Miracle-dz/UniFAR-FTUs huggingface dataset:
Pseudomonas aeruginosa: new insights into pathogenesis and host defenses.

Pseudomonas aeruginosa is a metabolically versatile bacterium that can cause a wide range of severe opportunistic infections in patients with serious underlying medical conditions. These infections are characterized by an intense neutrophilic response resulting in significant damage to host tissues and often exhibit resistance to antibiotics leading to mortality. Treatment of persistent infections is additionally hampered by adaptive resistance, due to the growth state of the bacterium in the patient including the microorganism's ability to grow as a biofilm. An array of P. aeruginosa virulence factors counteract host defences and can cause direct damage to host tissues or increase the bacterium's competitiveness. New prevention and treatment methods are urgently required to improve the outcome of patients with P. aeruginosa infections. This review describes the two main types of P. aeruginosa lung infections and provides an overview of the host response and how the genomic capacity of P. aeruginosa contributes to the pathogenesis and persistence of these infections.
The Design and Realization of Video Phone System in Embedded Platform

With the wide acceptance and development of the Internet, it is trend to integrate all of services and devices into Internet. At the same time, the fast development of communication technology that is evolved from narrowband dial-up networks to current broadband networks, from fixed PSTN phone to mobile phone and from wired network to wireless network. In the foreseeable future, the communication will be converged to IP centric networks to come up pervasive/ubiquitous network environments. In this paper, the functions of SIP protocol, video/audio codec, and video/audio streaming are integrated to realize a video/audio phone system in embedded platform. Based on the multi-thread environment, the modules of motion JPEG, SIP signaling protocol, and video/audio streaming are designed to come out a SIP-based video/audio streaming system. The system can be applied to the applications of remote surveillance, digital door phone, interphone, and Internet phone.
Hierarchical Verb Clustering Using Graph Factorization

Most previous research on verb clustering has focussed on acquiring flat classifications from corpus data, although many manually built classifications are taxonomic in nature. Also Natural Language Processing (nlp) applications benefit from taxonomic classifications because they vary in terms of the granularity they require from a classification. We introduce a new clustering method called Hierarchical Graph Factorization Clustering (hgfc) and extend it so that it is optimal for the task. Our results show that Hgfc outperforms the frequently used agglomerative clustering on a hierarchical test set extracted from VerbNet, and that it yields state-of-the-art performance also on a flat test set. We demonstrate how the method can be used to acquire novel classifications as well as to extend existing ones on the basis of some prior knowledge about the classification.
depmixS4: An R Package for Hidden Markov Models

depmixS4 implements a general framework for defining and estimating dependent mixture models in the R programming language. This includes standard Markov models, latent/hidden Markov models, and latent class and finite mixture distribution models. The models can be fitted on mixed multivariate data with distributions from the glm family, the (logistic) multinomial, or the multivariate normal distribution. Other distributions can be added easily, and an example is provided with the exgaus distribution. Parameters are estimated by the expectation-maximization (EM) algorithm or, when (linear) constraints are imposed on the parameters, by direct numerical optimization with the Rsolnp or Rdonlp2 routines.
What Drives the Crowd? A Meta-Analysis of the Motivation of Participants in Crowdsourcing

This paper presents the findings from a meta-analysis of the motivation of participants in crowdsourcing. We analysed quantitative primary studies of participation in crowdsourcing using metaanalytical statistical techniques. The findings of the meta-analysis are aggregated knowledge claims as far as they can be made based on the analysed studies and the available data. The findings show which intrinsic and extrinsic motivational factors are important, to which degree they are influential, and how much they are dependent on the particular context and type of crowdsourcing.
Rational Design of Push-Pull Fluorene Dyes: Synthesis and Structure-Photophysics Relationship.

