Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteomic Approaches to Unraveling the RB/E2F Regulatory Pathway

Correct entry into and progression through the cell cycle require an intact RB/E2F pathway, and its deregulation is now considered a general hallmark of cancer (Nevins 2001). Pioneer work in the early 90’s showed that E2F activity is controlled through the temporal association of E2F factors with Retinoblastoma (RB) tumor suppressor proteins (pRB, p107 and p130), also called pocket proteins (Bandara & La Thangue 1991; Chellappan et al. 1991). The additional finding that RB activity is regulated through phosphorylations by cyclin dependent kinases (CDKs) provided the groundwork for the current model of cell cycle control (Weinberg 1995). According to this model, non-phosphorylated RB binds to E2F in G0/G1, leading to the repression of E2F target genes. Subsequent phosphorylation of RB by CDKs in mid-to late G1 disrupts its association with E2F. As a result, free E2F triggers the expression of target genes necessary for entry into and progression through the cell cycle (Burkhart & Sage 2008). This pathway is thought to be disrupted in most human cancers, either by activation of positively acting components such as G1 cyclins and CDKs, or the inactivation of negatively acting components such as RB and cyclin kinase inhibitors (Nevins 2001). The predicted consequence of deficient RB-mediated regulation is that E2F activity is constantly unleashed from the inhibitory effects of RB (DeGregori & Johnson 2006; Dimova & Dyson 2005; Iaquinta & Lees 2007). Mammalian E2F is a family of related factors (E2F1-8), originally discovered for their pivotal role in transcriptional regulation of genes associated with DNA replication and G1/S progression (Attwooll et al. 2004; Trimarchi & Lees 2002). More recently, microarray expression profiling analyses and ChIP-chip analyses (chromatin immunoprecipitation coupled to microarray technology) in cells overexpressing individual E2Fs have revealed that the transactivation function of these factors exceeds beyond G1/S transition regulation. In fact, E2Fs regulate a wide spectrum of genes with diverse biological functions, including regulation of apoptosis, autophagy, mitosis, chromosome organization, macromolecule metabolism, or differentiation (Ma et al. 2002; Muller et al. 2001; Polager et al. 2008; Ren et al. 2002; Weinmann et al. 2002; Young et al. 2003). Thus, the role of E2F transcription factors in cellular physiology is probably more complex than it was originally thought to be.
CHARACTER OF CYTOCHROME OXIDASE 1 GENE (CO1) IN MITOCHONDRIAL DNA DAMSELFLY Agriocnemis femina FROM LINOW LAKE, TONDANO LAKE AND MOAT LAKE AT NORTH SULAWESI

This study aims to find the character gene cytochrome oxidase subunit 1 (CO1), mitochondrial DNA damselfly ( Agriocnemis femina ) derived from Tondano Lake, Linow Lake and Lake Moat. The research was conducted in several stages, sampling, extraction and purification of total DNA, CO1 gene amplification and sequencing. Sequencing results were analyzed using Geneous Software 5.6. 4. Further alignment analysis using NCBI BLAST (www.ncbi.nih.gov). Although the sample morphology Damselfly used for DNA analysis showed differences in the characteristics of phenotypically plastic. CO1 gene sequencing results of the six samples show the sequence of nitrogenous bases Damsefly have identical percentage (similarity), 99 percent or it can be said based gene CO1, six samples are the same species. Similarity 6 Damsefly samples from three different ecosystems that Tondano Lake, Lake and Lake Moat Linow average above 99% with Agriocnemis femina. Some differences morphological characters of each sample from a different lake ecosystems is not sufficient to give effect to CO1 gene mutations in mitochondrial DNA or gene conservation CO1 at Demselfly that live in three lake ecosystems is very high. Keywords: Character, CO1, Agriocnemis femina, Lake Tondano, Linow Lake, Lake Moat
LEGAL INSIDER TRADING, CEO’S INCENTIVES, AND QUALITY OF EARNINGS

