Miracle-dz/UniFAR-FTUs huggingface dataset:
The Crc Global Regulator Inhibits the Pseudomonas putida pWW0 Toluene/Xylene Assimilation Pathway by Repressing the Translation of Regulatory and Structural Genes*

In Pseudomonas putida, the expression of the pWW0 plasmid genes for the toluene/xylene assimilation pathway (the TOL pathway) is subject to complex regulation in response to environmental and physiological signals. This includes strong inhibition via catabolite repression, elicited by the carbon sources that the cells prefer to hydrocarbons. The Crc protein, a global regulator that controls carbon flow in pseudomonads, has an important role in this inhibition. Crc is a translational repressor that regulates the TOL genes, but how it does this has remained unknown. This study reports that Crc binds to sites located at the translation initiation regions of the mRNAs coding for XylR and XylS, two specific transcription activators of the TOL genes. Unexpectedly, eight additional Crc binding sites were found overlapping the translation initiation sites of genes coding for several enzymes of the pathway, all encoded within two polycistronic mRNAs. Evidence is provided supporting the idea that these sites are functional. This implies that Crc can differentially modulate the expression of particular genes within polycistronic mRNAs. It is proposed that Crc controls TOL genes in two ways. First, Crc inhibits the translation of the XylR and XylS regulators, thereby reducing the transcription of all TOL pathway genes. Second, Crc inhibits the translation of specific structural genes of the pathway, acting mainly on proteins involved in the first steps of toluene assimilation. This ensures a rapid inhibitory response that reduces the expression of the toluene/xylene degradation proteins when preferred carbon sources become available.
Systems Approaches to Materials Design: Past, Present, and Future

There is increasing awareness of the imperative to accelerate materials discovery, design, development, and deployment. Materials design is essentially a goal-oriented activity that views the material as a complex system of interacting subsystems with models and experiments at multiple scales of materials structure hierarchy. The goal of materials design is effectively to invert quantitative relationships between process path, structure, and materials properties or responses to identify feasible materials. We first briefly discuss challenges in framing process-structure-property relationships for materials and the critical role of quantifying uncertainty and tracking its propagation through analysis and design. A case study exploiting inductive design of ultrahigh-performance concrete is briefly presented. We focus on important recent directions and key scientific challenges regarding the highly collaborative intersections of materials design with systems engineering, uncertainty quantification and management, optimization, and materials data science and informatics, which are essential to fueling continued progress in systems-based materials design.
A Novel Continuous Breath Test Versus Scintigraphy for Gastric Emptying Rate Measurement

Background Gastric scintigraphy (GS) is considered the gold standard for gastric emptying rate (GER) measurement; however, it requires expensive equipment and special licensing for radioactive substances. Aim To compare a new nonradioactive, real-time, continuous breath test (CBT) method with GS for the GER measurement. Methods Simultaneous GER analysis by both GS and CBT was carried out on 8 dyspeptic patients and 6 healthy controls. After a 14 hour fast, participants ate a standard meal of 250 Kcal double labeled with 1 mCi of Tc-99m and 100 &mgr;g of C-13 labeled octanoic acid. The participants underwent simultaneous GS for 120 minutes on single-detector &ggr; camera and CBT carried out by attaching the nasal cannula of the system (Oridion, BreathID, Israel), which automatically and continuously collected and analyzed breath samples with real time display. A linear fit model was used to calculate gastric empting half-time. A half-time of more than 100 minutes for GS and 80 minutes for CBT were considered pathologic. The GS and CBT were compared by &kgr; test of agreement in normal/abnormal results. Results Good correlation was found for GER measurements between GS and the CBT methods with a linear correlation coefficient of R=0.74. The &kgr; test indicated excellent agreement with value of 0.86 for the qualitative determination of pathologic and normal results. Conclusions The novel CBT provides reliable and reasonably accurate data for on-line GER estimate, in a simple manner suitable for medical clinics or bedside setting, without the use of radioactive substances.
Space vector pulse width modulation of three-level inverter extending operation into overmodulation region

Multi-level voltage-fed inverters with space vector pulse width modulation have established their importance in high power high performance industrial drive applications. The paper proposes an overmodulation strategy of space vector PWM of a three-level inverter with linear transfer characteristic that easily extends from the undermodulation strategy previously developed by the authors for neural network implementation. The overmodulation strategy is very complex because of large number of inverter switching states, and hybrid in nature, that incorporates both undermodulation and overmodulation algorithms. The paper describes the algorithm development, system analysis, DSP based implementation, and evaluation study to validate the modulator performance. The modulator takes the command voltage and angle information at the input and generates symmetrical PWM waves for the three phases of an IGBT inverter that operates at 1.0 kHz switching frequency. The switching states are distributed such that the neutral point voltage always remains balanced. An open loop volts/Hz controlled induction motor drive has been evaluated extensively by smoothly varying the voltage and frequency in the whole speed range that covers both undermodulation and overmodulation regions, and performance was found to be excellent. The PWM algorithm can be easily extended to vector-controtied drive.
Age and aerobic performance in deer mice

