Miracle-dz/UniFAR-FTUs huggingface dataset:
Small RNA Profile in Moso Bamboo Root and Leaf Obtained by High Definition Adapters

Moso bamboo (Phyllostachy heterocycla cv. pubescens L.) is an economically important fast-growing tree. In order to gain better understanding of gene expression regulation in this important species we used next generation sequencing to profile small RNAs in leaf and roots of young seedlings. Since standard kits to produce cDNA of small RNAs are biased for certain small RNAs, we used High Definition adapters that reduce ligation bias. We identified and experimentally validated five new microRNAs and a few other small non-coding RNAs that were not microRNAs. The biological implication of microRNA expression levels and targets of microRNAs are discussed.
APIDiff: Detecting API breaking changes

Libraries are commonly used to increase productivity. As most software systems, they evolve over time and changes are required. However, this process may involve breaking compatibility with previous versions, leading clients to fail. In this context, it is important that libraries creators and clients frequently assess API stability in order to better support their maintenance practices. In this paper, we introduce APIDIFF, a tool to identify API breaking and non-breaking changes between two versions of a Java library. The tool detects changes on three API elements: types, methods, and fields. We also report usage scenarios of APIDIFF with four real-world Java libraries.
Study of an Outbreak of Highly Pathogenic Avian Influenza H5N8 in Commercial Pekin Ducks (Anas platyrhynchos domesticus) in California

SUMMARY A February 2015 outbreak of highly pathogenic avian influenza (HPAI) H5N8 in a flock of commercial Pekin ducks (Anas platyrhynchos domesticus) in California was investigated in detail. Approximately 17,349 five-wk-old ducks experienced an increased mortality from a normal of eight birds per day to 24, 18, 24, 33, and 61 birds per day, respectively, in the last 5 days prior to flock depopulation. Clinically, there was decreased water and feed consumption, and approximately 1.0% of the affected flock exhibited neurologic signs. Necropsy of five clinically ill ducks revealed pale, patchy areas on the epicardium in two birds, pale foci of necrosis in the liver of one bird, and airsacculitis in three birds. Histopathology revealed multifocal nonsuppurative encephalomyelitis, myocarditis, myositis, pancreatitis, hepatitis, and glossitis. Immunohistochemistry revealed avian influenza virus (AIV) nucleoprotein in the nucleus and cytoplasm of various cells in the aforementioned organs, as well as in the skin and feathers. Eight of the 10 sera samples tested were positive for avian influenza antibodies by agar gel immunodiffusion serology. Oropharyngeal and cloacal swabs taken from 15 birds, as well as from the lungs, livers, pancreas, and spleen, were positive for AIV by real-time reverse transcriptase (rRT) PCR. AIV was isolated and typed as Eurasian lineage HPAI H5N8, clade 2.3. 4.4, by the National Veterinary Services Laboratory, Ames, IA. Extensive surveillance of birds for AIV around the 10-km zone did not reveal any additional cases. Ducks on the affected premises were humanely euthanatized by foam and composted in-house, the houses were heated to 57 C for 4 days, and swabs were taken periodically from the compost to ensure negativity for AIV by rRT-PCR. The compost and litter were then removed, and the house was pressure cleaned, disinfected, and repopulated approximately 120 days after euthanatization of the ducks.
A flexibly projected AR system of wall-mounted buttons

User interface (UI) is an important factor for user experience (UX) because UI has s significant impact on feeling of use. Wall mounted buttons which are used as physical UI for elevators, room rights and so on. However, changing installation locations of wall mounted buttons is not easy. In addition, changing button labels and types is not easy, too. If we can change installation locations, labels and types of wall mounted buttons easily, their UX is improved. In this paper, a virtual wall-mounted button is proposed. The proposed system projects virtual wall mounted buttons on a wall by a projector. The proposed system gets user's height and change buttons' vertical position. In addition, users can change a button label and type. As a result of the user-test, the proposed system improves the problems of wall mounted buttons and has a possibility that it improves product and system UX. On the other hand, user-test shows necessity to improve buttons' visibility.
Fulminant hepatic failure: Summary of a workshop

