Alternative polyadenylation determines the functional landscape of inverted Alu repeats.

Inverted Alu repeats (IRAlus) are abundantly found in the transcriptome, especially in introns and 3' untranslated regions (UTRs). Yet, the biological significance of IRAlus embedded in 3' UTRs remains largely unknown. Here, we find that 3' UTR IRAlus silences genes involved in essential signaling pathways. We utilize J2 antibody to directly capture and map the double-stranded RNA structure of 3' UTR IRAlus in the transcriptome. Bioinformatic analysis reveals alternative polyadenylation as a major axis of IRAlus-mediated gene regulation. Notably, the expression of mouse double minute 2 (MDM2), an inhibitor of p53, is upregulated by the exclusion of IRAlus during UTR shortening, which is exploited to silence p53 during tumorigenesis. Moreover, the transcriptome-wide UTR lengthening in neural progenitor cells results in the global downregulation of genes associated with neurodegenerative diseases, including amyotrophic lateral sclerosis, via IRAlus inclusion. Our study establishes the functional landscape of 3' UTR IRAlus and its role in human pathophysiology.

Microscopic augmented-reality indicators for long-term live cell time-lapsed imaging.

Microscopic observations of cultured cells in many lab-on-a-chip applications mostly utilize digital image acquisition using CCD sensors connected to a personal computer. The functionalities of this digital imaging can be enhanced by implementing computer-vision based augmented reality technologies. In this study, we present a new method for precisely relocating biological specimens under microscopic inspections by using augmented reality patterns, called microscopic augmented reality indicators (µ-ARIs). Since the method only requires sticky films attached under sample containers of any shape, long-term live cell observations can be conducted at much less extra cost than with conventional methods. On these sticky films, multiple arrays of position-indicating patterns were imprinted to provide a reference coordinate system for recording and relocating the accurate position and rotation of the specimen under inspection. This approach can be useful for obtaining the exact locations of individual cells inside biological samples using µ-ARI imprinted transparent films in a rapid and controlled manner.

A kinematic analysis of directional effects on mouse control.

The directional effects associated with cursor movement controlled by a computer mouse have long been studied to improve mouse performance during precise tasks. However, those studies have rarely considered the kinematic variables associated with directional effects and have only analysed the projection of trajectories along the main axes of movement, eventually reducing the original dimensions of the data. In addition, as the angle of approach has a limited number of levels, it has been difficult to observe singular behaviour in the horizontal directions. In this study, we investigated the directional effects on kinematic variables when using a mouse to select circular targets. In this experiment, the measured trajectory of 16 different angles of approach was measured after separating the x and y components. The results revealed interesting biomechanical and cognitive features of mouse control and led to the suggestion of two improvements to be made upon the typical mouse design.

Fluorescence intensity ratio stereoscopic transform.

A novel approach to 3-D information processing of 2-D cell images is presented, called fluorescence intensity ratio stereoscopic transform (FIRST). Here, we describe its basic principle of image processing and show the results for the ratio of total internal reflection fluorescence (TIRF) to fluorescence intensity. A simple, intuitive transform algorithm would help us to easily obtain a clear stereoscopic image from two 2-D cell images with different fluorescence intensity. For this purpose, nonlinear evanescent-field (EF) imaging of cell-membrane surface and its intracellular structures by using on-chip grating coupler is achieved. This method enabled us to obtain cell images with different signal-to-background ratio and resolution under microfluidic environments. Specifically, we manipulated optic pathway to partially illuminate microscale objects within the microfluidic channel. These findings imply this method will enable selectively to detect optical signals of biomolecular interaction within the cell membrane in a controlled manner. Furthermore, we believe this approach will help to develop an optofluidic sensor for individually detecting dynamic behaviors of intracellular molecules in living cells under microfluidic cell culture environments.

Skyrmion Phase in MnSi Thin Films Grown on Sapphire by a Conventional Sputtering.

Topologically protected chiral skyrmions are an intriguing spin texture that has attracted much attention because of fundamental research and future spintronic applications. MnSi with a non-centrosymmetric structure is a well-known material hosting a skyrmion phase. To date, the preparation of MnSi crystals has been investigated by using special instruments with an ultrahigh vacuum chamber. Here, we introduce a facile way to grow MnSi films on a sapphire substrate using a relatively low vacuum environment of conventional magnetron sputtering. Although the as-grown MnSi films have a polycrystalline nature, a stable skyrmion phase in a broad range of temperatures and magnetic fields is observed via magnetotransport properties including phenomenological scaling analysis of the Hall resistivity contribution. Our findings provide not only a general way to prepare the materials possessing skyrmion phases but also insight into further research to stimulate more degrees of freedom in our inquisitiveness.

