. Finally, the potential multi-channel sensing utility of this device is demonstrated to show the importance of high ER feature.