Miracle-dz/UniFAR-FTUs huggingface dataset:
Determination of Vancomycin Resistant Enterococcus faecium Diversity in Tehran Sewage Using Plasmid Profile, Biochemical Fingerprinting and Antibiotic Resistance

Background: Sewage treatment plants are considered to be the hotspots for antibiotic resistance transfer among bacterial species. Many fecal bacteria including Enterococci circulate and are exposed to antibiotic residues in this environment. Being as one of the most common cause of nosocomial infections, special concerns have risen worldwide about the rate and characteristics of Enterococci (especially, isolates with high resistance against glycopeptides) which are available in raw sewages. Objectives: Study on the vancomycin Resistant E. faecium diversity in Tehran sewage by plasmid profile, biochemical fingerprinting and antibiotic resistance Materials and Methods: Forty isolates recovered from an urban sewage treatment plant were studied during 2009- 2010. The antibiotic resistance of isolates against 7 antibiotics was examined by disk diffusion method. Extraction of plasmid DNA was performed and identification of van genotype (vanA and vanB) was done by PCR. Biochemical fingerprinting was done by the use of Phene-Plate system (PhP). Results: All isolates were found to be resistant to erythromycin, ampicillin and ciprofloxacin. The PCR analyses showed that all E. faecium isolates harbored vanA gene and 5 (13%) isolates harbored vanA and vanB concomitantly. By plasmid profiling the VRE isolates differentiated into 11 types. PhP showed that VRE isolates were grouped into 23 biochemical types. Conclusions: The combination of plasmid profiling and PhP techniques revealed the presence of diverse population of VRE in sewage treatment plant in Tehran. Furthermore, the results showed that the PhP technique is a reliable method in determining the VRE clonal diversity.
Early-Life Determinants of Total and HDL Cholesterol Concentrations in 8-Year-Old Children; The PIAMA Birth Cohort Study

Background Adult cholesterol concentrations might be influenced by early-life factors, such as breastfeeding and birth weight, referred to as “early programming”. How such early factors exert their influence over the life course is still poorly understood. Evidence from studies in children and adolescents is scarce and conflicting. We investigated the influence of 6 different perinatal risk factors on childhood total and HDL cholesterol concentrations and total-to-HDL cholesterol ratio measured at 8 years of age, and additionally we studied the role of the child's current Body Mass Index (BMI). Methods Anthropometric measures and blood plasma samples were collected during a medical examination in 751 8-year-old children participating in the prospective Prevention and Incidence of Asthma and Mite Allergy (PIAMA) birth cohort study. Linear and logistic regression were performed to estimate associations of total and HDL cholesterol concentrations with breastfeeding, birth weight, infant weight gain, maternal overweight before pregnancy, gestational diabetes and maternal smoking during pregnancy, taking into account the child's current BMI. Results Linear regressions showed an association between total-to-HDL cholesterol ratio and maternal pre-pregnancy overweight (β = 0.15, Confidence Interval 95% (CI): 0.02, 0.28), rapid infant weight gain (β = 0.13, 95%CI: 0.01, 0.26), and maternal smoking during pregnancy (β = 0.14, 95%CI: 0.00, 0.29). These associations were partly mediated by the child's BMI. Conclusion Total-to-HDL cholesterol ratio in 8-year-old children was positively associated with maternal pre-pregnancy overweight, maternal smoking during pregnancy and rapid infant weight gain.
Designing Fitness Apps Using Persuasive Technology: A Text Mining Approach

Popularity and pervasiveness of mobile apps have great potential to motivate healthy behavioural modifications. Considering the increased prevalence of obesity, overweight and sedentary lifestyle in modern societies, this study takes an important step in proposing design elements for fitness apps that can stimulate enhanced physical activity behaviour. We posit that persuasive technology principles infused into social cognitive theory elements will lead to the design of successful fitness apps. We empirically validated our conceptualization using app descriptions and lifecycle data of mobile apps. Implications for practice and future research are discussed.
A methodology for the design of distributed search in P2P middleware

Important research efforts are being conducted in the area of search, lookup, and routing, and are even increasing in the quest for P2P middleware that is both scalable and decentralized. To structure and classify current as well as facilitate and give direction to future research, this methodology proposes a top-down two-dimensional design space. This design space has been developed for exhaustiveness so as to cover all possible design options, existing or yet to be conceived. A comprehensive survey of P2P search systems serves as a reference for the reader while at the same time validating the framework. An identification of areas in the design space not covered by current systems leads to the design of a novel peer-to-peer-based keyword routing scheme. Finally, an evaluation of possible design options along the most important requirement will help guide system designers.
Effect of oil overlay on inhibition potential of roscovitine in sheep cumulus-oocyte complexes.

