Miracle-dz/UniFAR-FTUs huggingface dataset:
Bis-(3′-5′)-cyclic dimeric GMP-linked quorum sensing controls swarming in Vibrio parahaemolyticus

Movement over and colonization of surfaces are important survival strategies for bacteria, and many find it advantageous to perform these activities as a group, using quorum sensing to sample population size and synchronize behavior. It is puzzling however, that swarming-proficient and virulent strains of Vibrio parahaemolyticus are silenced for the vibrio archetypal pathway of quorum sensing. Here we describe the S-signal, a pheromone that can be communicated between cells in coculture to regulate surface colonization. This signal was harvested in cell-free supernatants and demonstrated to stimulate swarming gene expression at low cell density. The S-signal was generated by the pyridoxal phosphate-dependent aminotransferase ScrA; signal reception required the periplasmic binding protein ScrB and the membrane-bound GGDEF-EAL domain-containing protein ScrC. ScrC is a bifunctional enzyme that has the ability to form and degrade the second messenger bis-(3′-5′) cyclic dimeric GMP (c-di-GMP). ScrA in neighboring cells was able to alter the activity of ScrC in a ScrB-dependent manner, transforming ScrC’s repressing ability to inducing activity with respect to swarming. Conversely, cell–cell signaling repressed capsule gene expression. In summary, we report that quorum sensing can stimulate swarming in V. parahaemolyticus; it does so via an alternative pathway capable of generating an autoinducing signal that influences c-di-GMP, thereby expanding the lexicon and language of cell–cell communication.
Cooperative application for lane change maneuver on Smart Mobile devices

This paper presents a cooperative advanced driving assistance application for lane change maneuvers. The application is deployed on a smart mobile device equipped with a stereo imaging system, that implements the image processing tasks, and performs the fuzzy logic reasoning to asses the safety of the maneuver. Since cooperative driving assistance systems have gained extreme importance in the last decade, they will become an important factor to increase the road safety and traffic efficiency. Our application incorporates not only relevant vehicle dynamics information, such as: vehicle speed, yaw rate and other CAN bus specific parameters, but also external sensors' data, such as: high accuracy GPS position and localization and vehicle to vehicle (V2V) communication. The application has been tested in both simulators and real driving scenarios.
Variable Selection for Model‐Based High‐Dimensional Clustering and Its Application to Microarray Data

Summary Variable selection in high‐dimensional clustering analysis is an important yet challenging problem. In this article, we propose two methods that simultaneously separate data points into similar clusters and select informative variables that contribute to the clustering. Our methods are in the framework of penalized model‐based clustering. Unlike the classical L1‐norm penalization, the penalty terms that we propose make use of the fact that parameters belonging to one variable should be treated as a natural “group. ” Numerical results indicate that the two new methods tend to remove noninformative variables more effectively and provide better clustering results than the L1‐norm approach.
Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing

ABSTRACT Deep metagenomic shotgun sequencing has emerged as a powerful tool to interrogate composition and function of complex microbial communities. Computational approaches to assemble genome fragments have been demonstrated to be an effective tool for de novo reconstruction of genomes from these communities. However, the resultant “genomes” are typically fragmented and incomplete due to the limited ability of short-read sequence data to assemble complex or low-coverage regions. Here, we use single-molecule, real-time (SMRT) sequencing to reconstruct a high-quality, closed genome of a previously uncharacterized Corynebacterium simulans and its companion bacteriophage from a skin metagenomic sample. Considerable improvement in assembly quality occurs in hybrid approaches incorporating short-read data, with even relatively small amounts of long-read data being sufficient to improve metagenome reconstruction. Using short-read data to evaluate strain variation of this C. simulans in its skin community at single-nucleotide resolution, we observed a dominant C. simulans strain with moderate allelic heterozygosity throughout the population. We demonstrate the utility of SMRT sequencing and hybrid approaches in metagenome quantitation, reconstruction, and annotation. IMPORTANCE The species comprising a microbial community are often difficult to deconvolute due to technical limitations inherent to most short-read sequencing technologies. Here, we leverage new advances in sequencing technology, single-molecule sequencing, to significantly improve reconstruction of a complex human skin microbial community. With this long-read technology, we were able to reconstruct and annotate a closed, high-quality genome of a previously uncharacterized skin species. We demonstrate that hybrid approaches with short-read technology are sufficiently powerful to reconstruct even single-nucleotide polymorphism level variation of species in this a community. The species comprising a microbial community are often difficult to deconvolute due to technical limitations inherent to most short-read sequencing technologies. Here, we leverage new advances in sequencing technology, single-molecule sequencing, to significantly improve reconstruction of a complex human skin microbial community. With this long-read technology, we were able to reconstruct and annotate a closed, high-quality genome of a previously uncharacterized skin species. We demonstrate that hybrid approaches with short-read technology are sufficiently powerful to reconstruct even single-nucleotide polymorphism level variation of species in this a community.
Using Process Indicators to Help the Verification of Goal Fulfillment