SUMMARY Age impacts the phenotype of all multicellular animals, but lifetime changes in physiological traits are poorly understood for all but a few species. Here, we describe a cross-sectional study of age effects on body composition, aerobic performance and ventilation in deer mice Peromyscus maniculatus. This species lives considerably longer in captivity (in excess of 5 years) than most laboratory rodents, and the adaptational biology of its aerobic physiology is well studied. Our deer mice grew throughout life, and, as is typical for mammals, their basal metabolic rate (BMR) and maximal oxygen consumption in exercise (V̇O2max) and thermogenesis (V̇O2sum) increased as power functions of mass. Age did not affect BMR, but we found abrupt decreases in growth rate, V̇O2max and V̇O2sum at approximately 485 days of age, and the mass-adjusted maximal aerobic performance of old mice (5 years of age) was 20% (V̇O2max) to 35% (V̇O2sum) less than that of young animals. Breathing frequency (f) and oxygen extraction (EO2) also declined with age but did not change abruptly. However, there were no consistent age-related changes in tidal volume (VT) or minute volume (V̇min) after accounting for the effects of mass and V̇O2sum. Age influenced several aspects of body composition (lean and fat mass). However, these changes were insufficient to explain the age-related declines in aerobic performance, suggesting that mass-specific oxidative capacity of lean tissue decreased with age. The performance changes we found could engender substantial reductions in the mobility and thermal tolerances of old deer mice. However, very few wild mice are likely to survive to ages where substantial performance decreases occur, so these declines are probably not subjected to strong selection in natural populations.
Asymmetric Suppression Outside the Classical Receptive Field of the Visual Cortex

Areas beyond the classical receptive field (CRF) can modulate responses of the majority of cells in the primary visual cortex of the cat (Walker et al., 1999). Although general characteristics of this phenomenon have been reported previously, little is known about the detailed spatial organization of the surrounds. Previous work suggests that the surrounds may be uniform regions that encircle the CRF or may be limited to the “ends” of the CRF. We have examined the spatial organization of surrounds of single-cell receptive fields in the primary visual cortex of anesthetized, paralyzed cats. The CRF was stimulated with an optimal drifting grating, whereas the surround was probed with a second small grating patch placed at discrete locations around the CRF. For most cells that exhibit suppression, the surrounds are spatially asymmetric, such that the suppression originates from a localized region. We find a variety of suppressive zone locations, but there is a slight bias for suppression to occur at the end zones of the CRF. The spatial pattern of suppression is independent of the parameters of the suppressive stimulus used, although the effect is clearest with iso-oriented surround stimuli. A subset of cells exhibit axially symmetric or uniform surround fields. These results demonstrate that the surrounds are more specific than previously realized, and this specialization has implications for the processing of visual information in the primary visual cortex. One possibility is that these localized surrounds may provide a substrate for figure–ground segmentation of visual scenes.
Les dimensions de la qualité de vie subjective à Dakar

L’ensemble des recherches participatives menées sur la qualité de vie subjective dans les pays en développement a mis en évidence l’importance de la santé physique au sein de ce concept. Cependant, au Sénégal, la qualité de vie subjective n’a jamais été étudiée. Ainsi, les objectifs principaux de cette étude qualitative étaient les suivants : en premier lieu, comprendre ce que signifie le concept de «qualité de vie » (dundu bu baax) et identifier ses dimensions émiques à Dakar ; deuxièmement, analyser le rôle de la santé physique dans la qualité de vie en déterminant ses relations avec les autres dimensions du concept. Huit groupes de discussion focalisés, homogènes en genre, âge et catégorie socioprofessionnelle, ont été menés afin de répondre à ces objectifs. Quatre dimensions de la qualité de vie ont émergé de ces entretiens : la santé physique, les relations sociales, les conditions matérielles d’existence et les caractéristiques psychologiques individuelles (comprenant les mécanismes d’ajustement). Par différents mécanismes, directs et indirects, collatéraux et de contagion, les problèmes de santé affectent l’ensemble des dimensions de la qualité de vie des individus et, par conséquent, leur expérience subjective du bien-être. Par ailleurs, la partie conceptuelle de notre analyse a permis de montrer comment les tensions entre individualisme et holisme, exacerbées en contexte africain-urbaincontemporain, sont susceptibles d’affecter la qualité de vie des jeunes générations.
Stability and Experimental Comparison of Prototypical Iterative Schemes for Total Variation Regularized Problems