Our work surveyed experimental and theoretical investigations to construct highly emissive D-π-A (D=donor, A=acceptor) fluorenes. The synthetic routes were optimised to be concise and gram-scalable. The molecular design was first rationalised by varying the electron-withdrawing group from an aldehyde, ketotriazole or succinyl to methylenemalonitrile or benzothiadiazole. The electron-donating group was next varied from aliphatic or aromatic amines to saturated cyclic amines ranging from aziridine to azepane. Spectroscopic studies correlated with TD-DFT calculations provided the optimised structures. The selected push-pull dyes exhibited visible absorptions, significant brightness, important solvatofluorochromism, mega-Stokes shifts (>250 nm) and dramatic shifts in emission to the near-infrared. The current library includes the comprehensive characterization of 16 prospective dyes for fluorescence applications. Among them, several fluorene derivatives bearing different conjugation anchors were tested for coupling and demonstrated to preserve the photophysical responses once further bound.
Factors associated with nonmelanoma skin cancer following renal transplantation in Queensland, Australia.

BACKGROUND Caucasian renal transplant recipients living in Queensland, Australia, have the highest risk of nonmelanoma skin cancer in the world. OBJECTIVE To determine clinical and environmental factors associated with posttransplantation nonmelanoma skin cancer in Queensland. METHODS 361 Caucasian adult recipients completed a structured interview and full skin examination. Skin cancer details were obtained from hospital records. RESULTS Squamous cell carcinoma was strongly associated with blue or hazel eyes, time resident in a hot climate, and pretransplantation squamous cell carcinoma; tumor numbers were associated with birth in a hot climate, childhood sunburn, pretransplantation actinic keratoses, and smoking. The risk of basal cell carcinoma was strongly associated with acute or intermittent sun exposure during childhood and pretransplantation basal cell carcinoma; numbers were associated with blue or hazel eyes, time spent living in a hot climate, and male gender. CONCLUSION Clinical and environmental factors can be used to identify recipients at risk of nonmelanoma skin cancer in Queensland.
Robust Person Detection by Classifier Cubes and Local Verification ∗

Classifier grids have shown to be an alternative to sliding window approaches for object detection from static cameras. However, existing approaches neglected two essential points: (a) temporal information is not used and (b) a standard non-maxima suppression is applied as post-processing step. Thus, the contribution of this paper is twofold. First, we introduce classifier cubes, which exploit the available temporal information within a classifier grid by adapting the local detection likelihood based on preceded detections. Second, we introduce a more sophisticated post-processing step to verify detection hypotheses by comparing a local figure/ground segmentation to a provided prototype model. Experiments on publicly available data demonstrate that both extensions improve the detection performance.
Influence of oxidation time on microstructure and composition of micro-arc oxidation coatings formed on zirconium

Abstract Zirconia ceramic coatings on zirconium were prepared by micro-arc oxidation (MAO) method in mixed electrolyte of calcium glycerophosphate and calcium acetate. Effect of oxidation time on microstructure, element composition and phase composition of the coatings were analysised by X-ray diffraction, scanning electron microscopy, Raman spectroscopy, respectively. The elemental composition of the coatings included Zr, O, Ca, and P. As oxidation time increased, Ca and P content of coatings correspondingly increased, and content of Zr reduced. The fabricated coatings with thickness from 20 to 30 μm were composed of c-ZrO2 and t-ZrO2, only trace amounts of m-ZrO2 phase were detected. Owing to the porous structure and components of coatings, ZrO2 coatings prepared by this method may provide available possibilities applied to biomedical materials.
Regulation of Nucleotide Excision Repair by Nuclear Lamin B1

