Miracle-dz/UniFAR-FTUs huggingface dataset:
Live Cell Imaging Reveals Novel Functions of Salmonella enterica SPI2-T3SS Effector Proteins in Remodeling of the Host Cell Endosomal System

Intracellular Salmonella enterica induce a massive remodeling of the endosomal system in infected host cells. One dramatic consequence of this interference is the induction of various extensive tubular aggregations of membrane vesicles, and tubules positive for late endosomal/lysosomal markers are referred to as Salmonella-induced filaments or SIF. SIF are highly dynamic in nature with extension and collapse velocities of 0.4–0.5 µm x sec−1. The induction of SIF depends on the function of the Salmonella Pathogenicity Island 2 (SPI2) encoded type III secretion system (T3SS) and a subset of effector proteins. In this study, we applied live cell imaging and electron microscopy to analyze the role of individual effector proteins in SIF morphology and dynamic properties of SIF. SIF in cells infected with sifB, sseJ, sseK1, sseK2, sseI, sseL, sspH1, sspH2, slrP, steC, gogB or pipB mutant strains showed a morphology and dynamics comparable to SIF induced by WT Salmonella. SIF were absent in cells infected with the sifA-deficient strain and live cell analyses allowed tracking of the loss of the SCV membrane of intracellular sifA Salmonella. In contrast to analyses in fixed cells, in living host cells SIF induced by sseF- or sseG-deficient strains were not discontinuous, but rather continuous and thinner in diameter. A very dramatic phenotype was observed for the pipB2-deficient strain that induced very bulky, non-dynamic aggregations of membrane vesicles. Our study underlines the requirement of the study of Salmonella-host interaction in living systems and reveals new phenotypes due to the intracellular activities of Salmonella.
Size and Bias Effects of Search Engines : Theory and Experimental Evidence Aurora

This paper analyzes equilibrium prices under incomplete and biased information provided to consumers by price-comparison search engines. Theoretical results predict a conflict of interests between users and non users of these engines. More (unbiased) information does not necessarily increase welfare. Experimental evidence supports some of the model’s predictions and rejects others. Data analysis indicates that divergence between empirical and theoretical price distributions can partly be due to systematic effects of agents’ attitudes towards risky choice. Two aspects of such attitudes are identified: a subject’s degree of risk aversion and whether the subject’s choices are compatible with theories assuming dominance. JEL classification: D43, D83, L13.
Treatment of bulimia nervosa in a primary care setting.

OBJECTIVE The authors' goal was to determine whether treatments known to be effective for bulimia nervosa in specialized treatment centers can be used successfully in primary health care settings. They examined the benefits of two treatments for bulimia: 1) fluoxetine, an antidepressant medication, and 2) guided self-help, an adaptation of cognitive behavior therapy. METHOD Ninety-one female patients in two primary care settings were randomly assigned to receive fluoxetine alone, placebo alone, fluoxetine plus guided self-help, or placebo and guided self-help. RESULTS The majority of the patients did not complete the treatment trial; many patients found the treatment program too demanding, but others indicated it was not sufficiently intensive. Patients assigned to fluoxetine attended more physician visits, exhibited a greater reduction in binge eating and vomiting, and had a greater improvement in psychological symptoms than those assigned to placebo. There was no evidence of benefit from guided self-help. CONCLUSIONS The treatment of patients with bulimia nervosa in a primary care setting is hampered by a high dropout rate. Guided self-help, a psychological treatment based on cognitive behavior therapy, appears ineffective, but treatment with fluoxetine is associated with better retention and substantial symptomatic improvement.
Romanian WordNet: New Developments and Applications

Among the existing ontologies, the multilingual lexical ontologies have a special status. Structured in a similar way to standard ontologies, the lexical ones are distinguished by the fundamental requirement that each conceptualized entity is lexicalized by one or more synonymous words (a synset) of the natural language vocabulary. Multilingually aligned wordnets, such as EuroWordNet or BalkaNet, represent one step further with great promises in the domain of multilingual processing. This paper gives an account for the development and current status of the Romanian wordnet, aligned to the Princeton WordNet 2.0 (PWN2.0), and discusses some of its applications.
A SURFACE-BASED TECHNIQUE FOR WARPING 3-DIMENSIONAL IMAGES OF THE BRAIN