Inhibitors of cyclin-dependent kinases, as roscovitine, have been used to prevent the spontaneous resumption of meiosis in vitro and to improve the oocyte developmental competence. In this study, the interference of oil overlay on the reversible arrest capacity of roscovitine in sheep oocytes as well as its effects on cumulus expansion was evaluated. For this, cumulus-oocyte complexes (COCs) were cultured for 20 h in TCM 199 with 10% foetal bovine serum (Control) containing 75 μm roscovitine (Rosco). Subsequently, they were in vitro matured (IVM) for further 18 h in inhibitor-free medium with LH and FSH. The culture was performed in Petri dishes under mineral oil (+) or in 96 well plates without oil overlay (-) at 38.5°C and 5% CO2 . At 20 and 38 h, the cumulus expansion and nuclear maturation were evaluated under stereomicroscope and by Hoechst 33342 staining, respectively. No group presented cumulus expansion at 20 h. After additional culture with gonadotrophins, a significant rate of COCs from both Control groups (+/-) exhibited total expansion while in both Rosco groups (+/-) the partial expansion prevailed. Among the oocytes treated with roscovitine, 65.2% were kept at GV in the absence of oil overlay while 40.6% of them reached MII under oil cover (p < 0.05). This meiotic arrest was reversible, and proper meiosis progression also occurred in the Control groups (+/-). So, the culture system without oil overlay improved the meiotic inhibition promoted by roscovitine without affecting the cumulus expansion rate or the subsequent meiosis progression.
Dimensioning bandwidth for elastic traffic in high-speed data networks

Simple and robust engineering rules for dimensioning bandwidth for elastic data traffic are derived for a single bottleneck link via normal approximations for a closed-queueing network (CQN) model in heavy traffic. Elastic data applications adapt to available bandwidth via a feedback control such as the transmission control protocol (TCP) or the available bit rate transfer capability in asynchronous transfer mode. The dimensioning rules satisfy a performance objective based on the mean or tail probability of the per-flow bandwidth. For the mean objective, we obtain a simple expression for the effective bandwidth of an elastic source. We provide a new derivation of the normal approximation in CQNs using more accurate asymptotic expansions and give an explicit estimate of the error in the normal approximation. A CQN model was chosen to obtain the desirable property that the results depend on the distribution of the file sizes only via the mean, and not the heavy-tail characteristics. We view the exogenous "load" in terms of the file sizes and consider the resulting flow of packets as dependent on the presence of other flows and the closed-loop controls. We compare the model with simulations, examine the accuracy of the asymptotic approximations, quantify the increase in bandwidth needed to satisfy the tail-probability performance objective as compared with the mean objective, and show regimes where statistical gain can and cannot be realized.
Adaptive playback algorithm for interactive audio streaming over wireless ad-hoc networks

Assuring effective real-time audio communication over an ad-hoc network composed of mobile wireless nodes is an important new challenge in the wireless arena. In this paper, we propose a new playback algorithm denoted PAA (Periodic Adaptive Algorithm) which adapts periodically the playback latency based on the observation of network delay. The parameters of the algorithm have been chosen off-line with traces generated from several simulated scenarios. We show that PAA outperforms both IPolicy and E-Policy algorithms with respect to Mean Opinion Scores (MOS) performance indicator.
What's in a Word? How Word Choice Can Develop (Mis)conceptions about the Nature of Science

Despite over 10 years of reform efforts, research still shows that students typically have inadequate conceptions of what science is and what scientists do (McComas 2004; Lederman 2007). Many science students, as well as some teachers, use a single “scientific method” that, “proves a hypothesis” by systematic data collection. By following a prescribed set of steps, and writing up a report requiring these steps, many students blindly accept that their data provide “proof” for their conclusion. In your own science class, you have probably heard statements such as “The data is right because it proves that the answer is true. ” This kind of statement overlooks the value of evidence in supporting conclusions, where evidence is a product of data interpretation and not the raw data itself. Such statements present science as rigid and objective. This view does not acknowledge creativity, inference, or tentativeness as characteristics of science. It not only misrepresents the nature of science, but likely makes science inaccessible to many students. The techniques included here raise awareness of common terminology and the image of the nature of science in general. How Word Choice Can Develop (Mis)conceptions About the Nature of Science
Issues on Nonlinear Digital Control

The purpose of this work is to show the real need to motivate theoretical research in nonlinear digital control not only for solving control problems which are specific to the context, but also for giving the intuition of new control methodologies. Digital control methods can, indeed, be used either for the design of piecewice constant feedback strategies or for the design of discontinuous and hybrid controllers.
Tgfβ signaling is required for atrioventricular cushion mesenchyme remodeling during in vivo cardiac development