The nuclear lamins play important roles in the structural organization and function of the metazoan cell nucleus. Recent studies on B-type lamins identified a requirement for lamin B1 (LB1) in the regulation of cell proliferation in normal diploid cells. In order to further investigate the function of LB1 in proliferation, we disrupted its normal expression in U-2 OS human osteosarcoma and other tumor cell lines. Silencing LB1 expression induced G1 cell cycle arrest without significant apoptosis. The arrested cells are unable to mount a timely and effective response to DNA damage induced by UV irradiation. Several proteins involved in the detection and repair of UV damage by the nucleotide excision repair (NER) pathway are down-regulated in LB1 silenced cells including DDB1, CSB and PCNA. We propose that LB1 regulates the DNA damage response to UV irradiation by modulating the expression of specific genes and activating persistent DNA damage signaling. Our findings are relevant to understanding the relationship between the loss of LB1 expression, DNA damage signaling, and replicative senescence.
Network coding: Connections between information theory and estimation theory

In this paper, we prove the existence of fundamental relations between information theory and estimation theory for network-coded flows. When the network is represented by a directed graph g = (V, ε) and under the assumption of uncorrelated noise over information flows between the directed links connecting transmitters, switches (relays), and receivers. We unveil that there yet exist closed-form relations for the gradient of the mutual information with respect to different components of the system matrix M. On the one hand, this result opens a new class of problems casting further insights into effects of the network topology, topological changes when nodes are mobile, and the impact of errors and delays in certain links into the network capacity which can be further studied in scenarios where one source multi-sinks multicasts and multi-source multicast where the invertibility and the rank of matrix M plays a significant role in the decoding process and therefore, on the network capacity. On the other hand, it opens further research questions of finding precoding solutions adapted to the network level.
Balloon dilatation of critical left heart stenoses in low birthweight infants

We describe the results of balloon angioplasty in 5 infants with body weights of 850‐2400 g. Three patients with severe aortic valve stenosis and two patients with isthmic coarctation of the aorta experienced relief of stenosis. Two patients with aortic valve stenosis developed thrombosis of the femoral artery; however, complete resolution of the compromised pulse occurred following thrombolytic therapy. In both patients with isthmic coarctation, pulses on the right leg remained diminished. All patients are doing well 0.28 to 3.32 y after the procedure; none has required additional therapy. Our results in a limited number of consecutive low birthweight infants show that balloon dilatation is feasible and can be performed successfully even in neonates with body weights <1500g. According to our experience, balloon dilatation in infants with body weights >2000 g does not differ significantly from standard procedures. In very small infants, however, balloon angioplasty requires special precautions to avoid temperature loss. Arterial access is the major problem in small children, and requires further improvement.
Expectation propagation for nonstationary heteroscedastic Gaussian process regression

This paper presents a novel approach for approximate integration over the uncertainty of noise and signal variances in Gaussian process (GP) regression. Our efficient and straightforward approach can also be applied to integration over input dependent noise variance (heteroscedasticity) and input dependent signal variance (non-stationarity) by setting independent GP priors for the noise and signal variances. We use expectation propagation (EP) for inference and compare results to Markov chain Monte Carlo in two simulated data sets and three empirical examples. The results show that EP produces comparable results with less computational burden.
Policymaking as design in complex systems - the international climate change regime

This paper explores policymaking as a design process in complex systems using the example of the international climate policy regime. Applying Johnson's (2008) framework on science and the designing of policy for complex futures, we establish that the evolution of international climate policy displays some characteristics of an ad hoc complexity-science policy-design process. The IPCC's emissions scenario approach is used as an example of the current climate-science policy regime's approach to dealing with policy uncertainty. We conclude that such an approach fails to capture the true relationships between policymakers, the complex models they seek to design and the actual uncertainty inherent in the environment. Further, we conclude that more formal linkages between climate policymaking and complex systems science could generate valuable new insights for both policymakers and scientists.
On decomposing speech into modulated components