We have devised, implemented and tested a fast, spatially accurate technique for calculating the high-dimensional deformation field relating the brain anatomies of an arbitrary pair of subjects. The resulting 3D deformation map can be used to quantify anatomic differences between subjects or within the same subject over time, and to transfer functional information between subjects or integrate that information on a single anatomic template. The new procedure is based on developmental processes responsible for variations in normal human anatomy, and is applicable to 3D brain images in general, regardless of modality. Hybrid surface models known as Chen surfaces (based on superquadrics and spherical harmonics) are used to efficiently initialize 3D active surfaces, and these then extract from both scans the developmentally fundamental surfaces of the ventricles and cortex. The construction of extremely complex surface deformation maps on the internal cortex is made easier by building a generic surface structure to model it. Connected systems of parametric meshes model several deep sulci whose trajectories represent critical functional boundaries. These sulci are sufficiently extended inside the brain to reflect subtle and distributed variations in neuroanatomy between subjects. The algorithm then calculates the high-dimensional volumetric warp (typically with 384x256x3 ≈ 0.1 billion degrees of freedom) deforming one 3D scan into structural correspondence with the other. Integral distortion functions are used to extend the deformation field required to elastically transform nested surfaces to their counterparts in the target scan. The algorithm’s accuracy is tested, by warping 3D MRI volumes from normal subjects and Alzheimer’s patients, and by warping full-color 1024 digital cryosection volumes of the human head onto MRI volumes. Applications are discussed, including the transfer of multi-subject 3D functional, vascular and histologic maps onto a single anatomic template, the mapping of 3D brain atlases onto the scans of new subjects, and the rapid detection, quantification and mapping of local shape changes in 3D medical images in disease, and during normal or abnormal growth and development.
Impact of semantic-aware radio resource management schemes on video streaming service

Current wireless networks have no knowledge on the type and characteristics of the specific mobile services and contents they are providing (they are agnostic). On the other hand, associated to richer content and more advanced devices, improvement of Quality of Experience (QoE) levels perceived by each user looks as one of the main goals of the different actors in the telecommunication's ecosystem. In this respect, network awareness of the transferred content types and their quality requirements can be important to deliver them fulfilling user requirements while optimizing the utilization of network resources. In this paper, we explore the effect of including semantic knowledge in the radio resource management (RRM) schemes of cellular systems as a way to reach this balance for video streaming service. To make this possible, we propose a number of semantic-aware RRM schemes using information about the video playback's current status, and investigate their performances based on the reduction of the total time of interruptions (TTI) perceived by users when a video streaming content is played. The achieved results are compared to those of the standard agnostic scheme implemented in the cellular networks. The outcomes show that incorporating semantic-aware RRM schemes, more users can receive the content provided by a network within a tolerable level of TTI, while the number of users receiving High Definition (HD) videos can be increased, which in general terms might reduce the investment in infrastructure to fulfill users' requirements.
LED modelling and input current ripple reduction of Cuk converter using magnetic coupling

Now a days LEDs are replacing traditional incandescent and fluorescent lamp in domestic and commercial applications due to their advantages of high efficiency, low power consumption and long life. The ripple content of current in both sides is reduced and performance improvement is obtained by controlling the forward current of LED using isolated/non-isolated dc-dc converters. Even though cuk and sepic converters have continuous currents on input and output sides but there exists more current ripple content on input side higher than acceptable limits. A magnetically coupled CUK converter proposed to steer the current either to input side or output side hence can have a control on ripple content of current without additional filters. This paper also analyses the effect of magnetic coupling in CUK converter. PI controller is used to control the output current of the converter. MATLAB model for the LED is modelled and used for the simulation. This paper discusses the design and simulation results for a 48W coupled inductor cuk converter at a constant switching frequency of 30kHz.
Cook up better code

The development of Smart Grid systems has proven to be a challenging task. Besides the inherent technical complexity, the involvement of different stakeholders from different disciplines is a major challenge. In order to maintain the strict security requirements, holistic systems engineering concepts and reference architectures are required that enable the integration, maintenance and evaluation of Smart Grid security. In this paper, a conceptual approach is presented on how to enable the integration of security by design in the development of Smart Grid Systems. A major cornerstone of this approach is the development of a domain-specific and standards-based modelling language on basis of the M/490 Smart Grid Architecture Model (SGAM). Furthermore, this modelling approach is utilized to develop a reference architecture model on basis of the National Institute of Standards and Technology (NIST) Logical Reference Model (LRM) with its integrated security concepts. The availability of a standards-based reference architecture model enables the instantiation of particular solutions with a profound basis for security. Moreover, it is demonstrated how such architecture models can be utilized to gain insights into potential security implications and furthermore can serve as a basis for implementation.
Knowing What to Imitate and Knowing When You Succeed

If we are to build robots that can imitate the actions of a human instructor, the robotics community must address a variety of issues. In this paper, we examine two of these issues. First, how does the robot know which things it should imitate? Second, how does the robot know when its actions are an adequate imitation of the original? We further describe an on-going research effort to implement systems for a humanoid robot that address these issues.
The Impact of Device-Width Quantization on Digital Circuit Design Using FinFET Structures