Abstract Various iterative methods are available for the approximate solution of non-smooth minimization problems. For a popular non-smooth minimization problem arising in image processing, we discuss the suitable application of three prototypical methods and their stability. The methods are compared experimentally with a focus on choice of stopping criteria, influence of rough initial data, step sizes as well as mesh sizes. An overview of existing algorithms is given.
A Cross-Cultural Comparison of Body Dissatisfaction in Estonian and Australian Young Adults and its Relationship with Media Exposure

The study investigated body image in young adults from two countries with different histories of media exposure. Questionnaires assessing body dissatisfaction, dieting, disordered eating, leisure pursuits, and media exposure were administered to 394 Australian university students and 415 Estonian university students. Although there were large gender differences between men and women, in contrast to prediction, there were relatively few differences on body concern between Australian and Estonian students.
A Quantitative Process for Enhancing End of Phase 2 Decisions

The objectives of the phase 2 stage in a drug development program are to evaluate the safety and tolerability of different doses, select a promising dose range, and look for early signs of activity. At the end of phase 2, a decision to initiate phase 3 studies is made that involves the commitment of considerable resources. This multifactorial decision, generally made by balancing the current condition of a development organization's portfolio, the future cost of development, the competitive landscape, and the expected safety and efficacy benefits of a new therapy, needs to be a good one. In this article, we present a practical quantitative process that has been implemented for drugs entering phase 2 at Amgen Ltd. to ensure a consistent and explicit evidence-based approach is used to contribute to decisions for new drug candidates. Broadly following this process will also help statisticians increase their strategic influence in drug development programs. The process is illustrated using an example from the pancreatic cancer indication. Embedded within the process is a predominantly Bayesian approach to predicting the probability of efficacy success in a future (frequentist) phase 3 program.
Vowel assessment and remediation: a case study

This study presents data from a preschooler (aged 4;11) with a phonological disorder involving the vocalic system. Assessment, using a revised version of Pollock and Keiser's stimulus word list for examining the vowels of English, shows that this child had a reduced, nine-vowel system. She lacked the front low vowel /æ/, the back vowels /u/, /υ/ and /o/, the low central vowel /a/, and the diphthong /au/. The low front vowel was always produced as a back vowel, while the back tense vowels were generally produced as diphthongs. Overall, 65% of her vowels were correct. Intervention strategies were developed, targeting the vowels /u/ and /æ/.
Statistical methods for dealing with publication bias in meta‐analysis

Publication bias is an inevitable problem in the systematic review and meta‐analysis. It is also one of the main threats to the validity of meta‐analysis. Although several statistical methods have been developed to detect and adjust for the publication bias since the beginning of 1980s, some of them are not well known and are not being used properly in both the statistical and clinical literature. In this paper, we provided a critical and extensive discussion on the methods for dealing with publication bias, including statistical principles, implementation, and software, as well as the advantages and limitations of these methods. We illustrated a practical application of these methods in a meta‐analysis of continuous support for women during childbirth. Copyright © 2014 John Wiley & Sons, Ltd.
Investigating the Dualistic Nature of Empathy and Empathizing

Empathy is often regarded as a warm feeling or experience towards others: just one. While this is correct, the literature points to two types of empathy that have different origins. In an attempt to reveal the two kinds of empathy, an expounding of the etymological and historical roots of empathy was resorted to. To explain how interrelated and often interchangeable the concept of empathy is in relation to other words of inter-subjective feeling such as pity, compassion and sympathy, the meanings of all four words were discussed. For an exploration of the implications of the new understanding of empathy on practice, the Roots of Empathy Program was selected. The theoretical basis for the program was then compared to two models presented in this paper. The two models represent processes resulting from cognitive and affective empathy. Content information from material pertaining to the program was plotted on two matrices : one for each model. Upon analysing the data, it was determined that the Roots of Empathy Program makes the assumption that knowledge of a “target’s” situation automatically leads to concern. It was also determined that the program resorted to “perspective taking”, and did not include “perceived similarity” in its implementation. Benefitting from the proposed models in this thesis could be helpful in introducing “perceived similarity” into empathy related practice.
An Overview on Coronary Heart Disease (A Comparative Evaluation of Turkey and Europe) and Cost-effectiveness of Diagnostic Strategies