The recent accounting scandals brought into light the failure of corporate governance mechanisms to curbing earnings management. This study focuses on the insiders who design the managers’ compensation contracts. The contract designers are seen as lacking the financial expertise to correctly uncover the true outcome. However by virtue of their knowledge of the contract details, they can discern the likelihood that the firm’s public report is not truthful. Modeling the firm as a principal-agent contract, we show that insiders induce earnings management and make trading gains by designing suboptimal incentives. Given that our results are driven largely by the lack of these directors’ financial expertise, our study has the policy implication that inclusion of financial experts in compensation committees can contribute to transparencies under the current insider trading rules in place.
Analysis the Simulation Performances of EOR Techniques in the Oil Recovery Enhancement

Physical and chemical properties of hydrocarbons might vary according to the different reservoir characteristics; in respect of the way, this alteration could divide produced oils into the high API grade (for low viscosity oil) to low API grade (for heavy crude oil with high viscosity). Therefore, the similar extraction methodology could not be used for various types of crude oil, and a set of different methods should be utilized. To achieve the high rate of hydrocarbon, petroleum engineers are always find novel solutions to address this issue. Due to the fact that, the efficiency of primary and secondary techniques in most of the reservoirs are being estimated about 35% to 50% of the total initial oil in [17]. The parametric mechanisms of natural drives are the primary techniques of hydrocarbon production and by passing the well lifelong pressure drop, the importance of enhanced oil recovery methodologies are urgently required for the reservoirs. Hence, enhanced oil recovery techniques are entailed; Improved water Flooding, Polymer Flooding, Microbial injection, Gas Flooding, Enriched gas injection, Light gas injection, Chemical Flooding, Nitrogen gas flooding, Carbon dioxide flooding, Miscible flooding, Thermal recovery, Steam Flooding and, Steam cycle Injection [8-12]. Chemical Flooding are being divided into two principal categories, Surfactant Flooding and Foam Flooding. Surfactant is a simple substance and only a small amount of it, would reduce the water surface tension. Surfactants are usually organic materials that contain hydrophobic (water repellant)and hydrophilic groups (water absorbent) which they are soluble in organic solvents and water soluble with the molecular structure and it subsequently reduce the surface tension and wateroil and oil-water interface. It also reduces the drainage of the water and oil interface by the liquidliquid interface. A large number of surfactant molecules can be coupled together in a soluble mass and form a mass called Micelle which is clearly shown in figure 1 [13-17].
Exhibition of circular Bragg phenomenon by hyperbolic, dielectric, structurally chiral materials

Abstract. The relative permittivity dyadic of a dielectric structurally chiral material (SCM) varies helicoidally along a fixed direction; in consequence, the SCM exhibits the circular Bragg phenomenon, which is the circular-polarization-selective reflection of light. The introduction of hyperbolicity in an SCM—by making either one or two but not all three eigenvalues of the relative permittivity dyadic acquire negative real parts—does not eliminate the circular Bragg phenomenon, but significantly alters the regime for its exhibition. Significantly wider circular-polarization-sensitive stopbands may be exhibited by hyperbolic SCMs in comparison to nonhyperbolic SCMs. Physical vapor deposition techniques appear to be suitable to fabricate hyperbolic SCMs.
Potential Role of Herbal Medicine in Alleviating Pain and Inflammation in Osteoarthritis: a Review

Osteoarthritis (OA) is a rheumatological disorder accompanied with imbalance between anabolic and catabolic mediators which leads to the destruction of homeostasis of articular cartilage. Currently, Steroids and non-steroidal anti-inflammatory drugs are commonly used in the management of OA. Besides the various side effects of these drugs, they can just alleviate symptoms of OA. Hence, to achieve safe and efficacious drugs, the research tendency toward exploration of novel sources has been grown up. Various previous researches have focused on the use of medicinal plants in the treatment of OA. This review focuses on the most efficacious medicinal plants and drugs considering related laboratory and clinical evidences. More investigations are needed to develop therapeutic agents with disease-modifying properties to treat OA.
Demand for Watershed Services: Understanding Local Preferences through a Choice Experiment in the Koshi Basin of Nepal

