Miracle-dz/UniFAR-FTUs huggingface dataset:
Focal adhesion sites and the removal of substratum-bound fibronectin

Fibronectin was not removed from the substratum beneath focal adhesion sites when fibroblasts spread in serum-free medium on adsorbed fibronectin substrata, or when fibroblasts spread in serum-containing medium on covalently cross-linked fibronectin substrata. Under these conditions, there was colocalization between 140-kD fibronectin receptors and focal adhesion sites. It was concluded that removal of adsorbed fibronectin from beneath focal adhesion sites was a mechanical process that required serum. The effect of serum was nonspecific since serum could be replaced by equivalent concentrations of serum albumin, ovalbumin, or gamma globulins. Quantitative measurements indicated that the presence of proteins in the incubation medium weakens the interaction of fibronectin with the substratum, thereby allowing the adsorbed protein to be removed from the substratum at sites of high stress. After removing fibronectin from the substratum, cells reorganized this material into patches and fibrils beneath cells, and the reorganized fibronectin colocalized with fibronectin receptors. Some of the patches of fibronectin were phagocytosed. The fibronectin fibrils were observed to be in register with actin filament bundles and sometimes translocated to the upper cell surfaces. It is proposed that removal of fibronectin from beneath focal adhesion sites is an example of how cells can modify their extracellular matrices through contractile activity.
Scalable and Versatile Genome Editing Using Linear DNAs with Microhomology to Cas9 Sites in Caenorhabditis elegans

Homology-directed repair (HDR) of double-strand DNA breaks is a promising method for genome editing, but is thought to be less efficient than error-prone nonhomologous end joining in most cell types. We have investigated HDR of double-strand breaks induced by CRISPR-associated protein 9 (Cas9) in Caenorhabditis elegans. We find that HDR is very robust in the C. elegans germline. Linear repair templates with short (∼30–60 bases) homology arms support the integration of base and gene-sized edits with high efficiency, bypassing the need for selection. Based on these findings, we developed a systematic method to mutate, tag, or delete any gene in the C. elegans genome without the use of co-integrated markers or long homology arms. We generated 23 unique edits at 11 genes, including premature stops, whole-gene deletions, and protein fusions to antigenic peptides and GFP. Whole-genome sequencing of five edited strains revealed the presence of passenger variants, but no mutations at predicted off-target sites. The method is scalable for multi-gene editing projects and could be applied to other animals with an accessible germline.
Using Social Cognitive Theory to Predict Physical Activity and Fitness in Underserved Middle School Children

Abstract Few researchers have used social cognitive theory and environment-based constructs to predict physical activity (PA) and fitness in underserved middle-school children. Hence, we evaluated social cognitive variables and perceptions of the school environment to predict PA and fitness in middle school children (N = 506, ages 10-14 years). Using multiple regression analyses we accounted for 12% of the variance in PA and 13-21% of the variance in fitness. The best predictors of PA were barrier self-efficacy, classmate social support, and gender; whereas, only gender predicted fitness. The results affirmed the importance of barrier self-efficacy and gender differences. Our findings regarding classmate social support are some of the first to illuminate the importance of school-specific peers in promoting PA.
Blink: 3D Display Multiplexing for Virtualized Applications

For management and security reasons, Virtual Machines are increasingly being deployed on Desktop PC’s, but because existing VMM technologies are mostly targeted at servers, graphical performance is a stumbling block to many modern applications such as games, simulation, and video-conferencing. Existing highperformance display systems sacrifice safety and provide applications with direct hardware access, but the aim of our work is to build a display system with Virtual Machine quality safety and isolation, while retaining performance comparable to less safe “direct” approaches. We are developing Blink, a Display System for Virtual Machines, the core component of which is a JIT-compiler for extended OpenGL programs which execute safely inside the address space of the display server. Our results show that this model can lead to fewer context switches than traditional client/server approaches, can eliminate redundant copying and clearing of graphics buffers, and reduce the visible effects of scheduler
YACOP: Enhanced gene prediction obtained by a combination of existing methods

The performance of gene-predicting tools varies considerably if evaluated with respect to the parameters sensitivity and specificity or their capability to identify the correct start codon. We were interested to validate tools for gene prediction and to implement a metatool named YACOP, which combines existing tools and has a higher performance. YACOP parses and combines the output of the three gene-predicting systems Criticia, Glimmer and ZCURVE. It outperforms each of the programs tested with its high sensitivity and specificity values combined with a larger number of correctly predicted gene starts. Performance of YACOP and the gene-finding programs was tested by comparing their output with a carefully selected set of annotated genomes. We found that the problem of identifying genes in prokaryotic genomes by means of computational analysis was solved satisfactorily. In contrast, the correct localization of the start codon still appeared to be a problem, as in all cases under test at least 7.8% and up to 32.3% of the positions given in the annotations differed from the locus predicted by any of the programs tested. YACOP can be downloaded from http://www.g2l. bio.uni-goettingen.de.
Campaign Spending with Office-Seeking Politicians, Rational Voters, and Multiple Lobbies

