Miracle-dz/UniFAR-FTUs huggingface dataset:
Purification and Characterization of Suicin 65, a Novel Class I Type B Lantibiotic Produced by Streptococcus suis

Bacteriocins are antimicrobial peptides of bacterial origin that are considered as a promising alternative to the use of conventional antibiotics. Recently, our laboratory reported the purification and characterization of two lantibiotics, suicin 90–1330 and suicin 3908, produced by the swine pathogen and zoonotic agent Streptococcus suis (serotype 2). In this study, a novel bacteriocin produced by S. suis has been identified and characterized. The producing strain S. suis 65 (serotype 2) was found to belong to the sequence type 28, that includes strains known to be weakly or avirulent in a mouse model. The bacteriocin, whose production was only possible following growth on solid culture medium, was purified to homogeneity by cationic exchange and reversed-phase high-pressure liquid chromatography. The bacteriocin, named suicin 65, was heat, pH and protease resistant. Suicin 65 was active against all S. suis isolates tested, including antibiotic resistant strains. Amino acid sequencing of the purified bacteriocin by Edman degradation revealed the presence of modified amino acids suggesting a lantibiotic. Using the partial sequence obtained, a blast was performed against published genomes of S. suis and allowed to identify a putative lantibiotic locus in the genome of S. suis 89–1591. From this genome, primers were designed and the gene cluster involved in the production of suicin 65 by S. suis 65 was amplified by PCR. Sequence analysis revealed the presence of ten open reading frames, including a duplicate of the structural gene. The structural genes (sssA and sssA’) of suicin 65 encodes a 25-amino acid residue leader peptide and a 26-amino acid residue mature peptide yielding an active bacteriocin with a deducted molecular mass of 3,005 Da. Mature suicin 65 showed a high degree of identity with class I type B lantibiotics (globular structure) produced by Streptococcus pyogenes (streptococcin FF22; 84.6%), Streptococcus macedonicus (macedocin ACA-DC 198; 84.6%), and Lactococcus lactis subsp. lactis (lacticin 481; 74.1%). Further studies will evaluate the ability of suicin 65 or the producing strain to prevent experimental S. suis infections in pigs.
Living wall: programmable wallpaper for interactive spaces

The Living Wall project explores the construction and application of interactive wallpaper. Using conductive, resistive, and magnetic paints we produced wallpaper that enables us to create dynamic, reconfigurable, programmable spaces. The wallpaper consists of circuitry that is painted onto a sheet of paper and a set of electronic modules that are attached to it with magnets. The wallpaper can be used for a multitude of functional and fanciful applications involving lighting, environmental sensing, appliance control, and ambient information display.
Global sensitivity analysis of the Indian monsoon during the Pleistocene

Abstract. The sensitivity of the Indian monsoon to the full spectrum of climatic conditions experienced during the Pleistocene is estimated using the climate model HadCM3. The methodology follows a global sensitivity analysis based on the emulator approach of Oakley and O'Hagan (2004) implemented following a three-step strategy: (1) development of an experiment plan, designed to efficiently sample a five-dimensional input space spanning Pleistocene astronomical configurations (three parameters), CO2 concentration and a Northern Hemisphere glaciation index; (2) development, calibration and validation of an emulator of HadCM3 in order to estimate the response of the Indian monsoon over the full input space spanned by the experiment design; and (3) estimation and interpreting of sensitivity diagnostics, including sensitivity measures, in order to synthesise the relative importance of input factors on monsoon dynamics, estimate the phase of the monsoon intensity response with respect to that of insolation, and detect potential non-linear phenomena. By focusing on surface temperature, precipitation, mixed-layer depth and sea-surface temperature over the monsoon region during the summer season (June-July-August-September), we show that precession controls the response of four variables: continental temperature in phase with June to July insolation, high glaciation favouring a late-phase response, sea-surface temperature in phase with May insolation, continental precipitation in phase with July insolation, and mixed-layer depth in antiphase with the latter. CO2 variations control temperature variance with an amplitude similar to that of precession. The effect of glaciation is dominated by the albedo forcing, and its effect on precipitation competes with that of precession. Obliquity is a secondary effect, negligible on most variables except sea-surface temperature. It is also shown that orography forcing reduces the glacial cooling, and even has a positive effect on precipitation. As regards the general methodology, it is shown that the emulator provides a powerful approach, not only to express model sensitivity but also to estimate internal variability and detect anomalous simulations.
Integrated Analysis for Identifying Radix Astragali and Its Adulterants Based on DNA Barcoding

