Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Coordinately Dysregulated Subnetworks in Complex Phenotypes

In the study of complex phenotypes, single gene markers can only provide limited insights into the manifestation of phenotype. To this end, protein-protein interaction (PPI) networks prove useful in the identification of multiple interacting markers. Recent studies show that, when considered together, many proteins that are connected via physical and functional interactions exhibit significant differential expression with respect to various complex phenotypes, including cancers. As compared to single gene markers, these "coordinately dysregulated subnetworks" improve diagnosis and prognosis of cancer significantly and offer novel insights into the network dynamics of phenotype. However, the problem of identifying coordinately dysregulated subnetworks presents significant algorithmic challenges. Existing approaches utilize heuristics that aim to greedily maximize information-theoretic class separability measures, however, by definition of "coordinate" dysregulation, such greedy algorithms do not suit well to this problem. In this paper, we formulate coordinate dysregulation in the context of the well-known set-cover problem, with a view to capturing the coordination between multiple genes at a sample-specific resolution. Based on this formulation, we adapt state-of-the-art approximation algorithms for set-cover to the identification of coordinately dysregulated subnetworks. Comprehensive experimental results on human colorectal cancer (CRC) show that, when compared to existing algorithms, the proposed algorithm, NETCOVER, improves diagnosis of cancer and prediction of metastasis significantly. Our results also demonstrate that subnetworks in the neighborhood of known CRC driver genes exhibit significant coordinate dysregulation, indicating that the notion of coordinate dysregulation may indeed be useful in understanding the network dynamics of complex phenotypes.
Creating initial digital soil properties map of Afghanistan

Rahmani, Shams R. M.S., Purdue University, December 2014. Creating Initial Digital Soil Properties Map of Afghanistan. Major Professor: Phillip Owens. Afghanistan is a country with a population of more than 31 million people and is located in south central Asia. The total arable land in the country is 12%, 5% is irrigated and the remaining 7% is rainfed. Lack of available soil information, poor farming practices, and poor land management planning, severely affect the yield of agricultural products. In order to ensure sustainable agriculture and prevent land degradation problems, understanding the spatial variability of soils is crucial. The overall objective of this research study was to use digital soil mapping techniques to identify the soil resources and to generate a spatially explicit soil map of a 8,358,160 ha pilot study area. The specific objective is to develop a version 1 map of the six Northern provinces of Afghanistan. Several techniques such as artificial neural networks, multiple regression analysis, and hybrid geostatisitcal approaches are used to create digital soil maps. However, most of these procedures required large amounts of data to create digital soil maps at a useful resolution. Countries like Afghanistan have limited available data and it is difficult to develop the map based on the aforementioned procedures. For this research, we utilized a
Apparent clustering and apparent background earthquakes biased by undetected seismicity

[1] In models of triggered seismicity and in their estimation from empirical data, the detection threshold md is commonly equated to the magnitude m0 of the smallest triggering earthquake. This unjustified assumption neglects the possibility of shocks below the detection threshold triggering observable events. We introduce a formalism that distinguishes between the detection threshold md and the minimum triggering earthquake m0 ≤ md. By considering the branching structure of one complete cascade of triggered events, we derive the apparent branching ratio na (which is the apparent fraction of aftershocks in a given catalog) and the apparent background source Sa observed when only the structure above the detection threshold md is known due to the presence of smaller undetected events capable of triggering larger events. If, as several recent analyses have shown, earthquake triggering is controlled in large part by the smallest magnitudes, this implies that previous estimates of the clustering parameters may significantly underestimate the true values: For instance, an observed fraction of 55% of aftershocks is renormalized into a true value of 75% of triggered events.
Impactos de Crescimentoe Bem-Estar da Reforma Tributária no Brasil

This article evaluates the impact on the Brazilian economy of a tax reform that reduces distortions and cumulative taxes, using for such experiment the current proposal of the Brazilian Treasury Department (Ministerio da Fazenda). We employ a standard dynamic recursive model calibrated as close as possible to the current Brazilian economy in our simulations, which are implemented by introducing in this arti cial economy parameters corresponding to the tax reform. It is estimated that the current proposal would lead to an increase of 1.2 percentile point in the output growth rate in the eight years following its implementation and a long run gain of 14% from its current trend. The impact on the investment level would be very expressive, 40% in the same period, so that the investment rate would from 20% for 26%. Estimated welfare gains were also very large. Keywords: Tax Reform; Growth ; Welfare; Dynamic Recursive Model. ANPEC Classi cation: AREA 5 JEL: E62; H20; E37
Nod Factors Induce Nod Factor Cleaving Enzymes in Pea Roots. Genetic and Pharmacological Approaches Indicate Different Activation Mechanisms1