I introduce a microfounded model of campaign finance with office-seeking politicians, a continuum of voters, and a large number of heterogeneous lobbies. Lobbies make contributions to politicians according to a common agency framework. Politicians use contributions to finance their electoral expenditures. Voters are not fooled by electoral expenditures: they are influenced in a way that is consistent with the equilibrium behavior of lobbies and politicians. The model is used to: (i) determine the relation between campaign spending and political deadweight; (ii) show the informational value of lobbies' contributions; (iii) evaluate the welfare implications of restricting campaign spending; and (iv) interpret the empirical finding that campaign expenditures have a very low effect on election outcome. One can say that this model makes the best case in favor of campaign contributions. Nevertheless, under reasonable parameter values, a ban on campaign contributions is welfare-improving.
Conditional gene knockout approach to investigate Delta opioid receptor functions in the forebrain

Delta opioid receptors (DORs) are G-protein coupled receptors belonging to the opioid system, which play a central role in chronic pain and emotional responses. DORs are strongly expressed in olfactory bulb, cortex, striatum, basolateral nucleus of the amygdala and pons nuclei. Using constitutive gene knockout, we have previously demonstrated the role of DORs in reducingchronic pain (Gaveriaux-Ruff, Nozaki et al. 2011), anxiety-related behaviors and impulsivity(Olmstead,Ouagazzal et al. 2009), regulating locomotor activity (Filliol, Ghozland et al. 2000) and facilitating context learning (Le Merrer, Faget et al. 2012; Le Merrer, Rezai et al. 2013), Although these functions are well-established, neuronal networks and mechanisms underlying DOR-regulated behaviors remain poorly understood. The aim of this thesis work was to identify neuronal populations and brain circuits that support DOR functions. Recent evidence showed that DOR is highly expressed in GABAergic neurons (Scherrer et al. 2006;Erbs et al., 2012; Rezai et al. 2012). We therefore developed a conditional knockout mouse line (Dlx-DOR)by breeding floxed DOR gene (Oprd1) with a transgenic Dlx-5/6-Cre mouse line (Monorv et al., 2006) in order to produce a specific deletion of DOR in GABAergic neurons of the forebrain. We first determined brain distribution of delta receptors in Dlx-DOR at mRNA and protein levels. Then, behavioral analysis were performed to assess whether DORs expressed in forebrain GABAergic neurons contribute to the regulation of emotional contrai, locomotor activity as well as epileptogenic effect of SNC80, the prototypal DOR agonist. Finally, we initiated a project focused on DORs detected at the level of BLA.
Bench Top Bioassay of Anti-tumor Activity of Black Cumin ( Nigella sativa ) Oil and Bee Honey Using the Indigenous Strain of Agrobacterium tumefaciens SDB0012

Sudan is endowed with natural products having anti-bacterial, anti-fungal and anti-cancer activities. Among these, bee honey and black cumin oil are recommended by botanist to be used as antibacterial and anti-cancer products; in addition to other health uses. In this study both bee honey, crude oil of black cumin and a mixture of them at a rate of 1:1 were studied for anti-bacterial and anti-tumor activities using the potato disc bioassay at the Microbiology Laboratory, Faculty of Engineering and Technology, University of Gezira. The indigenous strain SDB0012 used in this study was extracted from Tuti Island-Khartoun State and purified since 2005. The major characteristic of this strain was given by Yousif. Whereas, bee honey and black cumin oil were collected in Wad Medani market. Moreover, the crude oil of the black cumin was subjected to fractionation using thin layer chromatography and potato disc bioassay to identify the active anti-tumor components in these trials, the Complete Randomized Design was used with four replicates. Results indicated that both bee honey and the crude extract of the black cumin had no anti-bacterial activities against the indigenous strain of Agrobacterium tumefaciens “SDB0012”, which characterized by having resistance against penicillin (30 mg), chloramphenicol (30 mg) and ciprofloxacin (30 mg). Both bee honey and black cumin had anti-tumor activities with inhibition of 40% and 55%, respectively. The mixture of bee honey and cumin oil extract (1:1) gave 100% inhibition of tumor on the potato discs. Only one out of the eight components separated from the oil black cumin crude extract in thin layer chromatography showed complete inhibition of tumors and was considered as the active anti-tumor component of the black cumin.
Progress Toward Accurate Measurements of Power Consumptions of DBD Plasma Actuators