Fulminant hepatic failure (FHF) is defined by the appearance of severe liver injury with hepatic encephalopathy in a previously healthy person. There are an estimated 2,000 cases of FHF in the United States yearly, representing 0.1% of all deaths and, perhaps, 6% of liverrelated deaths. The causes of FHF are many, the chief ones in the United States being hepatitis A; B; non‐A, non‐B and drug induced liver disease. There are no specific therapies for FHF, however, liver transplantation is recommended for situations in which spontaneous recovery appears unlikely. Factors that are valuable in assessing the likelihood of spontaneous recovery are static features such as patient age and etiology of FHF and dynamic features including encephalopathy grade, prothrombin time, and serum bilirubin. Presently, approximately 7% of all liver transplants are done for FHF and the 1‐year patient survival rates average 63%, somewhat less than survival rates for nonfulminant liver disease, averaging 78%. The management of patients with FHF is challenging, particularly important being monitoring and early treatment of infections, hemodynamic abnormalities, and brain edema. Innovative approaches to management and therapy include use of cytoprotective or antiviral medications, hepatic support systems, extracorporeal liver support, hepatocyte transplantation, auxiliary liver transplantation, and xenotransplantation. None of these are of proven benefit, but many are promising as a means to support the patient with FHF until spontaneous recovery occurs or a suitable liver graft is available for transplantation. (Hepatology 1995;21:240–252).
Distributed Data Compression in Sensor Clusters: A Maximum Independent Flow Approach

Let a cluster (network) of sensors be connected by the communication links, each link having a capacity upper bound. Each sensor observes a discrete random variable in private and one sensor serves as the cluster header or sink. Here, we formulate the problem of how to let the sensors encode their observations such that the direction of compressed data is a feasible flow towards the sink. We demonstrate that this problem can be solved in a distributed manner by adapting an existing maximum independent flow (MIF) algorithm in polynomial time. Further, we reveal that this algorithm in fact determines an optimal solution by recursively pushing the remaining randomness in the sources via unsaturated communication links towards the sink. For those networks with integral communication capacities, we propose an integral MIF algorithm which completes much faster than MIF. Finally, we point out that the nature of the data compression problem in a sensor cluster is to seek the maximum independent information flow in the intersection of two submodular polyhedra, which can be further utilized to improve the MIF algorithm in the future.
A Generalized Policy Support System and Its Hierarchy Semantics

One common characteristic of many Policy Support Systems (PSSs) is their dependency on the concept of hierarchy. Hierarchy does not need to be limited to a hierarchy of roles (subject centric) as in traditional Role-Based Access Control (RBAC). Instead, it can be applied to other aspects of PSS such as object, environment, purpose and so on. In this paper, we propose a new generalized model forPSS. The model unifies Generalized Role-Based Access Control (GRBAC) and Enterprise Privacy Practices (E-P3P) policy support systems and generalizes their hierarchy semantics.
Identifying multiclass vehicles using global positioning system data

ABSTRACT It has been previously evidenced that global positioning system (GPS) data can be used to distinguish passenger cars from delivery trucks. In this paper, a machine learning approach is proposed to use GPS data to identify multiclass vehicles, including passenger cars, single unit trucks, and multi-trailer trucks. The method is acceleration and deceleration-based since it considers the variations of acceleration and deceleration as the most effective features to classify vehicles. The overall classification result for the three vehicle classes is about 75%. The major challenge is to distinguish single unit trucks from multitrailer trucks due to their somewhat similar mobility patterns. The paper also explores the impacts of GPS sampling frequency on vehicle classification. It is found that the proposed multiclass vehicle classification can be reasonably conducted if the data are collected frequently enough (i.e., every five seconds or more frequently) to capture the major acceleration and deceleration processes. The proposed method can be considered as a low-cost and non-intrusive approach to collect vehicle class information and to potentially supplement the existing classification schemes in urban areas.
Identification of key genes and pathways in regulating immune-induced diseases of dendritic cells by bioinformatic analysis

