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Long non-coding RNAs (lncRNAs) are the "dark matters"involved in gene regulation with complex mechanisms. However, the functions of most lncRNAs remain to be determined. Our previous work revealed a massive number of degradome-supported cleavage signatures on Arabidopsis lncRNAs. Some of them have been confirmed associated with miRNAs-like sRNAs production, while others without long stem structure remain unexplored. A systematical search for phasiRNAs generating ability of these lncRNAs was conducted. Eight novel small RNA triggered lncRNA-phasiRNA pathways were discovered and three of them were found to be conserved in Arabidopsis, Oryza sativa, Glycine max and Gossypium hirsutum. Besides, Five novel ta-siRNAs derived from these lncRNAs were further identified to be involved in the regulation of plant development, stress responses and aromatic amino acids synthesis. These results substantially expanded the gene regulation mechanisms of lncRNAs.

Additional file 4: Figure S2. 24-nt phasiRNAs generated from the novel PHAS lociin wild-type and DCL3 mutant. 24-nt phasiRNAs generated from transcripts of LOC_Os01g37325.1 (A), LOC_Os02g20200.1 (B), LOC_Os02g55550.1 (C), LOC_Os04g45834.2 (D) and LOC_Os09g14490.1 (E) in wild-type and osdcl3–1 mutant seedling, respectively. The black arrows indicate the sRNA trigger cleavage sites, the x-axis represent the phasiRNA position mapped within the PHAS loci, the y-axis represent the read abundance (in RMP, reads per million) of the small RNAs mapped to the sense and antisense strands of PHAS loci.

Additional file 3: Figure S1. 21-nt phasiRNAs generated from the novel PHAS loci in wild-type and DCL4 mutant. 21-nt phasiRNAs generated from transcripts of LOC_Os01g57968.1 (A) and LOC_Os05g43650.1 (D) in wild-type and osdcl4-1 seedling, LOC_Os02g18750.1 (B), LOC_Os04g25740.1 (C) and LOC_Os06g30680.1(E) in wild-type and osdcl4-1 mutant panicle, respectively. The black arrows indicate the sRNA trigger cleavage sites, the x-axis represent the phasiRNA position mapped within the PHAS loci, the y-axis represent the read abundance (in RMP, reads per million) of the small RNAs mapped to the sense and antisense strands of PHAS loci.

Additional file 6: Figure S3. Degradome sequencing-based validation of the phasiRNA-target interactions.Four libraries of degradome sequencing data libraries (GSM434596, GSM455938, GSM455939 and GSM476257) were recruited for T-plot profiling. The IDs of the target transcripts and the corresponding phasiRNAs generated from the transcripts of LOC_Os02g18750.1, LOC_Os05g43650.1, LOC_Os06g30680.1 and LOC_Os12g42380.1 are listed on the top. The y axis measure the normalized reads (in RMP, reads per million) of the degradome signals, and the x axis represent the position of the cleavage signals on the target transcripts. The binding sites of the phasiRNA on their target transcripts were denoted by gray horizontal lines, and the dominant cleavage signals were marked by black arrows.

Background The microRNAs(miRNA)-derived secondary phased small interfering RNAs (phasiRNAs) participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants. In rice, two miRNAs, miR2118 and miR2275, were mainly responsible for triggering of 21-nt and 24-nt phasiRNAs biogenesis, respectively. However, relative fewer phasiRNA biogenesis pathways have been discovered in rice compared to other plant species, which limits the comprehensive understanding of phasiRNA biogenesis and the miRNA-derived regulatory network. Results In this study, we performed a systematical searching for phasiRNA biogenesis pathways in rice. As a result, five novel 21-nt phasiRNA biogenesis pathways and five novel 24-nt phasiRNA biogenesis pathways were identified. Further investigation of their regulatory function revealed that eleven novel phasiRNAs in 21-nt length recognized forty-one target genes. Most of these genes were involved in the growth and development of rice. In addition, five novel 24-nt phasiRNAs targeted to the promoter of an OsCKI1 gene and thereafter resulted in higher level of methylation in panicle, which implied their regulatory function in transcription of OsCKI1,which acted as a regulator of rice development. Conclusions These results substantially extended the information of phasiRNA biogenesis pathways and their regulatory function in rice.