The accurate measurement of power consumption by Dielectric Barrier Discharge (DBD) plasma actuators is a challenge due to the characteristics of the actuator current signal. Micro-discharges generate high-amplitude, high-frequency current spike transients superimposed on a low-amplitude, low-frequency current. We have used a high-speed digital oscilloscope to measure the actuator power consumption using the Shunt Resistor method and the Monitor Capacitor method. The measurements were performed simultaneously and compared to each other in a time-accurate manner. It was found that low signal-to-noise ratios of the oscilloscopes used, in combination with the high dynamic range of the current spikes, make the Shunt Resistor method inaccurate. An innovative, nonlinear signal compression circuit was applied to the actuator current signal and yielded excellent agreement between the two methods. The paper describes the issues and challenges associated with performing accurate power measurements. It provides insights into the two methods including new insight into the Lissajous curve of the Monitor Capacitor method. Extension to a broad range of parameters and further development of the compression hardware will be performed in future work.
Neonatal CD8 T-cell Hierarchy Is Distinct from Adults and Is Influenced by Intrinsic T cell Properties in Respiratory Syncytial Virus Infected Mice

Following respiratory syncytial virus infection of adult CB6F1 hybrid mice, a predictable CD8+ T cell epitope hierarchy is established with a strongly dominant response to a Kd-restricted peptide (SYIGSINNI) from the M2 protein. The response to KdM282-90 is ∼5-fold higher than the response to a subdominant epitope from the M protein (NAITNAKII, DbM187-195). After infection of neonatal mice, a distinctly different epitope hierarchy emerges with codominant responses to KdM282-90 and DbM187-195. Adoptive transfer of naïve CD8+ T cells from adults into congenic neonates prior to infection indicates that intrinsic CD8+ T cell factors contribute to age-related differences in hierarchy. Epitope-specific precursor frequency differs between adults and neonates and influences, but does not predict the hierarchy following infection. Additionally, dominance of KdM282-90 –specific cells does not correlate with TdT activity. Epitope-specific Vβ repertoire usage is more restricted and functional avidity is lower in neonatal mice. The neonatal pattern of codominance changes after infection at 10 days of age, and rapidly shifts to the adult pattern of extreme KdM282- 90 -dominance. Thus, the functional properties of T cells are selectively modified by developmental factors in an epitope-specific and age-dependent manner.
The Effects Of Ability Homophily on Individual Performance

Abstract : Homophily is the sociological term for a principle that is easily observed and understood: similar people tend to associate with one another (or the well-known saying "Birds of a feather flock together"). Homophily creates divides among people with numerous demographic characteristics and causes people to surround themselves with others who are similar to themselves (McPherson et al., 2001). Race and ethnicity have the greatest influence on relationship choices followed by age, religion, education, occupation, and gender (McPherson et al., 2001). While studies of homophily of race and gender are quite common, few studies have examined homophily based on instrumental attributes such as a person's ability or intelligence. Most of the previous research on homophily related to ability comes from educational researchers. Homophily of ability could lead to grouping of people who have similar performance levels. Grouping by ability is of interest because it has been linked to increased performance in experiments involving undergraduate (Goethals, 2001) and primary (Lou et al., 1996; Tieso, 2003) school students. However, previous studies have not examined the consequences of ability grouping when it results from homophily occurring naturally rather than being imposed by a researcher or teacher. To determine if performance benefits are associated with ability homophily, a longitudinal study was conducted to measure the advice and friendship relationships of 404 adults in a military management training course. Performance was measured by an end-of-course formative test, instructor evaluations, and peer evaluations. The results confirm that ability homophily in advice relationships is related to increased performance. Ability homophily among friendship relationships was not related to increased performance.
Income Growth, Urbanization, and Food Demand in China

A complete demand system is estimated separately for urban and rural residents using a two-stage AIDS-QUAIDS model and pooled provincial and time-series data from 2000 to 2010. The estimated models are then used to project China’s rural and urban food demand in the future. Results suggest that with the continued rise in per capita income and urbanization rate, the budget shares of food grains and vegetables are expected to decrease while the shares of foods with animal origin and other high-valued foods are expected to rise. Moreover, urban residents will dominate the food demand in China.
Taming Dynamically Adaptive Systems using models and aspects

Since software systems need to be continuously available under varying conditions, their ability to evolve at runtime is increasingly seen as one key issue. Modern programming frameworks already provide support for dynamic adaptations. However the high-variability of features in Dynamic Adaptive Systems (DAS) introduces an explosion of possible runtime system configurations (often called modes) and mode transitions. Designing these configurations and their transitions is tedious and error-prone, making the system feature evolution difficult. While Aspect-Oriented Modeling (AOM) was introduced to improve the modularity of software, this paper presents how an AOM approach can be used to tame the combinatorial explosion of DAS modes. Using AOM techniques, we derive a wide range of modes by weaving aspects into an explicit model reflecting the runtime system. We use these generated modes to automatically adapt the system. We validate our approach on an adaptive middleware for home-automation currently deployed in Rennes metropolis.
Methodologies for realizing natural-language-facilitated human-robot cooperation: A review