Radix Astragali is a popular herb used in traditional Chinese medicine for its proimmune and antidiabetic properties. However, methods are needed to help distinguish Radix Astragali from its varied adulterants. DNA barcoding is a widely applicable molecular method used to identify medicinal plants. Yet, its use has been hampered by genetic distance, base variation, and limitations of the bio-NJ tree. Herein, we report the validation of an integrated analysis method for plant species identification using DNA barcoding that focuses on genetic distance, identification efficiency, inter- and intraspecific variation, and barcoding gap. We collected 478 sequences from six candidate DNA barcodes (ITS2, ITS, psbA-trnH, rbcL, matK, and COI) from 29 species of Radix Astragali and adulterants. The internal transcribed spacer (ITS) sequence was demonstrated as the optimal barcode for identifying Radix Astragali and its adulterants. This new analysis method is helpful in identifying Radix Astragali and expedites the utilization and data mining of DNA barcoding.
Heterogeneity of brain lesions in pediatric traumatic brain injury.

OBJECTIVE Magnetic resonance imaging (MRI) provides a method to identify and quantify abnormalities resulting from traumatic brain injury (TBI). MRI abnormalities in children with TBI have not been fully characterized according to the frequency, location, and quantitative measurement of a range of pathologies critical for studies of neuropsychological outcome. Here, we report MRI findings from a large, multicenter study of childhood TBI, the Social Outcomes of Brain Injury in Kids (SOBIK) study, which compared qualitative and quantitative neuroimaging findings in 72 children with complicated mild-to-severe TBI to 52 children with orthopedic injury (OI). METHOD Qualitative analyses of MRI scans coded white matter hyperintensities (WMHs), hemosiderin deposits reflecting prior hemorrhagic lesions, regions of encephalomalacia and/or atrophy, and corpus callosum atrophy and traumatic shear lesions. Two automated quantitative analyses were conducted: (a) FreeSurfer methods computed volumes for total brain, white matter (WM), gray matter (GM), corpus callosum, ventricles, amygdala, hippocampus, basal ganglia, and thalamus along with a ventricle-to-brain ratio (VBR); and (b) voxel-based morphometry (VBM) to identify WM, GM, and cerebrospinal fluid. We also examined performance on the Processing Speed Index (PSI) from the Wechsler Intelligence Scale for Children, Fourth Edition, in relation to the above-mentioned neuroimaging variables. RESULTS WMHs, hemosiderin deposits, and focal areas of encephalomalacia or atrophy were common in children with TBI, were related to injury severity, and were mostly observed within a frontotemporal distribution. Quantitative analyses showed volumetric changes related to injury severity, especially ventricular enlargement and reduced corpus callosum volume. VBM demonstrated similar findings, but, in addition, GM reductions in the inferior frontal, basal forebrain region, especially in the severe TBI group. The complicated mild TBI group showed few differences from the OI group. PSI was significantly associated with global atrophy, as measured by VBR. CONCLUSION MRI findings after childhood TBI are diverse and particularly influenced by injury severity, and they involve common features, group heterogeneity, and individual variability.
The Solution Design Using USB Key for Network Security Authentication

In recent years the identifying technology based on the USB Key has developed into a convenient, secure and reliable one. This paper, therefore, by applying this very technology, offers a solution to online identification, renders a way of actually realizing the task, builds a logical model for it, and provides a specific program as an example by employing ASP as a language, thus efficiently accomplishing the intended job.
Pulsed inductively coupled chlorine plasmas in the presence of a substrate bias