Establishment of symbiosis between legumes and rhizobia requires bacterial Nod factors (NFs). The concentration of these lipochitooligosaccharides in the rhizosphere is influenced by plant enzymes. NFs induce on pea (Pisum sativum) a particular extracellular NF hydrolase that releases lipodisaccharides from NFs from Sinorhizobium meliloti. Here, we investigated the ability of non-nodulating pea mutants to respond to NodRlv factors (NFs from Rhizobium leguminosarum bv viciae) with enhanced NF hydrolase activity. Mutants defective in the symbiotic genes sym10, sym8, sym19, and sym9/sym30 did not exhibit any stimulation of the NF hydrolase, indicating that the enzyme is induced via an NF signal transduction pathway that includes calcium spiking (transient increases in intracellular Ca2+ levels). Interestingly, the NF hydrolase activity in these sym mutants was even lower than in wild-type peas, which were not pretreated with NodRlv factors. Activation of the NF hydrolase in wild-type plants was a specific response to NodRlv factors. The induction of the NF hydrolase was blocked by α-amanitin, cycloheximide, tunicamycin, EGTA, U73122, and calyculin A. Inhibitory effects, albeit weaker, were also found for brefeldin A, BHQ and ethephon. In addition to this NF hydrolase, NFs and stress-related signals (ethylene and salicylic acid) stimulated a pea chitinase that released lipotrisaccharides from pentameric NFs from S. meliloti. NodRlv factors failed to stimulate the chitinase in mutants defective in the sym10 and sym8 genes, whereas other mutants (e.g. mutated in the sym19 gene) retained their ability to increase the chitinase activity. These findings indicate that calcium spiking is not implicated in stimulation of the chitinase. We suggest that downstream of Sym8, a stress-related signal transduction pathway branches off from the NF signal transduction pathway.
Promoting Inclusive Science Education Practices using Cogenerative Dialogues

Promoting self-determination has become an increasingly important goal for programs serving students with Special Education Needs (SEN). Research examining self-determination in relation to transition education has emerged as an important topic in the field of Special Education. While studies have shown self-determination training provides considerable benefits related to post-secondary outcomes, students continue to be excluded from participating in a decision-making capacity during planning sessions for Individualized Education Programs (IEP) or Individualized Transition Programs (ITP). In this paper, we draw from a body of research in the field of science education to argue for “cogenerative dialogue” as a beneficial instructional strategy special educators and content area teachers could use to expand selfdetermination practices of SEN students. We provide examples of how this structured discourse method has been implemented by teachers and researchers to engage students in participatory dialogue about how to improve science teaching and learning. We conclude by raising questions about the efficacy of utilizing this method in different cultural contexts and we offer directions for future research on using cogenerative dialogue to expand self-determination practices of SEN students in Korea.
Tsunami waves generated by submarine landslides of variable volume: analytical solutions for a basin of variable depth

Tsunami wave generation by submarine landslides of a variable volume in a basin of variable depth is studied within the shallow-water theory. The problem of landslide induced tsunami wave generation and propagation is studied analytically for two specific convex bottom profiles (h x 4/3 and h x 4 ). In these cases the basic equations can be reduced to the constant-coefficient wave equation with the forcing determined by the landslide motion. For certain conditions on the landslide characteristics (speed and volume per unit cross-section) the wave field can be described explicitly. It is represented by one forced wave propagating with the speed of the landslide and following its offshore direction, and two free waves propagating in opposite directions with the wave celerity. For the case of a near-resonant motion of the landslide along the power bottom profile h x the dynamics of the waves propagating offshore is studied using the asymptotic approach. If the landslide is moving in the fully resonant regime the explicit formula for the amplitude of the wave can be derived. It is demonstrated that generally tsunami wave amplitude varies non-monotonically with distance.
A Stochastic Geometry Based Approach to Modeling Interference Correlation in Cooperative Relay Networks

Future wireless networks are expected to be a convergence of many diverse network technologies and architectures, such as cellular networks, wireless local area networks, sensor networks, and device to device communications. Through cooperation between dissimilar wireless devices, this new combined network topology promises to unlock ever larger data rates and provide truly ubiquitous coverage for end users, as well as enabling higher spectral efficiency. However, it also increases the risk of co-channel interference and introduces the possibility of correlation in the aggregated interference that not only impacts the communication performance, but also makes the associated mathematical analysis much more complex. To address this problem and evaluate the communication performance of cooperative relay networks, we adopt a stochastic geometry based approach by assuming that the interfering nodes are randomly distributed according to a Poisson point process (PPP). We also use a random medium access protocol to counteract the effects of interference correlation. Using this approach, we derive novel closed-form expressions for the successful transmission probability and local delay of a relay network with correlated interference. As well as this, we find the optimal transmission probability $p$ that jointly maximizes the successful transmission probability and minimizes the local delay. Finally numerical results are provided to confirm that the proposed joint optimization strategy achieves a significant performance gain compared to a conventional scheme.
Migrants' utilization of somatic healthcare services in Europe--a systematic review.

