Miracle-dz/UniFAR-FTUs huggingface dataset:
Chapter 3 Targeted DNA Region Re-sequencing

Multiple re-sequencing approaches have been developed and reviewed (McCormack et al. 2013a ; Lemmon and Lemmon 2013 ). Below, we briefl y summarize the major re-sequencing methods, indicating their advantages and disadvantages (Table 3.1 ) and the scale at which they are most appropriate (Fig. 3.1 ). For all methods, we assume that sequencing coverage will be reasonably deep to achieve high accuracy (Table 3.2 ), especially at heterozygous sites. All methods are usually paired with DNA sequence tags (also known as barcodes, indexes, or molecular identifi ers, MID tags; see Faircloth and Glenn 2012 ) to identify individual samples from a pool of samples. We assume that lower costs will increase how widely the techniques will be adopted, and that total costs of ≤$100 US/sample, including personnel costs, are highly desirable.
The Nitsche Method of the Navier-Stokes Equations for Immersed and Moving Boundaries

The usual way for a ow simulation with complex boundaries is to generate an unstructured mesh that represents the boundary accurately. In this classical approach, the generation and handling of the mesh is a complex task and the nite element method (FEM) on unstructured meshes can generate signi cant computational overhead, especially in terms of memory requirements and access, an increasingly crucial aspect on massively parallel computing architectures. An alternative approach is the Immersed Boundary (IB) method. In this paper, we investigate the Nitsche Method for the Navier-Stokes equations (NSE) with immersed boundaries. This method avoids the usage of computationally costly unstructured meshes by using an adaptive Cartesian mesh instead. In contrast to unstructured meshes, Cartesian meshes can be partitioned in a loadbalanced way without a central storage of the whole mesh information and are highly storage e cient even in a sequential context. For an accurate simulation of our scenarios, no-slip boundary conditions need to be imposed on complex boundary, that is not represented by the mesh facets. For this purpose, we employ the Nitsche Method to impose these conditions in a weak form. We extend the approach for moving boundaries, which enables us to compute uid-structure interaction (FSI) scenarios. The results of various FSI benchmark scenarios, presented at the end of this paper, verify our approach.
Determinants of Income Diversification among Rural Farm Households: The Case of Leemo District, Hadiya Zone, South Nation Nationalities People Region, Ethiopia

This study was attempted on identifying and analyzing the determinants of income diversification and main income diversification sources among rural households in Leemo District, Hadiya Zone of South Nation Nationality Regional State using primary data. Structured questionnaires administered through personal interviews. Both descriptive statistics and econometric methods were used to analyses the data. Out of the total sampled households income, 57.84 % of their income obtained from farming activities, while 42.16% of their income earned from off-farm activities. In this study we identified that rural farm household’s income was basically categorized into two, viz. farm and non-farm income. Farm income sources constitutes: crop, livestock, other farm income source while nonfarm income constitutes agricultural wage, off-farm employment, nonfarm wage, self employed income sources and remittance (transfer payment). The simplest measure of income diversity was the average number of income sources (of the eight listed here) that households had. It was observed that rural households in the study area had an average of two sources of income. In Multiple regression model out of eleven explanatory variables included in the model, sex of household head, education level of household head, farm size, farm income and distance to market center were found significant in number of income diversification sources. While analysis of determinants of income diversification was done by logit regression model, in which probability of households’ participation in off-farm activities were used as dependent variable. In this case years of schooling of household head, farm income, landholding size/farm size, member ship in farmers cooperative and distance to the market center were found significant. Overall the result of this study suggests those stakeholders and concerned bodies who focus on promotion, encouragement and expansion of income diversification is expected to enhance educational level of household, to provide aids and subsidized inputs to improve agriculture which in turn increases farm income, to develop rural infrastructure, to create off-farm job opportunity and to take into consideration dwindling landholding size of households.
Risk , Limited Liability and Firm Scope