This study undertakes a choice experiment in order to identify differences in local demand for watershed services in the Koshi basin of Nepal. The paper first examines the possibility of using a non-monetary numA©raire to estimate household willingness-to-pay for watershed services. Survey results indicate that while some 50% of the population is willing to pay in monetary terms for environmental services, this number goes up to 75% when asked to contribute in labor time. Social benefits from environmental services are 1.4 to 2.2 times higher in labor hours relative to benefits estimated in monetary terms. Thus, in developing countries, households are more likely to express their demand for watershed services by offering their time rather than making a monetary payment. Results also suggest that locational differences matter. Down-stream community members, who practice commercial vegetable farming, have a higher demand for watershed services and are willing to pay a third more than upstream farmers for these services.
Correlations between energy consumption per capita, growth rate, industrialisation, trade volume and urbanisation: the case of Turkey

This study examines the relationship of energy consumption per capita with growth rate, industrialisation, trade volume and urbanisation in Turkish economy throughout the 1980–2015 period using the Engle-Granger, Fully modified ordinary least squares (FMOLS), canonical cointegration regression (CCR) and dynamic ordinary least squares (DOLS) methods. Analysis results revealed a long-run equilibrium relationship between the change in energy consumption per capita and growth rate, industrialisation, trade volume and urbanisation. Urbanisation, industrialisation, growth rate and trade volume positively influence the change in energy consumption per capita.
Vertical coordination from the angle of farmer loyalty and access to credit. Evidence from the Polish dairy sector

Numerous studies have shown that processing and retail industries have actively engaged in assisting farmers to join the modern food marketing systems. Data from the Polish dairy sector shows that assistance is provided not only for the traditional-channel farmers wishing to modernise, but also for farmers already included in the modern marketing channel. Drawing on the literature two explanations could be provided to account for this phenomenon: 1) even the modern-channel farmers lack sufficient funds to maintain required quality/quantity on their own; 2) after undertaking the necessary adjustments the modern-channel farmers are more likely to quit their relationship with current processor and turn elsewhere so the assistance is needed to prevent them from doing that. Basing on the household data, it is robustly found that these hypotheses could provide at most partial explanation for vertical linkages observed between modern-channel processors and farms. The present paper takes advantage of logit models, instrumental variables’ approach, panel data estimations as well as propensity score matching methods.
Population Dynamics in Diffusive Coupled Insect Population

A variety of ecological models exhibit chaotic dynamics because of nonlinearities in population growth and interactions. Here, we will study the LPA model (beetle Tribolium). The LPA model is known to exhibit chaos. In this project, we investigate two things which are the effect of noise constant and the effect of diffusion combined with the LPA model. The effect of noise is not only to change the dynamics of total population density but also to blur the bifurcation diagram. Numerical simulations of the model have shown that diffusion can drive the total population of insects into complex patterns of variability in time. We will compare these simulations with simulations without diffusion. And we conclude that the diffusion coefficient is a bifurcation parameter and that there exist parameter regions with chaotic behavior and periodic solutions. This study demonstrates how diffusion term can be used to influence the chaotic dynamics of an insect population.
A discrete crack propagation model for FRP-strengthened RC slabs

This manuscript presents a discrete crack approach enabling simulation of the progressive process of crack localisation and propagation, as well as its interaction with debonding of fibre-reinforced polymer (FRP) composites from concrete substrates. The numerical approach has been implemented with a non-iterative algorithm to efficiently overcome convergence difficulties produced by different sources of material non-linearity, such as concrete crushing and cracking, yielding of steel reinforcement and debonding of the FRP. The accuracy of the model has been validated against experimental results carried out on one-way simply-supported FRP-strengthened RC slabs, thus highlighting the ability of the proposed model to adequately capture the behaviour of the strengthened slab system.
Characterizing Visual Exploration Techniques for Temporal Data

Designing visualizations for exploration of temporal data requires several choices based on aspects of time and visual representation. Previous taxonomies have described existing visualizations based on these aspects without relating the visual representations. We propose to characterize existing visualization techniques based on both semantic aspects of time and visual representations. Our design space helps to identify how these different visual representations relate and give the possibility to combine attributes of representation from different techniques. We compare two examples of visualizations from the literature based on our taxonomy.
Genotypic analysis of secreted aspartyl proteinases in vaginal Candida albicans isolates