—FinFET structures enable scaling to very short gate lengths beyond 10nm, however, device-width quantization has been identified as a possible technology disrupter for its widespread adoption. Prior work has shown that the effect is more pronounced for circuits such as latches which are sensitive to the β β β β-ratio and that special tools and algorithms are required to migrate bulk CMOS designs to FinFET-based circuits. This paper investigates the effect of width granularity on functionality, performance, and power using three circuits that typify digital design: inverter network, SRAM cell, static SR flip-flop. We propose to employ HSPICE and Matlab scripts based on existing energy-delay optimization tools [6] to quantify the effects of width granularity.
A review on numerical calibration and de-embedding techniques in full-wave algorithms

This paper presents a brief review on the development of numerical calibration and de-embedding techniques. The earlier proposed short-open-calibration (SOC) technique was first implemented in the integral-equation based method of moments and extensively studied for computer-aided design of different microwave circuit structures. Unlike other de-embedding techniques, the SOC technique has no need to predefine the port discontinuities and feed network, but only consider them as a unified error box. Recent progress in this research will be discussed and clarified.
The Rapid Distraction of Attentional Resources toward the Source of Incongruent Stimulus Input during Multisensory Conflict

Neuroimaging work on multisensory conflict suggests that the relevant modality receives enhanced processing in the face of incongruency. However, the degree of stimulus processing in the irrelevant modality and the temporal cascade of the attentional modulations in either the relevant or irrelevant modalities are unknown. Here, we employed an audiovisual conflict paradigm with a sensory probe in the task-irrelevant modality (vision) to gauge the attentional allocation to that modality. ERPs were recorded as participants attended to and discriminated spoken auditory letters while ignoring simultaneous bilateral visual letter stimuli that were either fully congruent, fully incongruent, or partially incongruent (one side incongruent, one congruent) with the auditory stimulation. Half of the audiovisual letter stimuli were followed 500–700 msec later by a bilateral visual probe stimulus. As expected, ERPs to the audiovisual stimuli showed an incongruency ERP effect (fully incongruent versus fully congruent) of an enhanced, centrally distributed, negative-polarity wave starting ∼250 msec. More critically here, the sensory ERP components to the visual probes were larger when they followed fully incongruent versus fully congruent multisensory stimuli, with these enhancements greatest on fully incongruent trials with the slowest RTs. In addition, on the slowest-response partially incongruent trials, the P2 sensory component to the visual probes was larger contralateral to the preceding incongruent visual stimulus. These data suggest that, in response to conflicting multisensory stimulus input, the initial cognitive effect is a capture of attention by the incongruent irrelevant-modality input, pulling neural processing resources toward that modality, resulting in rapid enhancement, rather than rapid suppression, of that input.
Architecting Energy Efficient Servers

This dissertation investigates how energy efficient servers can be architected using current and future technology. We leverage recent trends in packaging and device technology to deliver low power and high throughput. Specifically at the package level, this dissertation looks at 3D stacking technology that has emerged as a promising solution in achieving energy efficiency by delivering high throughput at a low cost. It shows how one would leverage this new technology into a datacenter. 3D stacking technology can be used to implement a simple, low-power, high-performance chip multiprocessor suitable for throughput processing. Our proposed architecture leveraging this technology, PicoServer, employs 3D technology to bond one die containing several simple slow processing cores to multiple memory dies sufficient for a primary memory. The multiple memory dies are composed of DRAM. 3D stacking technology also enables wide low-latency buses between processors and memory. These remove the need for an L2 cache allowing its area to be re-allocated to additional simple cores. The additional cores allow the clock frequency to be lowered without impairing throughput. Lower clock frequency along with the integration of non-volatile memory in turn reduces power and means that thermal constraints, a concern with 3D stacking, are easily satisfied. The PicoServer architecture targets server applications, which exhibit a high degree of thread level parallelism. An architecture targeted to efficient throughput is ideal for this application domain. At the memory device level, this dissertation investigates how the system memory could be re-architected to reduce the rising power consumption of system memory and disk drives. Flash memory has emerged as a strong candidate to reduce system memory power while remaining cost effective than conventional system memory. This dissertation discusses how Flash could be integrated at the system level and provides insights on the architectural support for Flash in servers. Our architecture uses a two level disk cache composed of a relatively small DRAM, which includes a primary disk cache, and a Flash based secondary disk cache. Further, based on our observations, we found that the Flash based disk caches should be split into a read optimized disk cache and write optimized disk cache.
Dynamical consequences of CDM merger trees