: Process modelling is often criticized as lacking proper alignment with business goals. Although there is literature on different proposals to address the issue, the verification of this alignment remains an obstacle during process enactment. We make use of key process indicator (KPI) in a process design method to annotate processes/activities with proper information. The method derives this information from the business goals and uses it to calculate process indicators. We demonstrate through a real example, modelled with the ARIS business process model tool, how the method produces proper indicators, which should be used during process enactment.
Fuzzy Identity Based Encryption from Lattices

Cryptosystems based on the hardness of lattice problems have recently acquired much importance due to their average-case to worst-case equivalence, their conjectured resistance to quantum cryptanalysis, their ease of implementation and increasing practicality, and, lately, their promising potential as a platform for constructing advanced functionalities. In this work, we construct “Fuzzy” Identity Based Encryption from the hardness of the Learning With Errors (LWE) problem. We note that for our parameters, the underlying lattice problems (such as gapSVP or SIVP) are assumed to be hard to approximate within supexponential factors for adversaries running in subexponential time. We give CPA and CCA secure variants of our construction, for small and large universes of attributes. All are secure against selective-identity attacks in the standard model. Our construction is made possible by observing certain special properties that secret sharing schemes need to satisfy in order to be useful for Fuzzy IBE. We also discuss some obstacles towards realizing lattice-based attributebased encryption (ABE). ∗UCLA. E-mail: shweta@cs.ucla. edu Research supported in part from a DARPA/ONR PROCEED award, and NSF grants 1118096, 1065276, 0916574 and 0830803. †PARC—Palo Alto Research Center. E-mail: xb@boyen.org ‡University of Toronto. E-mail: vinodv@cs.toronto. edu §UCSD. E-mail: pvoulgar@cs.ucsd. edu ¶Queens College, CUNY. E-mail: hoeteck@cs.qc. edu. Supported by NSF CAREER Award CNS-0953626, and the US Army Research laboratory and the UK Ministry of Defence under agreement number W911NF-06-3-0001. The views and conclusions contained in this document are those of the author and should not be interpreted as representing the official policies, either expressed or implied, of the US Army Research Laboratory, the US Government, the UK Ministry of Defense, or the UK Government.
Thermal imaging of microwave power GaAs-FET with scanning thermal nanoprobe

Application of a new thermal nano-probe based on the changes of electrical resistivity of a nanometer-sized filament with temperature has been presented for the thermal imaging of microwave power active devices. The filament is integrated into an atomic force scanning probe piezoresistive type cantilever. The novel thermal probe has a spatial resolution better than 80 nm and a thermal resolution of the order of 10-3 K. The measurements have been successfully performed on a 30 fingers GaAs-MESFET with a maximum power dissipation of 2.5 W. The microwave transistor has been implemented in a circuit in such a way to prevent the undesired microwave oscillations. In this case the power dissipation is equal to the dc power input. The near-field measurements have been compared with three-dimensional finite element simulations. A good agreement between simulations and measurements is achieved.
Optimization of Feline Immunodeficiency Virus Vectors for RNA Interference