Natural Language (NL) for transferring knowledge from a human to a robot. Recently, research on using NL to support human-robot cooperation (HRC) has received increasing attention in several domains such as robotic daily assistance, robotic health caregiving, intelligent manufacturing, autonomous navigation and robot social accompany. However, a high-level review that can reveal the realization process and the latest methodologies of using NL to facilitate HRC is missing. In this review, a comprehensive summary about the methodology development of natural-language-facilitated human-robot cooperation (NLC) has been made. We first analyzed driving forces for NLC developments. Then, with a temporal realization order, we reviewed three main steps of NLC: human NL understanding, knowledge representation, and knowledge-world mapping. Last, based on our paper review and perspectives, potential research trends in NLC was discussed.
Learning to Specify Information Requirements: The Relationship between Application and Methodology

The systems development process involves establishing the information requirements of an application and successively transforming those requirements into a computer-based model of the application. Attention iS usually focused almost exclusively on the method of transformation, however, with little recognition of the role of the application. As a first step in examining the relevance of knowledge of the application to the systems development process, this study addresses whether there are synergistic effects of application and methodology knowledge in specifying information requirements. This was achieved via a repeated-measures protocol analysis study that manipulated both experience with the application and knowledge of the methodology. The results show that in learning to specify information requirements, novice analysts: • performed more effectively over time when trained to use a methodology applied the methodology more effectively when familiar with the application; • performed more effectively when they used procedural methodology knowledge rather than declarative methodology knowledge alone; • improved the effectiveness of their problem solving over time only when they used procedural methodology knowledge; • produced idiosyncratic results based on the application. Based on the findings of this research, it appears that research into the nature of applications, as well as methodologies, is warranted. From the viewpoint of the practitioner, since application knowledge is idiosyncratic, it may be necessary to include more than one application-knowledgable person on a systems development team.
THE PLEISTOCENE MANAGER: AN EMPIRICAL INVESTIGATION OF AGENCY SOCIAL CONTRACTS IN ORGANIZATIONS

This research project takes the position that there is a biological basis to social contract formation in business and to social contract dissolution. Its stance is that individuals cannot escape the natural forces that govern these relationships, by rite that these forces have on the structuring of the neural architecture of the human brain. While it is argued in this project that the neural algorithms in the brain are formed through evolutionary time to perform specific tasks that aided in the economizing activities of our ancestors, this structural design is not absolute. Rather, the neural circuits which formed in response to adaptive challenges facing our ancestors are susceptible to cultural influences, hierarchical arrangements, and organizational elaboration. So, although it is inescapable that biological forces shaped a fixed neural structure that guides and limits humans' abilities in the present day, naturally formed cultural variables in corporations moderate the activation of these neural circuits in ordinary business social contract situations.This dissertation attempts to inform the business ethics field with insights from evolutionary psychology by examining business respondents' behavior when confronted with a social contract situation that involves cheating. En route to this goal, the research project empirically tests for the presence of cheater-detection/social-contract neural algorithms in a sample of business practitioners and undergraduate business students, as an extension of the research conducted by evolutionary psychologists, Leda Cosmides and John Tooby. Based on the theoretical groundwork laid by evolutionary psychology and other natural science disciplines, the study examined whether human brain circuits are structured to recognize one specific type of social relationship in firms— agency arrangements.Ultimately, this study's central thesis is: Although corporate agents' minds are biologically evolved to identify cheaters in social contract situations, the neural circuits responsible for detecting these breaches are influenced by organizational and cultural components that affect the individuals' perceptions of the terms of the exchange. Results from the main study empirically confirm that cheater-detection algorithms are present within a business population but that these "hardwired" circuits are moderated by cultural influences in business organizations. Implications for organizations and ethical decision making are offered and discussed.
Grid Resource Management and Scheduling for Data Streaming Applications

Data streaming applications bring new challenges to resource management and scheduling for grid computing. Since real-time data streaming is required as data processing is going on, integrated grid resource management becomes essential among processing, storage and networking resources. Traditional scheduling approaches may not be sufficient for such applications, since usually only one aspect of grid resource scheduling is focused. In this work, an integrated resource scheduling approach is proposed and coordinated resource allocation of CPU cycles, storage capability and network bandwidth is implemented. Resource allocation is performed periodically with updated information on resources and applications and heuristic search for optimal solutions is used to assign various resources for running applications simultaneously. Performance metrics considered in this work include data throughput and utilization of processors, storage, and bandwidth, which are actually tightly coupled with each other when applied for grid data streaming applications. Experimental results show dramatic improvement of performance and scalability using our implementation.