We model a segment of filtered speech signal as a product of elementary signals as opposed to a sum of sinusoidal signals. Using this model, one can better appreciate the basic relationships between envelopes and phases or instantaneous frequencies (IFs) of signals. These relationships reveal some interesting properties of the signal's modulations. For instance, if the contribution due to a signal's envelope, specifically the Hilbert transform of its log-envelope, is removed from the signal's phase, then the resulting signal's IF is strictly positive. In addition, filtered speech signal having a bandwidth of B Hz can be essentially represented by the log-envelope and IF that have the same B Hz bandwidths. We extend the above ideas to decompose speech into modulated components. Specifically, a bank of data-adaptive filters (in a cross-coupled configuration) are used to decompose speech into its components; each adaptive filter is a simple single resonance bandpass filter (whose center-frequency or pole-location closely follows the desired formant frequency) supplemented by an adaptive all-zero filter (whose zero-locations sufficiently reduce unwanted leakage from neighboring formants). The filtered components are then represented by their respective log-envelopes and positive IFs; these small number of modulations closely approximate the speech signal.
The distribution of particles characterized by size and free mobility within polydisperse populations of protein‐polysaccharide conjugates, determined from two‐dimensional agarose electropherograms

New approaches for the characterization of polydisperse particle populations are presented Preliminary reports of this study were presented at the American Electrophoresis Society Meeting, Washington DC, USA, July 6–11, 1989; at the NIH/ADAMHA‐Industry Collaboration Forum, Bethesda, Maryland, USA, October 3, 1989; at the Electrophoresis Forum '89, Munich Germany, October 23–25, 1989; and at Frontiers in Bioprocessing II, Boulder, Colorado, USA, June 17–21, 1990. The investigated samples contain virus‐sized protein‐polysaccharide conjugates which had previously been prepared as immunogens against bacterial meningitis (Hib). The analysis is based on two‐dimensional agarose electrophoresis (Serwer‐type). This method, like the one of O'Farrell, achieves a separation according to size and charge. It relies on a different principle, however, and is applicable to nondenatured particles which are 100 to more than 1000 times larger in mass than regular uncrosslinked proteins. Data from stained gel patterns are evaluated by the computer program ELPHOFIT, which makes it possible to standardize the gel and to construct a nomogram which defines every position on the gel in terms of particle size and free mobility (related to surface net charge density). The output of ELPHOFIT, consisting of nomogram parameters, is transferred to the image processing program GELFIT. This software is used to evaluate the computer images obtained by digitizing the stained gel patterns: (i) The nomogram is electronically superimposed on the computer image. (ii) The gel pattern is transformed from a curvilinear to a rectangular coordinate system of particle size and free mobility. The center of gravity as well as density maxima are given in coordinates of particle size and free mobility. Ranges of grey levels can be accentuated by adding 16 pseudocolors. (iii) Using surface‐stripping techniques, GELFIT provides an estimate for the number of major subpopulations within each preparation. (iv) Numerical values or the distribution of particle size and free mobility are determined. Using program IMAGE, the quantitative physical assessment of a given conjugate preparation is presented in the form of a computer‐generated three‐dimensional plot, the shape of which serves to identify and characterize the preparation visually. The data analysis based on digitized two‐dimensional gel patterns is automated to an extent that a technician can perform routine evaluations. It uses the Macintosh II personal computer.
The effects of web site aesthetics and shopping task on consumer online purchasing behavior

This research-in-progress investigates the effects of website aesthetics and shopping task type on consumer attitude towards electronic shopping sites. The conceptualization of website aesthetics is based on the two-dimensional structure, namely, classical and expressive aesthetics, proposed by Lavie and Tractinsky (2004). The online shopping tasks are categorized as hedonic versus utilitarian shopping tasks. A pre-test was conducted for selection of utilitarian and hedonic products. Based on the results of the pre-test, a laboratory experiment was designed to capture the effects of website aesthetics on online consumer purchasing behavior across different shopping tasks.
Adaptive information-sharing for privacy-aware mobile social networks