BACKGROUND Utilization of services is an important aspect of migrants' access to healthcare. The aim was to review the European literature on utilization of somatic healthcare services related to screening, general practitioner, specialist, emergency room and hospital by adult first-generation migrants. Our study question was: 'Are there differences in migrants' utilization of somatic healthcare services compared to non-migrants? ' METHODS Publications were identified by a systematic search of PUBMED and EMBASE. Appropriateness of the studies was judged independently by two researchers based on the abstracts. Additional searches were conducted via the references of the selected articles. The final number of studies included was 21. RESULTS The results suggested a diverging picture regarding utilization of somatic healthcare services by migrants compared to non-migrants in Europe. Overall, migrants tended to have lower attendance and referral rates to mammography and cervical cancer screening, more contacts per patient to general practitioner but less use of consultation by telephone, and same or higher level of use of specialist care as compared to non-migrants. Emergency room utilization showed both higher, equal and lower levels of utilization for migrants compared to non-migrants, whereas hospitalization rates were higher than or equal to non-migrants. CONCLUSION Our review illustrates lack of appropriate epidemiological data and diversity in the categorization of migrants between studies, which makes valid cross-country comparisons most challenging. After adjusting for socio-economic factors and health status, the existing studies still show systematic variations in somatic healthcare utilization between migrants and non-migrants.
Cache-Fair Thread Scheduling for Multicore Processors

We present a new operating system scheduling algorithm for multicore processors. Our algorithm reduces the effects of unequal CPU cache sharing that occur on these processors and cause unfair CPU sharing, priority inversion, and inadequate CPU accounting. We describe the implementation of our algorithm in the Solaris operating system and demonstrate that it produces fairer schedules enabling better priority enforcement and improved performance stability for applications. With conventional scheduling algorithms, application performance on multicore processors varies by up to 36% depending on the runtime characteristics of concurrent processes. We reduce this variability by up to a factor of seven.
Modeling and control of the CCEA robotic arm

It is crucial to have safely physical interaction between people and machines in versatile situations. In this paper, a new and efficient actuation robotic arm, continuous-state coupled elastic actuation (CCEA), is proposed to provide human-machine systems with an intrinsically programmable stiffness capacity to shape output force corresponding to the deviation between human motions and set positions of the system. The bond graph approach is used to analyze the variable stiffness property of the CCEA system, and the backstepping controller based on bond graph is employed to control the robotic arm. Finally, some experiments about controlling the CCEA robotic arm has been conducted and shown satisfactory results.
Cross-Sectional Study on the Prevalence of Intestinal Parasites and Associated Risk Factors in Teda Health Centre, Northwest Ethiopia

Objective. To assess the magnitude of intestinal parasitic infection and associated risk factors in Teda Health Centre, Northwest Ethiopia. Method. A cross-sectional study was conducted in Teda Health Centre from February to April, 2011. Stool samples were collected from 410 study participants and analysed by direct wet mount and formal ether concentration techniques. Furthermore, sociodemographic data were collected by using standardized questionnaire. Result. The overall prevalence of intestinal parasitic infection in this study was 62.3%. Ascaris lumbricoides was the most predominant parasite (23.2%) followed by Giardia intestinalis (12.4%), Entamoeba histolytica/dispar (4.6%), Schistosoma mansoni (8.9%), hookworm (6.6%), Hymenolepis nana (1.5%), Enterobius vermicularis (0.4%), and Strongyloides stercoralis (0.2%). Absence of toilet and hand washing after toilet was shown to be associated with intestinal parasitic infection (P < 0.05 for both). Furthermore, swimming and less shoe wearing habits showed a significant prevalence of S. mansoni and hookworm infections, respectively. Conclusion. The present study showed high prevalence of intestinal parasitic infection in the study area. Absence of toilet and hand washing after toilet was found to be associated with intestinal parasitic infection. Therefore, there is a need for integrated control programme to have a lasting impact on transmission of intestinal parasitic infection.
A new LMI-based robust Sliding Mode Control for the uncertain discrete-time systems

In this paper, a new approach for designing a robust Discrete-time Sliding Mode Control (DSMC) is proposed for the uncertain discrete-time systems. To this end, an LMI approach is used to develop a new framework to design the linear sliding functions which are linear to the state. The LMI approach proposed in this paper is designed to deal with uncertain systems (matched and unmatched). It is wellknown that the finite sampling rate for the discrete-time systems leads to this fact that state move within a bound around the predetermined sliding surface referred to as quasi-sliding mode band. In this paper, this matter will be discussed in a new point of view and an innovative method will be used to obtain the ultimate bound on the system state.
Approximate nearest neighbor algorithms for Frechet distance via product metrics