The transforming growth factorβ (Tgfβ) signaling pathway plays crucial roles in many biological processes. To understand the role(s) of Tgfβ signaling during cardiogenesis in vivo and to overcome the early lethality of Tgfbr2-/- embryos, we applied a Cre/loxp system to specifically inactivate Tgfbr2 in either the myocardium or the endothelium of mouse embryos. Our results show that Tgfbr2 in the myocardium is dispensable for cardiogenesis in most embryos. Contrary to the prediction from results of previous in vitro collagen gel assays, inactivation of Tgfbr2 in the endocardium does not prevent atrioventricular cushion mesenchyme formation, arguing against its essential role in epithelium-mesenchyme transformation in vivo. We further demonstrate that Tgfβ signaling is required for the proper remodeling of the atrioventricular canal and for cardiac looping, and that perturbation in Tgfβ signaling causes the double-inlet left ventricle (DILV) defect. Thus, our study provides a unique mouse genetic model for DILV, further characterization of which suggests a potential cellular mechanism for the defect.
Multiplexed Modular Genetic Targeting of Quantum Dots

While DNA-directed nanotechnology is now a well-established platform for bioinspired nanoscale assembly in vitro, the direct targeting of various nanomaterials in living biological systems remains a significant challenge. Hybrid biological systems with integrated and targeted nanomaterials may have interesting and exploitable properties, so methods for targeting various nanomaterials to precise biological locations are required. Fluorescence imaging has benefited from the use of nanoparticles with superior optical properties compared to fluorescent organic dyes or fluorescent proteins. While single-particle tracking (SPT) in living cells with genetically encoded proteins is limited to very short trajectories, the high photon output of genetically targeted and multiplexed quantum dots (QDs) would enable long-trajectory analysis of multiple proteins. However, challenges with genetic targeting of QDs limit their application in these experiments. In this report, we establish a modular method for targeting QD nanoparticles selectively to multiple genetically encoded tags by precomplexing QD–streptavidin conjugates with cognate biotinylated hapten molecules. This approach enables labeling and SPT of multiple genetically encoded proteins on living cells at high speed and can label expressed proteins in the cytosol upon microinjection into living cells. While we demonstrate labeling with three distinct QD conjugates, the approach can be extended to other specific hapten–affinity molecule interactions and alternative nanoparticles, enabling precise directed targeting of nanoparticles in living biological systems.
Systematic reliability analysis of a class of application-specific embedded software framework

Dramatic advances in computer and communication technologies have made it economically feasible to extend the use of embedded computer systems to more and more critical applications. At the same time, these embedded computer systems are becoming more complex and distributed. As the bulk of the complex application-specific logic of these systems is realized by software, the need for certifying software systems has grown substantially. While relatively mature techniques exist for certifying hardware systems, methods of rigorously certifying software systems are still being actively researched. Possible certification methods for embedded software systems range from formal verification to statistical testing. These methods have different strengths and weaknesses and can be used to complement each other. One potentially useful approach is to decompose the specification into distinct aspects that can be independently certified using the method that is most effective for it. Even though substantial-research has been carried out to reduce the complexity of the software system through decomposition, one major hurdle is the need to certify the overall system on the basis of the aspect properties. One way to address this issue is to focus on architectures in which the aspects are relatively independent of each other. However, complex embedded systems are typically comprised of multiple architectures. We present an alternative approach based on the use of application-oriented-frameworks for implementing embedded systems. We show that it is possible to design such frameworks for embedded applications and derive expressions for determining the system reliability from the reliabilities of the framework and the aspects. The method is illustrated using a distributed multimedia collaboration system.
Escitalopram in the treatment of anxiety symptoms associated with depression

Most patients with depression have symptoms of anxiety associated with their illness. Our aim in this study was to investigate the efficacy of escitalopram, a proven antidepressant, on symptoms of anxiety in patients with major depressive disorder (MDD). Data from five placebo‐controlled escitalopram studies in MDD were analyzed. Three of the studies also included a comparison with citalopram. In all studies, anxiety was assessed using the Inner Tension item (item 3) of the Montgomery–Åsberg Depression Rating Scale (MADRS). In three studies, anxiety symptoms were also specifically assessed, either continuously over time or at baseline and end point, by using the Hamilton Rating Scale for Anxiety (HAM‐A), the Anxious Mood item of the HAM‐A (item 1), the Psychic Anxiety subscale of the HAM‐A (items 1‐6 and 14), the Anxiety Psychic item (item 10) of the Hamilton Rating Scale for Depression (HAM‐D‐24), and the Anxiety/Somatization subfactor (items 10–13, 15, and 17) of the HAM‐D‐24. Escitalopram was significantly superior to placebo in all comparisons. Citalopram was also consistently better than placebo in all comparisons, except in the HAM‐D‐24 Anxiety/Somatization subfactor. In some comparisons with placebo, escitalopram showed a significantly earlier onset of action or an earlier separation. Escitalopram was significantly more effective compared to placebo in treating both anxiety symptoms and the entire depression in the total depressive population, as well as in depressive patients with a high degree of anxiety. Depression and Anxiety 24:53–61, 2007. © 2006 Wiley‐Liss, Inc.
LANDSCAPE-SCALE PHYSIOLOGY: SITE DIFFERENCES IN REFUELING RATES INDICATED BY PLASMA METABOLITE ANALYSIS IN FREE-LIVING MIGRATORY SANDPIPERS