Pulsed inductively coupled plasmas (ICPs) sustained in electronegative gas mixtures using a substrate bias are being investigated to achieve improved etching characteristics in microelectronics fabrication. Experiments have shown that electron temperatures in pulsed ICPs without a substrate bias monotonically decrease during the afterglow. Under select conditions with a substrate bias, electron temperatures increase in the late afterglow. These trends suggest a transition in power deposition from inductive to capacitive. To investigate these processes, a two-dimensional, computationally parallel model was developed for pulsed ICPs. Results for Cl2 plasmas indicate that with a substrate bias the sheath thickness and speed, and hence electron heating, increase during the afterglow as the electron density decays. When the sheath reaches a critical thickness, capacitive electron heating begins.
Global pose estimation using multi-sensor fusion for outdoor Augmented Reality

Outdoor Augmented Reality typically requires tracking in unprepared environments. For global registration, Global Positioning System (GPS) is currently the best sensing technology, but its precision and update rate are not sufficient for high quality tracking. We present a system that uses Kalman filtering for fusion of Differential GPS (DGPS) or Real-Time Kinematic (RTK) based GPS with barometric heights and also for an inertial measurement unit with gyroscopes, magnetometers and accelerometers to improve the transient oscillation. Typically, inertial sensors are subjected to drift and magnetometer measurements are distorted by electro-magnetic fields in the environment. For compensation, we additionally apply a visual orientation tracker which is drift-free through online mapping of the unknown environment. This tracker allows for correction of distortions of the 3-axis magnetic compass, which increases the robustness and accuracy of the pose estimates. We present results of applying this approach in an industrial application scenario.
Size estimation of space target using cross-range profile

The size estimation of space target is useful to help monitor the collision of space targets. The traditional methods cannot obtain accurate size of three-axis stabilized targets via narrow-band radar. This paper presents a new algorithm based on cross-range profile. Through single range cell motion compensation and cross-range scaling, we can finally make the estimation of cross-range length. Simulation results verify the effectiveness of the algorithm.
Predicting Pedestrian Trajectories for Robot Navigation ( Extended Abstract )

We introduce a novel online method to predict pedestrian trajectories using agent-based velocity-space reasoning for improved human-robot interaction and collision-free navigation. Our formulation uses velocity obstacles to model the trajectory of each moving pedestrian in a robot’s environment and improves the motion model by adaptively learning relevant parameters based on sensor data. The resulting motion model for each agent is computed using statistical inferencing techniques, including a combination of Ensemble Kalman filters and a maximum-likelihood estimation algorithm. This allows a robot to learn individual motion parameters for every agent in the scene at interactive rates. We highlight the performance of our approach for collision-free robot navigation among pedestrians based on noisy, sparsely-sampled data and highlight the results in our simulator.
Reversible binding and rapid diffusion of proteins in complex with inositol lipids serves to coordinate free movement with spatial information

Polyphosphoinositol lipids convey spatial information partly by their interactions with cellular proteins within defined domains. However, these interactions are prevented when the lipids' head groups are masked by the recruitment of cytosolic effector proteins, whereas these effectors must also have sufficient mobility to maximize functional interactions. To investigate quantitatively how these conflicting functional needs are optimized, we used different fluorescence recovery after photobleaching techniques to investigate inositol lipid–effector protein kinetics in terms of the real-time dissociation from, and diffusion within, the plasma membrane. We find that the protein–lipid complexes retain a relatively rapid (∼0.1–1 µm2/s) diffusion coefficient in the membrane, likely dominated by protein–protein interactions, but the limited time scale (seconds) of these complexes, dictated principally by lipid–protein interactions, limits their range of action to a few microns. Moreover, our data reveal that GAP1IP4BP, a protein that binds PtdIns(4,5)P2 and PtdIns(3,4,5)P3 in vitro with similar affinity, is able to “read” PtdIns(3,4,5)P3 signals in terms of an elongated residence time at the membrane.
Feature Selection in Sentiment Analysis