The Nearest Neighbor Search (NNS) problem is: Given a set P of n points in a metric space X, preprocess P so as to eÆciently answer queries for nding the point in P closest to a query point q. NNS and its approximate versions are among the most extensively studied problems in the elds of Computational Geometry and Algorithms, resulting in discovery of many eÆcient algorithms. In particular, for the case when the metric spaceX is a low-dimensional Euclidean space l 2 , it is known how to construct data structure for exact [5, 15] or approximate [4, 13, 12, 9] NNS with query time (d+log n). Unfortunately, those data structures require space exponential in d. More recently, several data structures using space (quasi)-polynomial in n and d, and query time sublinear in n, have been discovered for approximate NNS under l1 and l2 [14, 12, 11] and l1 [10] norms. While many metrics of interest for nearest neighbor search are norms, quite a few of them are not. A prominent example of the latter is the Frechet metric. Unlike the norms, Frechet metric is de ned for sequences of points (possibly in nite and of di erent length), not vectors. More speci cally, the Frechet distance between two sequences of points is de ned as a minimum, over all alignments between the two sequences, of the maximum distance between two corresponding points (see Preliminaries for formal de nition). Frechet metric is a natural measure of similarity between sequences of points (e.g., handwritten signatures). It also has been studied in the Computational Geometry literature, e.g., in [2] (see also [3]). Unfortunately, the optimum alignment between any two sequences is not xed (i.e., it could be
The Influence of Credit on Farm Growth

This study was based on the hypothesis that lenders to the rural sector have the potential to affect the rate of agricultural adjustment directly via capital formation. Multi-period linear programming models were developed to quantify the effects of lender policy on farm growth for wheat growing, dairy and sheep properties. Three basic models were used to represent different farm management types for each industry group of models. The models included the production, marketing, taxation, consumption and investment subsystems of the farm. Emphasis in these models was focused on the financial linkages between these various subsystems. In particular, the models investigated the effects of increases in trading bank credit on farm growth.
Competing Human Interest: The Key Domain for an Effective Corporate Governance

Corporate governance is the latest addition to the ongoing search for excellence in the management of contemporary rising expectations of the middle class and the participants in the corporate affairs both as an insider as well as the stake holders. Corporate governance in its common parlance is about how to rule a corporate body in general whereas the governance defines the act of ruling the subjects within well defined procedures, organization, principle and various instruments of policy suitable for the purpose. Though the subject itself has taken prominence very recently but the roots of the concept are moderately old in the common enquiries of academia and the business fraternity as a subject. It is for the same reason it is both interesting and useful as well to go deeper into the subject matter and deal with the philosophy and nature of the subject in the present context. In the present paper, the imperatives and challenges to the corporate governance in the light of Stylized Fact of Social Behaviors (SFSB) have been studied. This is a neglected angle in the spectrum of studies in corporate governance at its core.
Links between maternal education and parenting quality during children's first three years: the moderating role of income and partner status

Socio-demographic factors have been consistently linked to parenting practices during children's first years of life. However, less is known about the unique contribution and interactive effects of key factors such as maternal education, income, and partner status. The purpose of the current study was to examine group differences in maternal sensitivity and cognitive stimulation based on maternal education, income, and partner status in a sample of 1,364 mothers with young children. Drawing from family stress theory, main effects of education, income, and partner status were examined, and income and partner status were examined as moderators of differences in maternal behavior based on education. A secondary goal was to examine group differences in maternal behavior based on education and partner status among low-income mothers and group differences based on education and cumulative income. Results of a series of analyses of covariance revealed that income and partner status did moderate education-based differences on maternal behavior, but in varying ways. The primary results indicated that there were larger group differences based on education among low-income mothers than middle/upper income mothers but for partner status there were larger education-based group differences for partnered mothers than single mothers. For the secondary analyses, group differences based on education were larger for low-income partnered mothers than low-income single mothers. Additionally, there were main effects of cumulative income on maternal behavior, and a significant interaction between education and cumulative income on maternal sensitivity. Post-hoc tests revealed that there were no differences in maternal behavior based on education for mothers who were chronically low-income, whereas there were differences in maternal behavior based on education for mothers who did not experience low-income, or experienced low-income intermittently (i.e., 1, 2, or 3 times). Taken together, the results indicate that education is an important resource to mothers who experience some aspects of socio-demographic stress (i.e., low income), but not among mothers who experience multiple or chronic sources of economic stress.