Abstract Variation in plasma metabolite profiles can provide information on physiological state and relative rates of mass change in free-living birds caught only once, and this technique could be used to compare rates of mass change (fattening) among populations or sites in relation to habitat quality. We compared plasma metabolite levels, as an index of relative refueling rates, in migratory Arctic-nesting Western Sandpipers (Calidris mauri), on a landscape scale at as many as nine sites over two years and during three different migratory stages within the Georgia Basin-Puget Sound region of British Columbia and Washington. There was significant intersite variation in plasma triglyceride levels in both years, but only for the northward migration. By contrast, there was little evidence of intrasite variability (i.e. metabolite profiles of birds using the same site were consistent between years and migratory stages), though we documented intrasite variation resulting from birds' use of different microhabitats at the same site. Plasma glycerol levels did not vary systematically among sites, though they varied among years; on average, birds had higher glycerol levels during northward migration than during southward migration. For the northward migration only, there was a positive relationship between plasma triglyceride levels and total macrofaunal prey abundance among sites. Birds using smaller sites with a lower index of mudflat exposure (mean number of kilometer-hours of mudflat exposed in a 24-h period, reflecting the opportunity to forage at each site) tended to have lower triglyceride levels. Fisiología a Escala de Paisaje: Diferencias entre Sitios en las Tasas de Reabastecimiento Indicadas por Análisis de Metabolitos del Plasma en Chorlos Migratorios Silvestres
Mechanical energy optimization in trajectory planning for six DOF robot manipulators based on eighth-degree polynomial functions and a genetic algorithm

Optimal trajectory planning for robot manipulators is a very important issue in the research field of robotics. Many applications require smooth trajectories and the minimization of a performance index, usually the traveling time or the mechanical energy of the actuators. This paper presents a novel method that uses eighth-degree polynomial functions to generate smooth trajectories for the parametric representation of a given path. The optimization algorithm presented in this paper minimizes the mechanical energy consumed in the robot manipulator. To solve the optimization model, a genetic algorithm is implemented. A software platform has been developed to test this optimal trajectory-planning algorithm. The software includes modules to solve the direct kinematics, the inverse kinematics, and the dynamics of the robot manipulator.
Automatic Speaker's Role Classification With a Bottom-up Acoustic Feature Selection

The objective of the current study is to automatically identify the role played by the speaker in a dialogue. By using machine learning procedures over acoustic feature, we wish to automatically trace the footprints of this information through the speech signal. The acoustic feature set was selected from a large statistic-based feature sets including 1,583 dimension features. The analysis is carried out on interactive dialogues of a Map Task setting. The paper first describes the methodology of choosing the 100 most effective attributes among the 1,583 features that were extracted, and then presents the classification results test of the same speaker in two different roles, and a gender-based classification. Results show an average of a 71% classification rate of the role the same speaker played, 65% for all women together and 65% for all men together.
Investigating the role of phoneme-level modifications in emotional speech resynthesis

Recent studies in our lab show that emotions in speech are manifested as, besides supra-segmental trends, distinct variations in phoneme-level prosodic and spectral parameters. In this paper, we further investigate the significance of this finding in the context of emotional speech synthesis. Specifically, we study phoneme-level signal property manipulation in transforming the emotional information conveyed in a speech utterance. We analyze the effect of individual and combined modifications of F0, duration, energy and spectrum using data recorded by a professional actress with happy, angry, sad and neutral expressiveness. We use content matched source-target pairs and apply TDPSOLA for prosody and LPC for spectrum modifications by directly extracting the required parameters from the target speech. Listening tests conducted with 10 naive raters show that modification of prosody and spectral envelope parameters by themselves is not sufficient. However, when applied together, modifying spectrum and prosody at the phone level gives successful results for most emotion pairs, except conversion to happy targets. We also observe that at the phoneme level, spectral envelope modifications are more effective than local prosodic modifications; and that, duration modifications are more effective than pitch modifications. The results confirm our hypothesis that phoneme level modifications can be used to fine tune the ensuing suprasegmental-parameter-based modifications to improve the overall quality of synthesized emotions.