Simultaneous counting of two subsets of leukocytes using fluorescent silica nanoparticles in a sheathless microchip flow cytometer.

A portable flow cytometer has been recognized as an important tool for many clinical applications such as HIV/AIDS screening in developing countries and regions with limited medical facilities and resources. Conventional flow cytometers typically require multiple detectors for simultaneous identification of multiple subsets of immune cell. To minimize the number of detectors toward portable flow cytometry or to analyze multi-parametric cellular information with minimum number of detectors in conventional flow cytometers, we propose a versatile multiplexed cell-counting method using functional silica nanoparticles (SiNPs). FITC-doped SiNPs, which are 100 times brighter than the FITC molecules itself, were used as new intensity-based fluorescent dye complexes to simultaneously measure two subsets of leukocytes using a single detector. CD45(+)CD4(+) cells tagged with these FITC-doped SiNPs were 50 times brighter than CD45(+)CD4(-) cells tagged only with FITC. To make the overall system compact, a disposable microchip flow cytometer that does not require sheath flow was developed. Combining these dye-doped SiNPs based detection schemes and the sheathless microchip flow cytometer scheme, we successfully identified and counted two subsets of leukocytes simultaneously (R(2) = 0.876). These approaches can be the building blocks for a truly portable and disposable flow cytometer for various clinical cytometry applications.

Effect of drying treatment on the leachability of metallic elements from weathered solid mine wastes.

Leaching of toxic metallic elements (Cu, Zn, As, Cd, and Pb) from two solid mine wastes was characterized under different drying treatments. During 14 batch decant-refill leaching steps, samples were intermittently dried four times in 40 °C oven or -20 °C freezer. For all leachates, the pH, pE, Fe2+/Fe3+, and SO42- were analyzed. The parameters of the two-site model (kfast, kslow, and ffast) and labile fractions (F1 + F2) were determined. High levels of toxic metallic elements were determined in waste samples; however, their leaching was limited, as evidenced by the magnitudes of F1 + F2, ffast, and kslow. Leachate solutions were acidic, at pH 3-4, and oxic, at 150 mV < Eh 300 < mV, thus having negligible Fe2+. Leachate concentrations of toxic metallic elements increased (4-58%) after drying at 40 °C and were strongly correlated (r2 = 0.780) with those of sulfate in liquid phase. The mass of element elution was in the order of 40 °C drying > -20 °C drying ≥ continuous wetting. Results indicate that the element leachability is increased through drying events and the leachate concentration is associated with the dissolution reaction of sulfur-bearing minerals. Frequent occurrence of prolonged droughts along with high temperatures over the mine waste disposal site, can enhance the leaching potential of toxic metallic elements.

A sleep-like state in Hydra unravels conserved sleep mechanisms during the evolutionary development of the central nervous system.

Sleep behaviors are observed even in nematodes and arthropods, yet little is known about how sleep-regulatory mechanisms have emerged during evolution. Here, we report a sleep-like state in the cnidarian Hydra vulgaris with a primitive nervous organization. Hydra sleep was shaped by homeostasis and necessary for cell proliferation, but it lacked free-running circadian rhythms. Instead, we detected 4-hour rhythms that might be generated by ultradian oscillators underlying Hydra sleep. Microarray analysis in sleep-deprived Hydra revealed sleep-dependent expression of 212 genes, including cGMP-dependent protein kinase 1 (PRKG1) and ornithine aminotransferase. Sleep-promoting effects of melatonin, GABA, and PRKG1 were conserved in Hydra However, arousing dopamine unexpectedly induced Hydra sleep. Opposing effects of ornithine metabolism on sleep were also evident between Hydra and Drosophila, suggesting the evolutionary switch of their sleep-regulatory functions. Thus, sleep-relevant physiology and sleep-regulatory components may have already been acquired at molecular levels in a brain-less metazoan phylum and reprogrammed accordingly.

Highly Reduced Saturation Magnetization in Epitaxially Grown Ferrimagnetic Heusler Thin Films.