In this article, we propose a new method for feature selection and sentiment classi- fication. To identify the most salient features belonging to the specific categories, we use the Z score measure. Based on this score, we can identify confident features and use the Infor- mation Gain (IG) measure to obtain scores for terms appearing in the neighborhood of the confident features. Based on this information, we propose a new weighting scheme to per- form sentiment classification. The proposed feature selection and classification method was evaluated on two publicly available datasets using various text representation schemes. Accuracy rates over 10 fold cross-validation indicate that the proposed approach performs on the same level, and sometimes outperforms, other schemes like SVM and Naive Bayes. RESUME . Dans cette communication, nous proposons une nouvelle methode pour la selection des termes et la classification automatique de sentiments. Pour determiner les caracteristiques les plus adequates d'une categorie, nous nous appuyons sur le score Z. Cette mesure nous permet de definir les termes pertinents et, recourant a la mesure du gain d'information, nous pouvons egalement evaluer les termes dans le voisinage des termes pertinents. Sur ces deux elements, nous proposons un nouveau modele de classification. Notre modele a ete evalue en recourant a deux collections tests et sur la base de plusieurs representations. La performance de notre modele (validation croisee) s'avere egale voire superieure a des approches connues basees sur le modele SVM ou Naive Bayes.
The association between school attendance, HIV infection and sexual behaviour among young people in rural South Africa

Objectives: To investigate whether the prevalence of HIV infection among young people, and sexual behaviours associated with increased HIV risk, are differentially distributed between students and those not attending school or college. Design: A random population sample of unmarried young people (916 males, 1003 females) aged 14–25 years from rural South Africa in 2001. Methods: Data on school attendance and HIV risk characteristics came from structured face-to-face interviews. HIV serostatus was assessed by oral fluid ELISA. Logistic regression models specified HIV serostatus and high-risk behaviours as outcome variables. The primary exposure was school attendance. Models were adjusted for potential confounders. Results: HIV knowledge, communication about sex and HIV testing were similarly distributed among students and non-students. The lifetime number of partners was lower for students of both sexes (adjusted odds ratio (aOR) for more than three partners for men 0.67; 95% CI 0.44 to 1.00; aOR for more than two partners for women 0.69; 95% CI 0.46 to 1.04). Among young women, fewer students reported having partners more than three years older than themselves (aOR 0.58; 95% CI 0.37 to 0.92), having sex more than five times with a partner (aOR 0.57; 95% CI 0.37 to 0.87) and unprotected intercourse during the past year (aOR 0.60; 95% CI 0.40 to 0.91). Male students were less likely to be HIV positive than non-students (aOR 0.21; 95% CI 0.06 to 0.71). Conclusions: Attending school was associated with lower-risk sexual behaviours and, among young men, lower HIV prevalence. Secondary school attendance may influence the structure of sexual networks and reduce HIV risk. Maximising school attendance may reduce HIV transmission among young people.
Multiple In Vivo Biological Processes Are Mediated by Functionally Redundant Activities of Drosophila mir-279 and mir-996

While most miRNA knockouts exhibit only subtle defects, a handful of miRNAs are profoundly required for development or physiology. A particularly compelling locus is Drosophila mir-279, which was reported as essential to restrict the emergence of CO2-sensing neurons, to maintain circadian rhythm, and to regulate ovarian border cells. The mir-996 locus is located near mir-279 and bears a similar seed, but they otherwise have distinct, conserved, non-seed sequences, suggesting their evolutionary maintenance for separate functions. We generated single and double deletion mutants of the mir-279 and mir-996 hairpins, and cursory analysis suggested that miR-996 was dispensable. However, discrepancies in the strength of individual mir-279 deletion alleles led us to uncover that all extant mir-279 mutants are deficient for mature miR-996, even though they retain its genomic locus. We therefore engineered a panel of genomic rescue transgenes into the double deletion background, allowing a pure assessment of miR-279 and miR-996 requirements. Surprisingly, detailed analyses of viability, olfactory neuron specification, and circadian rhythm indicate that miR-279 is completely dispensable. Instead, an endogenous supply of either mir-279 or mir-996 suffices for normal development and behavior. Sensor tests of nine key miR-279/996 targets showed their similar regulatory capacities, although transgenic gain-of-function experiments indicate partially distinct activities of these miRNAs that may underlie that co-maintenance in genomes. Altogether, we elucidate the unexpected genetics of this critical miRNA operon, and provide a foundation for their further study. More importantly, these studies demonstrate that multiple, vital, loss-of-function phenotypes can be rescued by endogenous expression of divergent seed family members, highlighting the importance of this miRNA region for in vivo function.
An Improved Privacy-Preserving Navigation Protocol in {VANET}s