Dendritic cells (DCs) serve crucial roles in the activation of the immune response, and imbalance in the activation or inhibition of DCs has been associated with an increased susceptibility to develop immune-induced diseases. However, the molecular mechanisms of regulating immune-induced diseases of DCs are not well understood. The aim of the present study was to identify the gene signatures and uncover the potential regulatory mechanisms in DCs. A total of 4 gene expression profiles (GSE52894, GSE72893, GSE75938 and GSE77969) were integrated and analyzed in depth. In total, 241 upregulated genes and 365 downregulated genes were detected. Gene ontology and pathway enrichment analysis showed that the differentially expressed genes (DEGs) were significantly enriched in the inflammatory response, the tumor necrosis factor (TNF) signaling pathway, the nuclear factor (NF)-κB signaling pathway and antigen processing. The top 10 hub genes were identified from the protein-protein analysis. The most significant 2 modules were filtered from the protein-protein network. The genes in 2 modules were involved in type I interferon signaling, the NF-κB signaling pathway and the TNF signaling pathway. Furthermore, the microRNA-mRNA network analysis was performed. The results of the present study revealed that the identified DEGs and pathways may improve our understanding of the mechanisms of the maturation of DCs, and the candidate hub genes that may be therapeutic targets for immune-induced diseases.
An unsupervised learning method for perceived stress level recognition based on office working behavior

The health issues in office workers regarding of working environment and working behavior have raised many concerns, both in medical field and technological field. For medical field, the concerns were related to physical injuries and stress due to either bad environment or bad working behaviors. In technological field, the main concern was to find a proper solution to prevent and raise awareness to these issues. In this paper, we discussed the possibility of using unsupervised learning for clustering office working behavior to show the relationship of the working behavior and stress level. We used the data collected from the device which include both behavior data and environment data. The results successfully demonstrated the two clusters that represents the working behavior related to either high or low stress level. The results can be used further to develop a classification model and to raise awareness in office workers.
North Atlantic Migratory Bird Flyways Provide Routes for Intercontinental Movement of Avian Influenza Viruses

Avian influenza virus (AIV) in wild birds has been of increasing interest over the last decade due to the emergence of AIVs that cause significant disease and mortality in both poultry and humans. While research clearly demonstrates that AIVs can move across the Pacific or Atlantic Ocean, there has been no data to support the mechanism of how this occurs. In spring and autumn of 2010 and autumn of 2011 we obtained cloacal swab samples from 1078 waterfowl, gulls, and shorebirds of various species in southwest and west Iceland and tested them for AIV. From these, we isolated and fully sequenced the genomes of 29 AIVs from wild caught gulls (Charadriiformes) and waterfowl (Anseriformes) in Iceland. We detected viruses that were entirely (8 of 8 genomic segments) of American lineage, viruses that were entirely of Eurasian lineage, and viruses with mixed American-Eurasian lineage. Prior to this work only 2 AIVs had been reported from wild birds in Iceland and only the sequence from one segment was available in GenBank. This is the first report of finding AIVs of entirely American lineage and Eurasian lineage, as well as reassortant viruses, together in the same geographic location. Our study demonstrates the importance of the North Atlantic as a corridor for the movement of AIVs between Europe and North America.
A Fully Integrated Shark-Fin Antenna for MIMO-LTE, GPS, WLAN, and WAVE Applications

In this study, a three-dimensional compact antenna solution for the automotive industry is proposed. The antenna solution is designed to fit in a shark-fin case and is easily fabricated from a printed circuit board and a metal sheet with low-cost process and materials. The antenna solution covers Long Term Evolution (LTE), GPS, WLAN, and Wireless Access in the Vehicular Environment (WAVE) bands (850 MHz, 1575 MHz, 2.4 GHz, and 5.9 GHz, respectively). The planar inverted-F antennas are used as multiple-input–multiple-output antennas for the LTE band due to their low-profile structure. Modified planar monopoles are used to obtain omnidirectional radiation patterns for WLAN and WAVE bands. Antenna characteristics such as return loss, isolation, and radiation pattern have been simulated and measured to confirm the possibility for use in automotive applications.
Using Drosophila to Understand Biochemical and Behavioral Responses to Exercise