Mental Health issues affect millions of people every year and deter the ability of an individual to live a fulfilling life. 1 in 5 U.S. adults experience some type of mental illness every year. Even though in the U.S. there are progressive policies and initiatives to help those with mental illnesses, there are still many people suffering and not receiving the help they need. There are different factors and reasons behind why some individuals are hesitant to receive care. Location, stigma, and the fear of treatment are some of the reasons, but with the help of technology like machine learning there can be a access to help everywhere. This work provides general overview on the mental disease particularly to review the machine learning application in the mental disease analysis to provide the best overview of this emerging direction.

Cybersickness in Virtual Reality (VR) is a serious issue affecting the overall experience. Many research papers have investigated the causes of cybersickness and offered potential solutions for reducing cybersickness. In this paper, we demonstrate a method to reduce cybersickness by using a novel rendering technique in the virtual environment (VE)- Dynamic Mono-Stereoscopic Rendering System (DMSRS). The DMSRS system uses two different cameras to create a hybrid rendering that includes monoscopic and stereoscopic systems. By default, VEs are rendered using stereoscopic or monoscopic rendering exclusively. The results indicate that cybersickness decreased amongst users with little to no VR experience hindered when using the DMSRS.

The 10th annual IEEE 3DUI Contest focuses on the development of 3D User Interfaces (3DUIs) using passive haptic feedback in Mixed Reality Environments. Material properties of real objects are enhanced with virtual behaviors while used for interaction in a mixed reality scenario. The contest was open to anyone interested in 3DUIs, from researchers to students, enthusiasts, and professionals. The purpose of the contest is to stimulate innovative and creative solutions to challenging 3DUI problems.

MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in eukaryotes. However, the information about miRNAs population and their regulatory functions involving in soybean seed development remains incomplete. Base on the Dicer-like1-mediated cleavage signals during miRNA processing could be employed for novel miRNA discovery, a genome-wide search for miRNA candidates involved in seed development was carried out. As a result, 17 novel miRNAs, 14 isoforms of miRNA (isomiRs) and 31 previously validated miRNAs were discovered. These novel miRNAs and isomiRs represented tissue-specific expression and the isomiRs showed significantly higher abundance than that of their miRNA counterparts in different tissues. After target prediction and degradome sequencing data-based validation, 13 novel miRNA–target pairs were further identified. Besides, five targets of 22-nt iso-gma-miR393h were found to be triggered to produce secondary trans-acting siRNA (ta-siRNAs). Summarily, our results could expand the repertoire of miRNAs with potentially important functions in soybean.

Latency (i.e., time delay) in a virtual environment is known to disrupt user performance, presence and induce simulator sickness. Thus, with emerging use of virtual rehabilitation, the target populations' latency perception thresholds need to be considered to fully understand and possibly control the implications of latency in a Virtual Rehabilitation environment. We present a study that quantifies the latency discrimination thresholds of a yet untested population-a specific subset of mobility impaired participants where participants suffer from Multiple Sclerosis-and compare the results to a control group of healthy participants. The study was modeled after previous latency discrimination research and shows significant differences in latency perception between the two populations with MS participants showing lower sensitivity to latency than healthy participants.

Virtual and Augmented Reality applications need a detailed model of the surrounding environment as well as their own location within it to provide users with immersive, interactive experiences. However, current techniques to build such models are often time-consuming, and require manual correction as the area they represent changes and evolves. As the model of the environment is often completed before the application put into use, it is unable to benefit from new information detected by the location's tracking sensors. This paper proposes a solution that utilizes aggregate position data from an area to develop that space's walkable mesh model. Participant locations were measured from Bluetooth Low Energy beacons via mobile devices, and that data set was then grouped together and filtered to produce an estimation of the total environment in the form of a two dimensional navigation mesh. The experiments produced several meshes that conformed to the walkable pathways of distinct layouts in an academic building.

A prototype of adaptive virtual environments therapy system (AVET) was developed which will enable innovative Virtual Reality (VR)-based therapy approach for children with attention deficit on the autism spectrum. Many systems have successfully used VR in Autism Spectrum Disorders (ASD) therapies. Most of them use VR as an alternative way to conduct therapies by simulating traditional therapies or real-life experiences. The AVET employed VR-exclusive "impossible experiences" (e.g., a chair that deforms upon the user's gaze, a transparent human) which are not available in real world. The AVET identifies, influences the user's cognition, and delivers a customized Prolonged Exposure (PE)-style VR therapy for children with attention deficits on the autism spectrum. We conducted a preliminary evaluation to the current AVET prototype with the experts. Based on the interview feedbacks, we anticipate the AVET will have a great potential to deliver innovative and effective ASD attention training therapies.