Introduction: Candida albicans is the most common etiologic agent of fungal vaginitis. These yeasts produce secreted aspartyl proteinases encoded by a family of 10 genes (SAP1-10). Objective: The purpose of this study was to analyze the presence of genes SAP1-7 in vulvovaginal C. albicans. Materials and method: The study included 26 C. albicans vaginal isolates. Detection of aspartyl proteases genes (SAP1-7) was performed by polymerase chain reaction (PCR). Results: The most frequent gene in C. albicans isolated from colonization was SAP6 (93.33%), and from infection, SAP7 (100%). We observed a statistical difference (p = 0.049) in SAP1 gene frequency between isolates from vulvovaginal colonization and infection. Conclusion: High frequency of SAP genes was observed in vulvovaginal C. albicans. The results suggest SAP1 participation in vulvovaginal candidiasis infection.
1 ESSENTIAL ELEMENTS OF A PROTEOMICS LABORATORY

The genomic revolution and the emergence of proteomics are transforming cancer research. Cancer has long been understood as a disease of genomic instability and growth dysregulation [Loeb, 2001; Sieber et al., 2003]. Altered gene forms and aberrant gene expression patterns give rise to altered biochemistry, cell biology, and tissue function that characterizes neoplastic disease. Just as genes translate ultimately to function, genetic instability translates to dysfunction, which is manifested at the level of proteins and proteomes. In cancer, these protein changes may provide tumor-specific targets for therapeutic intervention and highly informative biomarkers for disease [Petricoin et al., 2002b; Wulfkuhle et al., 2003]. The ability of new technologies to detect and analyze these changes is rapidly attracting researchers to use proteomics approaches in cancer research. A dedicated proteomics laboratory is the most logical means of establishing essential instrumentation and expertise in proteomics. From a purely practical standpoint, this makes sense in several ways. Mass spectrometry (MS) instrumentation is costly and requires skilled operators. Necessary expertise in protein and peptide separations, MS data analysis, and bioinformatics often requires individuals with complementary, overlapping skills. Finally, by establishing a relatively small portfolio of experimental capabilities and implementing robotics and automation, a proteomics laboratory can serve a large and diverse group of investigators. In short, a proteomics laboratory offers economy of scale, centralized expertise, and a means to foster interdisciplinary research.
SOIL DEVELOPMENT IN RELATION TO VEGETATION AND SURFACE AGE AT GLACIER BAY, ALASKA*

rate of change, over a short period, of many soil properties, with most of the above difficulties reduced to the minimum. This especially applies to those properties which relate directly to vegetation. At Glacier Bay a fairly detailed knowledge of the history of recent deglaciation has been established (Cooper, 1937; Field, 1947), and along with Cooper's (1923, 1931, 1939) classic vegetation succession studies it affords an exceptionally good basis for this kind of investigation. In the present paper the rate of development of some of the characteristics of the forest floor, and changes in the mineral-soil properties of reaction (pH), organic carbon, total nitrogen, calcium carbonate, and bulk density of the fine earth are reported. These changes are related both to age of the surface and to the
Genetic differentiation among populations of Chromobotia macracanthus Bleeker from Sumatra and Kalimantan based on sequencing gene of MtDNA Cytochrome b and Nucleus DNA RAG2