The development of endurance exercise paradigms in Drosophila has facilitated study of genetic factors that control individual response to exercise. Recent work in Drosophila has demonstrated that activation of octopaminergic neurons is alone sufficient to confer exercise adaptations to sedentary flies. These results suggest that adrenergic activity is both necessary and sufficient to promote endurance exercise adaptations.
A Redescription of Serrasentis sagittifer (Rhadinorhynchidae: Serrasentinae) from Rachycentron canadum (Rachycentridae) with Comments on its Biology and its Relationship to Other Species of Serrasentis

Abstract Adult and cystacanth forms of the acanthocephalan Serrasentis sagittifer from Australian coastal waters are redescribed and verified as the same species using both molecular and morphological data. This study provides the baseline 18S rDNA, 28S rDNA, and cox1 sequence data to serve as genetic barcode for S. sagittifer. The validity of the currently recognized species of Serrasentis is discussed. The most recently described species are junior synonyms of either Serrasentis nadakali or S. sagittifer, and a number of species are species inquirenda. When using morphological characters to distinguish the species of Serrasentis, consideration needs to be given to the maturity of the specimens, since the trunk elongates and the number and distribution of the ventral combs changes as worms mature, although the proboscis armature itself does not change. A simple key to assist in the identification of species of Serrasentis is provided. Adult S. sagittifer appear to be highly host specific to the cobia, Rachycentron canadum, in northern Australian waters, whereas cystacanths have been reported from a wide range of fish species. The relationship between host length and number of cystacanths shows that most paratenic infections are acquired as young fish, most likely via a crustacean intermediate host.
Effects of low-intensity endurance and resistance training on mobility in chronic stroke survivors: a pilot randomized controlled study.

BACKGROUND Chronic stroke survivors are exposed to long-term disability and physical deconditioning, effects that may impact their independence and quality of life. Community-based programs optimizing the dose of exercise therapy that are simultaneously low risk and able to achieve high adherence should be identified. AIM We tested the hypothesis that an 8-week, community-based, progressive mixed endurance-resistance exercise program at lower cardiovascular and muscular load yielded more mobility benefits than a higher-intensity program in chronic stroke survivors. DESIGN A two-arm, parallel-group, pilot randomized, controlled clinical trial. SETTING Hospital (recruitment); community-based adapted physical activity center (training). POPULATION Thirty-five chronic stroke patients (mean age: 68.4±10.4 years; 27 males). METHODS Participants were randomized to a low-intensity experimental (LI-E; N.=18) or a high-intensity active control group (HI-C; N.=17). Patients in the LI-E group performed over-ground intermittent walking (weeks 1-8) and muscle power training with portable tools (weeks 5-8); patients in the HI-C group executed treadmill walking (weeks 1-8) and strength training with gym machines (weeks 5-8). Changes in mobility, assessed using the 6-Minute Walking Distance test, were the primary outcome. Secondary outcomes included quality of life (Short-Form-36 Questionnaire), gait speed (10-Meter Walking Test), balance (Berg Balance Scale) and muscle performance of the lower limbs (strength and power of the quadriceps and femoral biceps). RESULTS After 8 weeks, the 6MWD revealed more improvement for the LI-E group than the HI-C group (P=0.009). The SF36 physical activity domain (P=0.012) and peak power of the femoral quadriceps and biceps were also significantly improved for the LI-E group (P=0.008 and P<0.001, respectively) compared with the HI-C. Gait speed, balance and lower-limb strength increased in both groups; no significant differences were noted. The muscle power of the affected limb was the muscle parameter most correlated with mobility in the entire population. CONCLUSIONS A low-intensity exercise program exhibited better results in terms of mobility, quality of life and muscle power compared with a higher-intensity program. Data need to be confirmed in a larger trial. CLINICAL REHABILITATION IMPACT The effectiveness, low-intensity and possible implementation in poorly equipped community-based settings make the LI-E program potentially suitable for stroke survivors and frail individuals.
Epidemiologic studies of cellular telephones and cancer risk: a review