The key of spintronic devices using the spin-transfer torque phenomenon is the effective reduction of switching current density by lowering the damping constant and the saturation magnetization while retaining strong perpendicular magnetic anisotropy. To reduce the saturation magnetization, particular conditions such as specific substitutions or buffer layers are required. Herein, we demonstrate highly reduced saturation magnetization in tetragonal D022 Mn3-x Ga thin films prepared by rf magnetron sputtering, where the epitaxial growth is examined on various substrates without any buffer layer. As the lattice mismatch between the sample and the substrate decreases from LaAlO3 and (LaAlO3)0.3(Sr2AlTaO6)0.7 to SrTiO3, the quality of Mn3-x Ga films is improved together with the magnetic and electronic properties. Especially, the Mn3-x Ga thin film epitaxially grown on the SrTiO3 substrate, fully oriented along the c axis perpendicular to the film plane, exhibits significantly reduced saturation magnetization as low as 0.06 µB, compared to previous results. By the structural and chemical analyses, we find that the predominant removal of Mn II atoms and the large population of Mn3+ ions affect the reduced saturation magnetization. Our findings provide insights into the magnetic properties of Mn3-x Ga crystals, which promise great potential for spin-related device applications.

An impulsive, electropulsation-driven backflow in microchannels during electroporation.

We describe for the first time an impulsive, electropulsation-driven backflow in microchannels for on-chip cell electroporation.

Design and Evaluation of Smart Glasses for Food Intake and Physical Activity Classification.

This study presents a series of protocols of designing and manufacturing a glasses-type wearable device that detects the patterns of temporalis muscle activities during food intake and other physical activities. We fabricated a 3D-printed frame of the glasses and a load cell-integrated printed circuit board (PCB) module inserted in both hinges of the frame. The module was used to acquire the force signals, and transmit them wirelessly. These procedures provide the system with higher mobility, which can be evaluated in practical wearing conditions such as walking and waggling. A performance of the classification is also evaluated by distinguishing the patterns of food intake from those physical activities. A series of algorithms were used to preprocess the signals, generate feature vectors, and recognize the patterns of several featured activities (chewing and winking), and other physical activities (sedentary rest, talking, and walking). The results showed that the average F1 score of the classification among the featured activities was 91.4%. We believe this approach can be potentially useful for automatic and objective monitoring of ingestive behaviors with higher accuracy as practical means to treat ingestive problems.

On-chip erythrocyte deformability test under optical pressure.

This paper presents a novel method for an on-chip erythrocyte deformability test under optical pressure, especially to enhance the level of sensitivity with respect to the detection of cancerous diseases. To demonstrate the performance and sensitivity of the combined method, we introduce the concept of transit velocity, a modified elongation index, and shape recovery time of individual erythrocytes in a strictly confined region (2 microm deep, 4 microm wide, and 100 microm long). Finally, we investigate a synergy or convergence effect due to the combination of these parameters for in situ detection of cancerous diseases under optical pressure.

A glasses-type wearable device for monitoring the patterns of food intake and facial activity.

Here we present a new method for automatic and objective monitoring of ingestive behaviors in comparison with other facial activities through load cells embedded in a pair of glasses, named GlasSense. Typically, activated by subtle contraction and relaxation of a temporalis muscle, there is a cyclic movement of the temporomandibular joint during mastication. However, such muscular signals are, in general, too weak to sense without amplification or an electromyographic analysis. To detect these oscillatory facial signals without any use of obtrusive device, we incorporated a load cell into each hinge which was used as a lever mechanism on both sides of the glasses. Thus, the signal measured at the load cells can detect the force amplified mechanically by the hinge. We demonstrated a proof-of-concept validation of the amplification by differentiating the force signals between the hinge and the temple. A pattern recognition was applied to extract statistical features and classify featured behavioral patterns, such as natural head movement, chewing, talking, and wink. The overall results showed that the average F1 score of the classification was about 94.0% and the accuracy above 89%. We believe this approach will be helpful for designing a non-intrusive and un-obtrusive eyewear-based ingestive behavior monitoring system.

Expansion channel for microchip flow cytometers.

This paper presents a novel way of designing a flow focusing channel for microchip flow cytometers. With this method we increased throughput and sensitivity of particle detection at the same time. Generally, to increase the detection throughput of a flow cytometer, the speed of the flow inside the focusing channel needs to be increased, hence reducing the time of exposure to laser beam. With the shorter exposure time, both the fluorescence and scatter signal from the target particles become dimmer. To increase the sensitivity of signal detection, however, the speed of the flow should be decreased so as to decrease throughput of detection. To overcome this dilemmatic problem, we integrated an expansion channel inside a focusing channel. Signals from particles in an expansion channel were about 10 times brighter than those in a normal channel. With this enhanced sensitivity, we could also speed up the inlet flow, which in turn increases the overall throughput of detection.