ABSTRACT RNA interference (RNAi) occurs naturally in plant and animal cells as a means for modulating gene expression. This process has been experimentally manipulated to achieve targeted gene silencing in cells, tissues, and animals, using a variety of vector systems. Here, we tested the hypothesis that vectors based on feline immunodeficiency virus (FIV) could be used for coexpression of reporter constructs and RNAi expression cassettes. We found, unexpectedly, in our initial constructs that placement of RNAi expression cassettes downstream from a polymerase II (pol II)-expressed reporter gene inhibited reporter expression but not vector titer. Through a series of intermediate vector constructs, we found that placement of the RNAi expression cassette relative to the Rev response element and the pol II expression cassette was critical for efficient RNAi and reporter gene expression. These results suggested that steric factors, including RNA structure and recruitment of competing transcriptional machinery, may affect gene expression from FIV vectors. In a second series of studies, we show that target sequence silencing can be achieved in cells transduced by FIV vectors coexpressing reporter genes and 3′ untranslated region resident microRNAs. The optimized FIV-based RNAi expression vectors will find broad use given the extensive tropism of pseudotyped FIV vectors for many cell types in vitro and in vivo.
Adapting the Edinburgh Geoparser for Historical Georeferencing

Place name mentions in text may have more than one potential referent (e.g. Peru, the country vs. Peru, the city in Indiana). The Edinburgh Language Technology Group (LTG) has developed the Edinburgh Geoparser, a system that can automatically recognise place name mentions in text and disambiguate them with respect to a gazetteer. The recognition step is required to identify location mentions in a given piece of text. The subsequent disambiguation step, generally referred to as georesolution, grounds location mentions to their corresponding gazetteer entries with latitude and longitude values, for example, to visualise them on a map. Geoparsing is not only useful for mapping purposes but also for making document collections more accessible as it can provide additional metadata about the geographical content of documents. Combined with other information mined from text such as person names and date expressions, complex relations between such pieces of information can be identified. The Edinburgh Geoparser c.
Parametric Characterization and Macroscopic Quantum Tunneling of  $\hbox{Nb}/\hbox{AlO}_{\rm x}/\hbox{Nb}$ Josephson Junctions

Parameters of Nb/AlOx/Nb Josephson including its critical current and capacitance which determine the dynamic energy consumption and speed of the superconducting electronics have been measured. The critical current of a 22 × 22 μm2 junction is 1801 ± 52 μA calculated from the dependent curve between the lifetime of zero-voltage and switching current. The specific capacitance is 0.051 ± 0.008 pF/μm2 obtained by observing Fiske self-resonant step when applied several Gauss magnetic field. Critical current distributions had been measured as a function of temperature from 900 mK to 40 mK. The distribution widths become independent of temperature below 200 mK, which indicates the transition between thermal activation and macroscopic quantum tunneling of junction phase.
Bimodal speech recognition using coupled hidden Markov models

In this paper we present a bimodal speech recognition system in which the audio and visual modalities are modeled and integrated using coupled hidden Markov models (CHMMs). CHMMs are probabilistic inference graphs that have hidden Markov models as sub-graphs. Chains in the corresponding inference graph are coupled through matrices of conditional probabilities modeling temporal influences between their hidden state variables. The coupling probabilities are both cross chain and cross time. The later is essential for allowing temporal influences between chains, which is important in modeling bimodal speech. Our bimodal speech recognition system employs a two-chain CHMM, with one chain being associated with the acoustic observations, the other with the visual features. A deterministic approximation for maximum a posteriori (MAP) estimation is used to enable fast classification and parameter estimation. We evaluated the system on a speaker independent connected-digit task. Comparing with an acoustic-only ASR system trained using only the audio channel of the same database, the bimodal system consistently demonstrates improved noise robustness at all SNRs. We further compare the CHMM system reported in this paper with our earlier bimodal speech recognition system in which the two modalities are fused by concatenating the audio and visual features. The recognition results clearly show the advantages of the CHMM framework in the context of bimodal speech recognition .
Damage detection monitoring applications in self-healing concrete structures using embedded piezoelectric transducers and recovery