Recent advance of vehicular technology offers opportunities for developing new navigation systems to overcome the problems of popular global positioning system (GPS) based navigation systems. In order to integrate vehicular technology into conventional GPS-based navigation systems securely, a secure and privacy-preserving navigation protocol that utilizes the real-time road information collected by a vehicular ad hoc network (VANET) was proposed in recent year. In this paper, we address the limitations of the previous work and propose an improved secure and privacy-preserving navigation protocol in VANETs. In particular, we focus on eliminating the system master secret distribution and update procedures for anonymous credential acquisition, and the need of an additional tamperproof device to use and store the system master key. Moreover, the proposed protocol does not need conventional public key certificates, which put a heavy burden of pubic key management over a VANET. In order to achieve these goals, we consider the concept of a two person multisignature and identity-based cryptographic schemes as our building blocks.
Geography preservice teachers’ disposition toward teaching spatial thinking through geography: a comparison between China and Korea

ABSTRACT Although geography education researchers in both China and Korea acknowledge that the education of spatial thinking and the development of teachers’ dispositions toward teaching spatial thinking are important, very few studies are available on the topic. This article examines the dispositions of Chinese and Korean geography preservice teachers’ dispositions toward teaching spatial thinking through geography, and it identifies the similarities and differences between the two countries. A survey was conducted with 979 Chinese and 323 Korean geography preservice teachers using the Teaching Spatial Thinking through Geography Disposition Inventory. Overall, both Chinese and Korean preservice teachers showed low-to-moderate dispositions toward teaching spatial thinking in their future classrooms. Chinese participants exhibited more positive dispositions in all five subcategories of the disposition inventory than did their Korean counterparts. Participants from both countries expressed low confidence in utilizing geospatial technologies. No specific score differences were observed by gender, grade level, and overall geography course experiences. The results reveal the current conditions of spatial thinking education in China and Korea and will help to establish strategies for successful spatial thinking education in geography in the future.
Cluster Computing using Intel Concurrent Collections

The Intel Corporation is developing a new parallel software and compiler called Concurrent Collections (CnC) to make programming in parallel easier for the user. CnC provides a system of collections comprised of steps, items, and tags. A CnC user specifies their algorithm in a graph representation using these constructs. Using this graph of dependencies, CnC automatically identifies parallelizable code segments and executes code in parallel. The present work focuses on the distributed version of CnC, where parallel code is run across multiple compute nodes. Specific accomplishments included getting distributed CnC working on the cluster tara in the UMBC High Performance Computing Facility, running timing tests, analyzing the data, and creating a generalized portable version of the distributed CnC code. This work allows a user in the distributed mode to have independent control over the number of threads, cores, and nodes to be used by a program. Several performance studies were ran in order to analyze the efficiency of the parallelism. Results for a parameter study show that Distributed CnC achieves a near-ideal speed-up for an increasing number of nodes.
Reduced Depth and Visual Hulls of Complex 3D Scenes

Depth and visual hulls are useful for quick reconstruction and rendering of a 3D object based on a number of reference views. However, for many scenes, especially multi‐object, these hulls may contain significant artifacts known as phantom geometry. In depth hulls the phantom geometry appears behind the scene objects in regions occluded from all the reference views. In visual hulls the phantom geometry may also appear in front of the objects because there is not enough information to unambiguously imply the object positions.