QR-on-a-chip: a computer-recognizable micro-pattern engraved microfluidic device for high-throughput image acquisition.

This study proposes a novel way to achieve high-throughput image acquisition based on a computer-recognizable micro-pattern implemented on a microfluidic device. We integrated the QR code, a two-dimensional barcode system, onto the microfluidic device to simplify imaging of multiple ROIs (regions of interest). A standard QR code pattern was modified to arrays of cylindrical structures of polydimethylsiloxane (PDMS). Utilizing the recognition of the micro-pattern, the proposed system enables: (1) device identification, which allows referencing additional information of the device, such as device imaging sequences or the ROIs and (2) composing a coordinate system for an arbitrarily located microfluidic device with respect to the stage. Based on these functionalities, the proposed method performs one-step high-throughput imaging for data acquisition in microfluidic devices without further manual exploration and locating of the desired ROIs. In our experience, the proposed method significantly reduced the time for the preparation of an acquisition. We expect that the method will innovatively improve the prototype device data acquisition and analysis.

Upper Extremity Functional Evaluation by Fugl-Meyer Assessment Scoring Using Depth-Sensing Camera in Hemiplegic Stroke Patients.

Virtual home-based rehabilitation is an emerging area in stroke rehabilitation. Functional assessment tools are essential to monitor recovery and provide current function-based rehabilitation. We developed the Fugl-Meyer Assessment (FMA) tool using Kinect (Microsoft, USA) and validated it for hemiplegic stroke patients. Forty-one patients with hemiplegic stroke were enrolled. Thirteen of 33 items were selected for upper extremity motor FMA. One occupational therapist assessed the motor FMA while recording upper extremity motion with Kinect. FMA score was calculated using principal component analysis and artificial neural network learning from the saved motion data. The degree of jerky motion was also transformed to jerky scores. Prediction accuracy for each of the 13 items and correlations between real FMA scores and scores using Kinect were analyzed. Prediction accuracies ranged from 65% to 87% in each item and exceeded 70% for 9 items. Correlations were high for the summed score for the 13 items between real FMA scores and scores obtained using Kinect (Pearson's correlation coefficient = 0.873, P<0.0001) and those between total upper extremity scores (66 in full score) and scores using Kinect (26 in full score) (Pearson's correlation coefficient = 0.799, P<0.0001). Log transformed jerky scores were significantly higher in the hemiplegic side (1.81 ± 0.76) compared to non-hemiplegic side (1.21 ± 0.43) and showed significant negative correlations with Brunnstrom stage (3 to 6; Spearman correlation coefficient = -0.387, P = 0.046). FMA using Kinect is a valid way to assess upper extremity function and can provide additional results for movement quality in stroke patients. This may be useful in the setting of unsupervised home-based rehabilitation.

Upper-Limb Function Assessment Using VBBTs for Stroke Patients.

Evaluating and quantifying the upper-limb functions are essential to planning effective patient rehabilitation. The box and block test (BBT) is a conventional, simple, and easy-to-apply assessment tool that is used in hospitals, and previous studies have demonstrated its usefulness in stroke rehabilitation. Using a conventional depth-sensing camera, the authors developed a virtual box and block test (VBBT) system for hand, finger, and grasping assessments based on the BBT used for the grasping ability test in hospitals. Such a virtual upper-limb-function assessment tool that can be implemented in a home setting could be a key component in a home-based virtual rehabilitation system. Comparison results between the real and virtual BBTs show the possibilities for virtualizing conventional and unsupervised assessments.

Time-lapse microscopy using smartphone with augmented reality markers.

A prototype system that replaces the conventional time-lapse imaging in microscopic inspection for use with smartphones is presented. Existing time-lapse imaging requires a video data feed between a microscope and a computer that varies depending on the type of image grabber. Even with proper hardware setups, a series of tedious and repetitive tasks is still required to relocate to the region-of-interest (ROI) of the specimens. In order to simplify the system and improve the efficiency of time-lapse imaging tasks, a smartphone-based platform utilizing microscopic augmented reality (µ-AR) markers is proposed. To evaluate the feasibility and efficiency of the proposed system, a user test was designed and performed, measuring the elapse time for a trial of the task starting from the execution of the application software to the completion of restoring and imaging of an ROI saved in advance. The results of the user test showed that the average elapse time was 65.3 ± 15.2 s with 6.86 ± 3.61 µm of position error and 0.08 ± 0.40 degrees of angle error. This indicates that the time-lapse imaging task was accomplished rapidly with a high level of accuracy. Thus, simplification of both the system and the task was achieved via our proposed system.