The 9th annual IEEE 3DUI Contest focuses on the development of 3D User Interfaces (3DUIs) for three different tasks in fully immersive Virtual Environments (VEs): 1) Ladder Climbing, 2) First-Person View Flying, and 3) Tower Stacking. The 3DUI Contest is part of the 2018 IEEE Conference on Virtual Reality and 3D User Interfaces held in Reutlingen, Germany. The contest is open to anyone interested in 3DUIs, from researchers to students, enthusiasts, and professionals. The purpose of the contest is to stimulate innovative and creative solutions to challenging 3DUI problems.

Virtual environments VEs have been shown to be beneficial in physical rehabilitation, increasing motivation and the range of exercises that can be safely performed. However, little is known about how disabilities may impact a user's responses to a VE, which could affect rehabilitation motivation. Thus, the primary objective of this research is to understand how VEs affect users with mobility impairments MI. Specifically, we investigate the influence of full body avatars that have canes. To begin investigating this, we designed a VE that included a range of multimodal feedback to induce a strong sense of presence and was novel to the participants. Using this VE, we conducted a study with two different populations: eight persons with MI and eight healthy persons as a control. The healthy participants were of similar demographics e.g., age, weight, height, and previous VE experience to the participants with MI who walked with a cane i.e., on the basis of strict selection criteria to maintain homogeneity. This is one of the first studies to investigate how a VE can affect the gait of the users with MI, physiological response, presence, behavior, and the influence of avatars. Results of the study suggest generalizable guidelines for the design of VEs for users with MI. Copyright © 2014 John Wiley & Sons, Ltd.

The highly conserved eukaryotic WD40 repeat protein, Receptor for Activated C Kinase 1 (RACK1), is involved in the abscisic acid (ABA) response in Arabidopsis. However, the regulation of RACK1 and the proteins with which it interacts are poorly understood. Here, we show that RACK1B is sumoylated at four residues, Lys50, Lys276, Lys281 and Lys291. Sumoylation increases RACK1B stability and its tolerance to ubiquitination-mediated degradation in ABA response. As a result, sumoylation leads to enhanced interaction between RACK1B and RAP2.6, an AP2/ERF family transcription factor. RACK1B binds directly to the AP2 domain of RAP2.6, which alters the affinity of RAP2.6 for CE1 and GCC cis-acting regulatory elements. Taken together, our findings illustrate that protein stability controlled by dynamic post-transcriptional modification is a critical regulatory mechanism for RACK1B, which functions as scaffold protein for RAP2.6 in ABA signaling.

This research analyzes if and how the Head Related Transfer Function (HRTF) can be used to support effective Human-Computer Interaction when people in a Virtual Environment (VE) without visual feedback. If sounds can be located in a VE by using HRTF only, designing and developing considerably safer but diversified training environments might greatly benefit individuals with visual impairments. To investigate this, we ran 2 usability studies: 1) to ascertain whether the HRTF could provide sufficient position information in VEs; 2) to learn whether the HRTF could provide sufficient distance and direction information in VEs. The results showed that a continuous audio feedback could help navigate in a VE without vision feedback.

The objective of this research is evaluating a novel method to enable any sedentary commercial game to be utilized as an effective exercise game (exergame). In general there are significantly fewer exergames than sedentary games. This limits game choice and potentially has negative implications for long-term use. Previous work on exergames has been focused on deriving guidelines for designing the most effective exergames, but has rarely leveraged the mass amounts of existing sedentary games. To address this issue, we present a potentially generalizable approach to utilize sedentary commercial games as exergames. Specifically, we developed a visual overlay technique that interfaces with a Microsoft Kinect and disrupts the user's visual perception of a game as a consequence for lower exercise performance. To evaluate this approach, we conducted a two user studies with 14 and 20 undergraduate students that evaluated use in single-player and two-player competitive modes, respectively. Results indicate that although we expected intermittently blocking players' view would be annoying, it actually made the game more exciting, while at the same time providing a vigorous workout.