Personal and contextual information are increasingly shared via mobile social networks. Users' locations, activities and their co-presence can be shared easily with online "friends", as their smartphones already access such information from embedded sensors and storage. Yet, people usually exhibit selective sharing behavior depending on contextual attributes, thus showing that privacy, utility, and usability are paramount to the success of such online services. In this paper, we present SPISM, a novel information-sharing system that decides (semi-)automatically whether to share information with others, whenever they request it, and at what granularity. Based on active machine learning and context, SPISM adapts to each user's behavior and it predicts the level of detail for each sharing decision, without revealing any personal information to a third-party. Based on a personalized survey about information sharing involving 70 participants, our results provide insight into the most influential features behind a sharing decision. Moreover, we investigate the reasons for the users' decisions and their confidence in them. We show that SPISM outperforms other kinds of global and individual policies, by achieving up to 90% of correct decisions.
Optical microvariability of EGRET blazars

We present results of a photometric CCD study of the incidence of microvariability in the optical emission of a sample of 20 blazars detected at gamma-ray energies by the EGRET instrument of the Compton Gamma-Ray Observatory. We have observed strong outbursts in some sources, but many others displayed no significant variability on timescales of hours. The typical minimum timescale results to be of ∼ several hours, not tens of minutes as claimed by some authors. The duty cycle for optical intranight microvariations of gamma- ray blazars, as estimated from our observations, seems to be ∼ 50 %, lower than what is usually assumed. For night-to-night variations, instead, the duty cycle approaches to what is observed in radio-selected BL Lacs and flat-spectrum radio quasars (i.e. ∼ 70 %).
Arrival and departure dynamics in social networks

In this paper, we consider the natural arrival and departure of users in a social network, and ask whether the dynamics of arrival, which have been studied in some depth, also explain the dynamics of departure, which are not as well studied. Through study of the DBLP co-authorship network and a large online social network, we show that the dynamics of departure behave differently from the dynamics of formation. In particular, the probability of departure of a user with few friends may be understood most accurately as a function of the raw number of friends who are active. For users with more friends, however, the probability of departure is best predicted by the overall fraction of the user's neighborhood that is active, independent of size. We then study global properties of the sub-graphs induced by active and inactive users, and show that active users tend to belong to a core that is densifying and is significantly denser than the inactive users. Further, the inactive set of users exhibit a higher density and lower conductance than the degree distribution alone can explain. These two aspects suggest that nodes at the fringe are more likely to depart and subsequent departure are correlated among neighboring nodes in tightly-knit communities.
Surface Deformation Models for Nonrigid 3D Shape Recovery

Three-dimensional detection and shape recovery of a nonrigid surface from video sequences require deformation models to effectively take advantage of potentially noisy image data. Here, we introduce an approach to creating such models for deformable 3D surfaces. We exploit the fact that the shape of an inextensible triangulated mesh can be parameterized in terms of a small subset of the angles between its facets. We use this set of angles to create a representative set of potential shapes, which we feed to a simple dimensionality reduction technique to produce low-dimensional 3D deformation models. We show that these models can be used to accurately model a wide range of deforming 3D surfaces from video sequences acquired under realistic conditions.
MAC-aware routing metric for 802.11 wireless mesh networks

We develop a new wireless link quality metric, ECOT (Estimated Channel Occupancy Time) that enables a high throughput route setup in wireless mesh networks. The key feature of ECOT is being applicable to diverse mesh network environments where IEEE 802.11 MAC (Medium Access Control) variants are used. We take into account the detailed operational features of various 802.11 MAC protocols, such as 802.11 DCF (Distributed Coordination Function), 802.11e EDCA (Enhanced Distributed Channel Access) with BACK (Block Acknowledgment), and 802.11n A-MPDU (Aggregate MAC Protocol Data Unit), and derive an integrated link metric that enables finding maximum throughput end-to-end routes. Through simulations in randomized topological environments, we evaluate the performance of the proposed link metric and routing strategy to demonstrate that our proposed schemes can achieve up to 354.4% throughput gain over existing ones.