Research on genetic differentiation among populations of Chromobotia macracanthus Bleeker from Sumatra, based on sequencing gene of mtDNA Cytochrome b and nucleus DNA RAG2 has been done. The objectives of the study were to obtain the representation of genetic differentiation among population of clown loach fishes or botia ( Chromobotia macracanthus ) from Sumatra and Kalimantan and to estimate the time divergence of both population group of botia. Samples of botia population were taken from 3 rivers in Sumatra namely Batanghari, Musi, and Tulang Bawang and one river from Kalimantan namely Kapuas. The genetic analysis was based on the sequencing of mtDNA Cytochrome b and nucleus DNA RAG2. The statistical analysis was done by using APE package on R language. The parameters observed were: nucleotide diversity, genetic distance, and neighbor-joining tree. The result showed that the highest nucleotide diversity was fish population of Musi, while the other two populations, Tulang Bawang (Sumatra) and Kapuas (Kalimantan), were considered as the lowest genetic diversity especially based on nucleus DNA RAG2 sequencing. Based on mtDNA Cytochrome-b sequencing, the most distinct population among those populations based on genetic distance were fish populations of Musi and Kapuas. According to the result of neighbor-joining tree analysis, the populations of botia were classified into two groups namely group of Sumatra and group of Kalimantan. The estimation of time divergence among group of population of Sumatra and Kalimantan based on mtDNA Cytochrome b was about 9.25—9.46 million years (Miocene era). The high genetic differences between groups of Sumatra and Kalimantan suggested that the effort of restocking botia from Sumatra into Kalimantan has to be done carefully, because it may disturb the gene originality of both botia populations.
The Effects of Large Disturbances on On-Line Reinforcement Learning for aWalking Robot

Reinforcement Learning is a promising paradigm for adding learning capabilities to humanoid robots. One of the difficulties of the real world is the presence of disturbances. In Reinforcement Learning, disturbances are typically dealt with stochastically. However, large and infrequent disturbances do not fit well in this framework; essentially, they are outliers and not part of the underlying (stochastic) Markov Decision Process. Therefore, they can negatively influence learning. The main reasons for such disturbances for a humanoid robot are sudden changes in the dynamics (such as a sudden push), sensor noise and sampling time irregularities. We investigate the effects of these types of outliers on the on-line learning process of a simple walking robot simulation. We propose to exclude the outliers from the learning process with the aim to improve convergence and the final solution. While infrequent sensor and timing outliers had a negligible influence, infrequent pushes heavily disrupted the learning process. By excluding the outliers from the learning process, performance was again restored.
The Innovation‐Employment Nexus: A Critical Survey of Theory and Empirics

Understanding whether technical change is beneficial or detrimental for employment is at the center of the policy debate, especially in phases of economic recession. So far, the effects of innovation â€“ in its manifold declinations and intrinsic complexity â€“ on labor demand have proven to be not unequivocal. This essay critically reviews the role of technical change in shaping employment dynamics at different levels of aggregation. First, it disentangles theoretically the role of different compensation mechanisms through which employment adjusts after an innovation is introduced. Second, it critically presents the most recent empirical evidence on the topic, with a focus on methods and limitations. Finally, it provides an attempt to conceptualize a number of stylized facts and empirical regularities on the innovationâ€ employment nexus.
The interaction of minimum wage and severance payments in a frictional labor market: theory and estimation

We introduce a minimum wage and severance payments in an equilibrium labor market model with search frictions. We analyze how these policies affect endogenous job creation and destruction decisions and, more generally, the general equilibrium allocation. We structurally estimate the model's parameters and, with the resulting sets of estimates, we perform a quantitative welfare analysis. We conclude that when the dispersion in wages found in the sample is low and the share that workers receive from the surplus their job generates is below a particular level, the maximum level of welfare can be attained using either any of the two policies by themselves or an appropriate combination. However, as dispersion in wages increases, the minimum wage, by itself, can no longer reach the economy's maximum level of welfare; and when it is high enough, no policy in isolation can attain the economy's maximum level of welfare, a combination is required.
A Compliant End-Effector to Passively Limit the Force in Tele-Operated Tissue-Cutting

This paper presents a compliant end-effector that cuts soft tissues and senses the cutting forces. The end-effector is designed to have an upper threshold on cutting forces to facilitate safe handling of tissue during automated cutting. This is demonstrated with nonlinear finite element analysis and experimental results obtained by cutting inhomogeneous phantom tissue. The cutting forces are estimated using a vision-based technique that uses amplified elastic deformation of the compliant end-effector. We also demonstrate an immersive tele-operated tissue-cutting system together with a haptic device that gives real-time force feedback to the user. DOI: 10.1115/1.4007638]