SUMMARY: Cellular telephones emit and receive radiofrequency (RF) signals between about 450 and 2200 MHz which fall in the microwave region of the electromagnetic spectrum. A RF wave from a cellular telephone contains billions of times less energy than an x-ray and is not capable of inducing ionizations or damaging DNA. The rapid and widespread use of this technology, however, has raised concern over possible adverse health effects, in particular brain cancer. A few studies which addressed this concern in the United States and Sweden are non-informative, either because the follow up was too short and numbers of cancers too small (USA) or because of serious methodological limitations (Sweden). In contrast, five well-designed epidemiologic studies have been conducted in three countries by investigators using different designs: three hospital-based case-control studies in the United States, a registry-based case-control study in Finland, and a registry-based cohort study of over 400,000 cellular phone users in Denmark. In our view, a consistent picture has emerged from these studies that appears to rule out, with a reasonable degree of certainty, a causal association between cellular telephones and cancer to date. No consistent evidence was observed for increased risk of brain cancer, meningioma, acoustic neuroma, ocular melanoma, or salivary gland cancer, examined over a wide range of exposure measures, including type of phone (analogue or digital), duration of use, frequency of use, total cumulative hours of use, tumor location and laterality (concurrence of tumor location with hand normally used during phone conversations). These methodologically sound epidemio-logic investigations have limitations associated with any non-experimental study, and although they are not the same across each of the studies, the influence of bias, confounding and uncertainties in exposure assessment cannot be completely discounted. However, increased risks of 20% or higher can be excluded with a high level of confidence. Complementing the human data are the emerging results of experimental studies which have failed to confirm earlier reports of possible adverse outcomes from RF exposure. Moreover, there is no biologically plausible mechanism to support a carcinogenic effect of non-ionizing RF waves. While the current state of the science is reassuring , ongoing case-control studies being conducted in 13 countries using a shared protocol, and continued follow-up of cohorts of cellular phone users, should provide further evidence regarding any possible carcinogenic effect associated with long-term cellular telephone use. The conclusions and viewpoints presented in the report are those of the author …
The effect of low-frequency mechanical vibration on retention in an orthodontic relapse model.

OBJECTIVE To investigate the effect of low-frequency mechanical vibration (LFMV) on the prevention of relapse after active orthodontic tooth movement, bone volume fraction (BVF), tissue density, and the integrity of periodontal ligament. MATERIALS AND METHODS Thirty male CD1, 12-week-old mice were used for the study. Mice were randomly divided into three groups: 1. control group, 2. relapse group, and 3. relapse + 30 Hz vibration group. In the control group, first molar was moved mesially for 7 days using nickel-titanium coil spring delivering 10g of force, whereas in relapse and relapse + 30 Hz groups, first molar was moved mesially for 7 days and then orthodontic force was removed and molar was allowed to relapse for 7 days. In relapse + 30 Hz group, LFMVs were applied at 30 Hz. Micro-focus computed tomography (micro-CT) was used for tooth movement measurements (relapse), BVF, and tissue density. Additionally, immunostaining for sclerostin, tartrate-resistant acid phosphatase staining, and picro-sirius red staining were performed on histological sections. RESULTS LFMV at 30 Hz showed a tendency to decrease relapse but was not statistically significant. Micro-CT analysis showed a trend towards increase in BVF and tissue density with application of LFMV. Sclerostin expression was decreased with 30 Hz vibration. Additionally, the picro-sirius staining showed that LFMV at 30 Hz helped in maintaining the thickness and integrity of collagen fibres in periodontal ligament. LIMITATIONS This is an animal study and extrapolation of the current findings to the clinical situation must be done with caution, as there is no osteonal remodelling (secondary remodelling) in mice when compared to humans. CONCLUSION There was no statistically significant difference in the amount of relapse between the relapse-only and relapse + 30 Hz groups. However, there was a trend of decrease in relapse with 30 Hz mechanical vibration.