Within the context of the standard structure formation scenario, massive present-day elliptical galaxies are sometimes thought of as the result of a major merger of spiral systems. Through extensive smooth particle hydrodynamic (SPH) simulations of merging spirals, we have explored these processes with the aim of quantifying their relaxation times. This is important, as it sets a minimum time interval between the onset of a merger and the appearance of an elliptical galaxy. We then compare this constraint with predictions of the hierarchical scenario, computed through Press-Schechter merger trees. We find evidence for elliptical systems that appear not to have been formed by a major merger of spirals.
Structure of rrn operons in pathogenic non-cultivable treponemes: sequence but not genomic position of intergenic spacers correlates with classification of Treponema pallidum and Treponema paraluiscuniculi strains

This study examined the sequences of the two rRNA (rrn) operons of pathogenic non-cultivable treponemes, comprising 11 strains of T. pallidum ssp. pallidum (TPA), five strains of T. pallidum ssp. pertenue (TPE), two strains of T. pallidum ssp. endemicum (TEN), a simian Fribourg-Blanc strain and a rabbit T. paraluiscuniculi (TPc) strain. PCR was used to determine the type of 16S–23S ribosomal intergenic spacers in the rrn operons from 30 clinical samples belonging to five different genotypes. When compared with the TPA strains, TPc Cuniculi A strain had a 17 bp deletion, and the TPE, TEN and Fribourg-Blanc isolates had a deletion of 33 bp. Other than these deletions, only 17 heterogeneous sites were found within the entire region (excluding the 16S–23S intergenic spacer region encoding tRNA-Ile or tRNA-Ala). The pattern of nucleotide changes in the rrn operons corresponded to the classification of treponemal strains, whilst two different rrn spacer patterns (Ile/Ala and Ala/Ile) appeared to be distributed randomly across species/subspecies classification, time and geographical source of the treponemal strains. It is suggested that the random distribution of tRNA genes is caused by reciprocal translocation between repetitive sequences mediated by a recBCD-like system.
Traditional medicines and globalization: current and future perspectives in ethnopharmacology

The ethnopharmacological approach toward the understanding and appraisal of traditional and herbal medicines is characterized by the inclusions of the social as well as the natural sciences. Anthropological field-observations describing the local use of nature-derived medicines are the basis for ethnopharmacological enquiries. The multidisciplinary scientific validation of indigenous drugs is of relevance to modern societies at large and helps to sustain local health care practices. Especially with respect to therapies related to aging related, chronic and infectious diseases traditional medicines offer promising alternatives to biomedicine. Bioassays applied in ethnopharmacology represent the molecular characteristics and complexities of the disease or symptoms for which an indigenous drug is used in “traditional” medicine to variable depth and extent. One-dimensional in vitro approaches rarely cope with the complexity of human diseases and ignore the concept of polypharmacological synergies. The recent focus on holistic approaches and systems biology in medicinal plant research represents the trend toward the description and the understanding of complex multi-parameter systems. Ethnopharmacopoeias are non-static cultural constructs shaped by belief and knowledge systems. Intensified globalization and economic liberalism currently accelerates the interchange between local and global pharmacopoeias via international trade, television, the World Wide Web and print media. The increased infiltration of newly generated biomedical knowledge and introduction of “foreign” medicines into local pharmacopoeias leads to syncretic developments and generates a feedback loop. While modern and post-modern cultures and knowledge systems adapt and transform the global impact, they become more relevant for ethnopharmacology. Moreover, what is traditional, alternative or complementary medicine depends on the adopted historic-cultural perspective.
A Computer Architecture with Hardwarebased Malware Detection

In the past the computer architetures and technologies have only been optimized for speed - never for security. The aspects of IT-security were always disregarded. [1] shows that it is possible to write malware that can not be detected or removed from an infected system by software. Stealth-features are possible by special properties of the x86 architecture. This work describes a general hardware architecture, that will improve the security.
Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments

Probabilistic inference of a phylogenetic tree from molecular sequence data is predicated on a substitution model describing the relative rates of change between character states along the tree for each site in the multiple sequence alignment. Commonly, one assumes that the substitution model is homogeneous across sites within large partitions of the alignment, assigns these partitions a priori, and then fixes their underlying substitution model to the best-fitting model from a hierarchy of named models. Here, we introduce an automatic model selection and model averaging approach within a Bayesian framework that simultaneously estimates the number of partitions, the assignment of sites to partitions, the substitution model for each partition, and the uncertainty in these selections. This new approach is implemented as an add-on to the BEAST 2 software platform. We find that this approach dramatically improves the fit of the nucleotide substitution model compared with existing approaches, and we show, using a number of example data sets, that as many as nine partitions are required to explain the heterogeneity in nucleotide substitution process across sites in a single gene analysis. In some instances, this improved modeling of the substitution process can have a measurable effect on downstream inference, including the estimated phylogeny, relative divergence times, and effective population size histories.