The ageing, operational and ambient loadings have a great impact in the operational and maintenance cost of concrete structures. Their service life prolongation is of utmost importance and this can be efficiently achieved by using reliable and low-cost monitoring and self-healing techniques. In the present study, the ultrasonic pulse velocity (UPV) method using embedded small-size and low-cost piezoelectric PZT (lead zirconate titanate) ceramic transducers in concrete with self-healing properties is implemented for monitoring not only the setting and hardening phases of concrete since casting time, but also for the detection of damage initiation, propagation and recovery of integrity after healing. A couple of small-scale notched unreinforced concrete beams are subjected to mode-I fracture through three-point bending tests. After a 24-hour healing agent curing period, the beams are reloaded using the same loading scenario. The results demonstrate the excellent performance of the proposed monitoring technique during the hydration, damage generation and recovery periods.
The ant and the grasshopper: fast and accurate pointer analysis for millions of lines of code

Pointer information is a prerequisite for most program analyses, and the quality of this information can greatly affect their precision and performance. Inclusion-based (i.e. Andersen-style) pointer analysis is an important point in the space of pointer analyses, offering a potential sweet-spot in the trade-off between precision and performance. However, current techniques for inclusion-based pointer analysis can have difficulties delivering on this potential. We introduce and evaluate two novel techniques for inclusion-based pointer analysis---one lazy, one eager1---that significantly improve upon the current state-of-the-art without impacting precision. These techniques focus on the problem of online cycle detection, a critical optimization for scaling such analyses. Using a suite of six open-source C programs, which range in size from 169K to 2.17M LOC, we compare our techniques against the three best inclusion-based analyses--described by Heintze and Tardieu [11], by Pearce et al. [21], and by Berndl et al. [4]. The combination of our two techniques results in an algorithm which is on average 3.2 xfaster than Heintze and Tardieu's algorithm, 6.4 xfaster than Pearce et al.'s algorithm, and 20.6 faster than Berndl et al.'s algorithm. We also investigate the use of different data structures to represent points-to sets, examining the impact on both performance and memory consumption. We compare a sparse-bitmap implementation used in the GCC compiler with a BDD-based implementation, and we find that the BDD implementation is on average 2x slower than using sparse bitmaps but uses 5.5x less memory.
Baseline Characteristics of Patients With Paclitaxel-or Sirolimus-Eluting Stents Before Propensity-Score Matching *

Background—Drug-eluting stents are more effective in reducing restenosis than bare-metal stents. Less certain is the relative performance of 2 widely used drug-eluting stents—sirolimusand paclitaxel-eluting stents—in diabetic and nondiabetic patients undergoing percutaneous coronary intervention in routine clinical practice. We therefore studied the long-term effectiveness and safety of sirolimus versus paclitaxel stents overall and stratified by the absence or presence of diabetes. Methods and Results—We compared sirolimus and paclitaxel stents in a propensity-score matched cohort of 2054 pairs of patients (835 matched pairs of diabetic patients and 1219 matched pairs of nondiabetic patients) undergoing percutaneous coronary intervention in Ontario between December 1, 2003 and March 31, 2006. The cohort was derived from the Cardiac Care Network of Ontario percutaneous coronary intervention registry and linked to population-based administrative health databases. In the overall cohort, there was no difference in rates of target-vessel revascularization (P 0.47), myocardial infarction (P 0.71), or death (P 0.49). As compared with paclitaxel stents, the use of sirolimus stents was associated with a significantly lower 3-year rate of target-vessel revascularization in nondiabetic patients (8.3% versus 10.0%, P 0.01), but not in diabetic patients (12.7% versus 10.3%, P 0.07). Rates of all-cause mortality were similar in patients receiving sirolimus stents versus paclitaxel stents in both the diabetic (8.4% versus 9.2%, P 0.91) and nondiabetic (4.6% versus 3.0%, P 0.22) groups. Conclusions—In this large observational study, patients receiving paclitaxel and sirolimus stents had similar mortality rates, but nondiabetic patients receiving sirolimus stents were significantly less likely to require repeat revascularization. (Circ Cardiovasc Qual Outcomes. 2009;2:96-107.)
Progressive Enhancement of Delayed Hyperalgesia Induced by Repeated Heroin Administration: A Sensitization Process