Objective: Coronary heart disease (CHD) is the leading cause of death for men and women in Turkey as it is in Europe and US. The prevalence of the disease is 3.8% in Turkey and 200,000 patients are added to the pool of CHD annually Because of genetic predisposition and high proportions of physical inactivity, smoking habit, and obesity, CHD is encountered in earlier ages in our country So, the economic burden of the disease is expected to be relatively high, but the amount of health expenditure is not always parallel to the prevalence of a disease in the community. This article was written to overview CHD statistics to make a comparison between Turkey and some European countries and to investigate the value of myocardial perfusion scan (MPS) as a gatekeeper in diagnosing CHD before invasive coronary angiography (ICA). The consequences were evaluated for Turkey In diagnosis; noninvasive testing gains importance in connection with the new approaches in treatment strategies, because a direct ICA strategy results in higher rates of revascularization without improvement in clinical outcomes. A "gatekeeper" is needed to select the patients who are not required to undergo angiography. MPS with its proved power in diagnosis and predicting prognosis, provides a cost-effective solution, and is accepted in some extensive analyses as a "gatekeeper" particularly in intermediate and high risk patients and in patients with known CHD. In conclusion, MPS may provide an optimal solution better than the ongoing situation in Turkey as well, when it is approved as a "gatekeeper in an algorithm before ICA. Conflict of interest:None declared.
The same but different students' understandings of primitive and object variables

From qualitative analysis of student interviews emerged three sets of categories, or outcome spaces, describing introductory students' understandings of variables. One outcome space describes different ways of understanding primitive variables. Another describes different understandings of object variables. The third outcome space describes the relationship between the primitive and object variables, again from the point of view of the student cohort. The results show that learners create various kinds of mental models of programming concepts, and that the concept of variable, which is fundamental to most types of programming, is understood in various non-viable ways. With the help of the outcome spaces, teaching materials and tools can be developed to explicitly address potential pitfalls and highlight educationally critical aspects of variables to students. A software tool, which would engage students to interact with and manipulate a visualization of a notional machine, suggests itself as an intriguing avenue for future work.
Turkish Version of Children's Response Styles Questionnaire Validity and Reliability in Turkish Early Adolescents

This study examines the basic psychometric properties of the Children’s Response Styles Questionnaire (CRSQ; Abela, Rochon, & Vanderbilt, 2000). The Children’ Response Style Questionnaires and The Children’s Depression Inventory were administered to 312 (46.6%) participants from the fourth and 358 (53.4%) from the seventh grade. Participants were recruited via convenient sampling and were between the age of 9 and 15 years. Factor structures, convergent validity, and internal reliability were examined for the two samples. Two factor structures were confirmed for both samples via confirmatory factor analyses. The CRSQ was found to have satisfactory internal reliability and convergent validity for both samples. MANOVA was utilized to examine gender and grade differences, and the results revealed further validity evidences. As the theory suggests, the seventh-grade females had more ruminative tendencies than the fourth-grade females and seventh-grade males. Results are discussed in light of the related litera.
Dependable Dynamic Partial Reconfiguration with minimal area & time overheads on Xilinx FPGAS

Thanks to their flexibility, FPGAs are nowadays widely used to implement digital systems' prototypes and, more frequently, their final releases. Reconfiguration traditionally required an external controller to upload contents in the FPGA. Dynamic Partial Reconfiguration (DPR) opens new horizons in FPGAs' applications, providing many new utilization paradigms, as it enables an FPGA to reconfigure itself: no external controller is required since it can be included in the FPGA. However, DPR also introduces reliability issues related to errors in the partial reconfiguration bitstreams. FPGA manufacturers currently provide solutions that are not efficient. In this paper new DfD (Design for Dependability) techniques are proposed. Exploiting information density of configuration data, they improve the performance while providing the same reliability characteristics as the previous ones.
Positioning, participation, and possibility: using post-structural concepts for social change in Asia-Pacific youth HIV prevention

ABSTRACT This article addresses one of the areas of global concern for Southern youth: HIV rates amongst young people from key communities. In the Asia-Pacific region 95% of all new infections occur amongst those under 25. Furthermore, in this region the nature of the epidemic is concentrated, chiefly affecting people from certain sub-groups such as those who inject drugs, sell sex, participate in male-to-male sex and people who are transgender. In this article we discuss an innovative peer-led leadership and advocacy program for youth which uses post-structural theoretical frames and concepts in an effort to steer against the dominant medicalised and individualising storylines which tend to inform approaches to HIV prevention. We draw on examples and data collected from the NewGen Asia Leadership training program to illustrate the ways post-structural concepts can be used to inform program design as well as analysis and critique of the impact of change efforts. Rather than the traditional focus on transmission of knowledge, skills, and attitudes in prevention efforts, we aim to show how the concepts of positioning, platform, and possibility may be mobilised in strategies used to address the challenge of HIV prevention amongst key youth populations.