Previous research on healthy subjects showed that a higher sense of presence can be elicited through full body avatars versus no avatar. However, minimal avatar research has been conducted with persons with mobility impairments. For these users, Virtual Environments (VEs) and avatars are becoming more common as tools for rehabilitation. If we can maximize presence in these VEs, users may be more effectively distracted from the pain and repetitiveness of rehabilitation, thereby increasing users' motivation. To investigate this we replicated the classic virtual pit experiment and included a responsive full body avatar (or lack thereof) as a 3D user interface. We recruited from two different populations: mobility impaired persons and healthy persons as a control. Results give insight into many other differences between healthy and mobility impaired users' experience of presence in VEs.

The objective of this research is to effectively design a cane interface for assistive and rehabilitative interactions in games. Current 3D interfaces for games are not usable for many populations with physical impairments and are often not adaptable to rehabilitation exercises (e.g., balance exercise, assistive device training). To address this, we present the design of a novel cane-based 3D interface for rehabilitation games. We report results from a user study, which offers insight into the future design and potential effectiveness of canes as rehabilitation game interfaces.

We are investigating if/how Mobility Impaired (MI) persons and healthy persons respond differently to Virtual Environments (VE). Previous research on healthy users has investigated a VE's effects on presence, gait (i.e., walking patterns), and physiological responses (e.g., heart rate). However, almost all of the previous research studies have been conducted only with healthy persons. Thus, it very little is known about how MI persons respond to a VE physiologically, how a VE will affect their gait (i.e., walking patterns), or how their sense of presence may differ from healthy persons. To begin investigating this, we designed a VE that included a range of multimodal feedback to induce a strong sense of presence and was novel to the participants. Using this VE, we conducted a study with two different populations: 8 MI persons and 8 healthy persons. The healthy participants were of similar demographics (e.g., age, weight, height) to the MI participants. The MI population was symptomatically homogeneous (e.g., they all walked with canes) and no participants had cognitive impairment. This is one of the first studies to investigate how a VE can affect MI users' gait, physiological response, and presence.

One of the major challenges in designing exercise games (exergames) is maintaining engagement and motivation over time. Previous research has shown that games can increase the motivation exercise. However, these games are typically developed with limited set of specific exercises in mind, which limits genre choices, and potentially long term motivation. To address this critical issue, we are interested in employing any exercise as an interface to common, existing, sedentary games, such as a car racing game. Specifically, in this paper, we aim to take initial steps toward this goal. As a proof of concept, we developed 2 exercised based interfaces for a car racing game - a game genre minimally used for exergames. We present the evaluation of our novel exercise interfaces to the racing game, and offer general guidelines for converting common classes of sedentary games to exergames.

We are investigating how persons with mobility impairments due to multiple sclerosis (MS) experience the sense of presence in a Virtual Environment (VE). Since the mid 90's, virtual reality (VR) research has produced a rich knowledge of how design and interaction features of VEs affect presence. However, to our knowledge almost all of the previous research studies have been conducted only with healthy persons. Thus, it is not known how these factors affect the presence of mobility impaired persons, which could have implications for VR-based rehabilitation. To begin investigating this, we replicated a classic VR experiment that has been replicated many times before, but we ran the study with a different population: 10 persons with mobility impairments caused by MS and another 5 healthy persons of similar demographics (e.g., age) as our MS population. This paper compares how these two groups experience presence and discusses the differences we found in our study.

Microarray images, which allow the analysis of hybridization expressions of genes, have been one of the most widely used high-throughput technologies with many different applications. Accurate and automatic microarray image analysis is very important since researchers trust the information provided in these experiments and construct conclusions based on the results produced by the software responsible in analyzing the hybridized arrays. Every microarray image contains thousands of spots, so how to do the spots finding in microarray images accurately and automatically is very meaningful. There are always some problems, such as rotation and distortion, in a microarray image caused by mechanical errors and/or optical errors in the system. All these problems will hinder "doi"ng analysis automatically. Early research has worked out several algorithms to deal with the rotation problem, but those algorithms can not handle microarray images with distortions. In this paper, we propose a robust spots finding method to deal with both rotation and/or distortion in microarray images. The proposed method provides automatic gridding and can handle a microarray image with different type of rotation (global or sub-array rotation) and optical distortions.