It is difficult to conceive that tolerance and sensitization processes, two apparently opposite phenomena, can concomitantly modify one given biological process, i.e., the processing of pain. We have shown recently that opiates produce not only analgesia but also long-lasting hyperalgesia in rats. This suggests that tolerance to the analgesic effect of an opiate, especially heroin, could be in part the result of an actual sensitization of pronociceptive systems. Here, we show that both magnitude and duration of heroin-induced delayed hyperalgesia increase with intermittent heroin administrations, leading to an apparent decrease in the analgesic effectiveness of a given heroin dose. Our observation that a small dose of heroin which is ineffective for triggering a delayed hyperalgesia in non-heroin-treated rats induced an enhancement in pain sensitivity for several days after a series of heroin administrations is in agreement with the sensitization hypothesis. The effectiveness of the opioid receptor antagonist naloxone to precipitate hyperalgesia in rats that had recovered their pre-drug nociceptive value after single or repeated heroin administrations indicates that heroin-deprived rats were in a new biological state associated with a high level balance between opioid-dependent analgesic systems and pronociceptive systems. Because the NMDA receptor antagonist dizocilpine maleate (MK-801) prevented both heroin-induced long-lasting enhancement in pain sensitivity and naloxone-precipitated hyperalgesia, these findings further suggest that tolerance, sensitization, and one withdrawal symptom, hyperalgesia, are issued from a neuroadaptive process in which NMDA systems play a critical role.
Combined Promoter Methylation Analysis of CADM1 and MAL: An Objective Triage Tool for High-Risk Human Papillomavirus DNA–Positive Women

Purpose: Screening women for high-grade cervical intraepithelial neoplasia or cervical cancer (CIN3+) by high-risk human papillomavirus (hrHPV) testing has as side-effect the detection of hrHPV-positive women without clinically relevant lesions. Here, we developed an objective assay assessing the methylation status of the promoter regions of CADM1 and MAL to triage hrHPV-positive women for CIN3+. Experimental Design: In a training set (51 women with CIN3+ and 224 without CIN2+), panels consisting of one to four quantitative methylation-specific PCR (qMSP) assays (CADM1-m12,CADM1-m18,MAL-m1,MAL-m2) were analyzed. Cross-validated receiver-operating characteristics (ROC) curves were constructed and the panel with highest partial cross-validated area under the curve (AUC) was used for validation in an independent set of 236 consecutive hrHPV-positive women from a screening cohort. In the validation set, the ROC curve of the panel was compared with CIN3+ sensitivity and specificity of cytology and of cytology combined with HPV16/18 genotyping. Results: In the training set, CADM1-m18 combined with MAL-m1 was the best panel (cross-validated partial AUC = 0.719). In the validation set, this panel revealed CIN3+ sensitivities ranging from 100% (95% CI: 92.4–100) to 60.5% (95% CI: 47.1–74.6), with corresponding specificities ranging from 22.7% (95% CI: 20.2–25.2) to 83.3% (95% CI: 78.4–87.4). For cytology these were 65.8% (95% CI: 52.3–79.0) and 78.8% (95% CI: 73.7–83.1) and for cytology/HPV16/18, these were 84.2% (95% CI: 72.0–92.7) and 54.0% (95% CI: 49.2–58.7), respectively. The point estimates of both cytology and cytology/HPV16/18 were equal to the values of the ROC curve of CADM1-m18/MAL-m1. Conclusions: We developed an objective methylation marker panel that was equally discriminatory for CIN3+ as cytology or cytology with HPV16/18 genotyping in hrHPV-positive women. This opens the possibility for complete cervical screening by objective, nonmorphological molecular methods. Clin Cancer Res; 17(8); 2459–65. ©2011 AACR.