This paper provides a new explanation for the relationship between firm scope, agent's effort and corporate risk. I set up a moral hazard in teams model with multiple agents and departments under the assumption that both the principal and the agents are protected by limited liability. Each agent exerts effort to reduce the probability of loss of his department. The two-sided limited liability assumption creates an externality between agents, since the bad performance of an agent could reduce the firm’s expected profit, and decrease the expected payoff of a good performing agent within the same firm. This would lower the incentive for other agents to exert effort, which causes 'Contagious shirking'. I prove for the optimal contract and derive conditions for effort to increase or decrease with scope, and explain why ‘contagious effect’ could better answer this question than diversification when firm scope is large. 1 Department of Mathematical Sciences and School of Economics and Management, Tsinghua University, Beijing, China. The author is indebted to (in alphabetic order) Chong-En Bai, Li Chen, Ming Gao, Ping He, Jaimie Lien, Hong Ma and Qing Liu for their comments, instructions and discussions. The author also benefited a lot from the discussions with Yuliy Sannikov, Lemin Wu and many others. 2 'Nothing can be so unjust as for a few persons abounding in wealth to offer a portion of their excess for the information of a company, to play with that excess, to lend the importance of their whole name and credit to the society, and then should the funds prove insufficient to answer all demands, to retire into the security of their unhazarded fortune, and leave the bait to be devoured by the poor deceived fish. ' ---The Times of London, 1824.5. 25
Viscous Faraday waves in two-dimensional large-aspect-ratio containers

A weakly nonlinear analysis of one-dimensional viscous Faraday waves in two-dimensional large-aspect-ratio containers is presented. The surface wave is coupled to a viscous long-wave mean flow that is slaved to the free-surface deformation. The relevant Ginzburg–Landau-like amplitude equations are derived from first principles, and can be of three different types, depending on the ratio between wavelength, depth and the viscous length. These three equations are new in the context of Faraday waves. The coefficients of these equations are calculated for arbitrary viscosity and compared with their counterparts in the literature for small viscosity; a discrepancy in the cubic coefficient is due to a dramatic sensitivity of this coefficient on a small wavenumber shift due to interplay between viscous effects and parametric forcing.
Uses of Mathematics in Computer Animation and 3D Rendering Software

- Abstract - As the title suggests, this paper discusses the applications of several mathematical concepts to computer animation software generally used in the creation of movies and video games. Topics covered will include differential forms, conformal maps, surface texturing, and lighting techniques. It is not the goal of this paper to present anything particularly novel to the mathematical community, but rather to present something that is entertaining to read that will hopefully engage both mathematicians and sane people alike. This paper has been carefully crafted so that it should be accessible to most people with a Calc. I background. That being said, the ﬁnal section of this paper, which contains some of the applications of math in animation software, should be readable to most people so long as they don’t freak out when they encounter the rendering equation.
Chaos synchronization of Yin and Yang T-S fuzzy models of Hénon map system

Based on the Chinese philosophy, Yin is the decreasing, negative, historical or feminine principle in nature, while Yang is the increasing, positive, contemporary or masculine principle in nature. Yin and Yang are two fundamental opposites in Chinese philosophy. Since the discrete Hénon map system is an invertible map, Yin–Yang T-S fuzzy model of chaotic Hénon map systems with increasing and decreasing argument can be studied. The Yang T-S fuzzy model of chaotic Hénon map system is presented. The Yin T-S fuzzy model of chaotic Hénon map system and Yin T-S fuzzy rules are obtained by invertible matrix in linear system theory. Chaos synchronization of Yang T-S fuzzy model of Hénon map systems is achieved by parallel distributed compensation technique, and the fuzzy controller for chaos synchronization of Yin T-S fuzzy model of Hénon map systems is also obtained by invertible matrix in linear system theory. The design of the Yin fuzzy controller is fleetly obtained by the inverse of Yang fuzzy controller, the concern is the Yin chaotic system must be an inverse of the Yang chaotic system. T-S fuzzy model scheme is used in the nonlinear discrete chaotic map system, so the nonlinear discrete chaotic map system can be analyzed by linear system theory.
Production competence revisited – a critique of the literature and a new measurement approach

Purpose – The purpose of this paper is to seek remedy to two major flaws of the production competence literature, which concern: the way the production competence construct is operationalized and the way its effects on performance are measured. Design/methodology/approach – The paper proposes to measure production competence as the two-dimensional operational level construct it actually is, and to use Slack’s (1994) importance-performance matrix to study its business level performance effects. The three hypotheses developed are tested using a subsample of the International Manufacturing Strategy Survey database, which includes 465 manufacturing companies from 21 countries. Findings – The study offers additional empirical support for production competence theory. Going beyond supporting existing theory, the results give more detailed insight by indicating that low operational performance on even one important competitive factor leads to lower business performance (order-losing effect); excessive investment.
Starting Compulsory English Early in Pakistan: A Study of Newly Emerged Scenario in the Light of TEYL Principles

The purpose of this article is to describe and analy s e complex and important issues surrounding the new scenario that has emerged after compulsory English has been introduced from class-1 in Pakistan . This paper attempts to explore these vital issues in the light of TEYL principles. A literature review of the problem is presented enumerating the TEYL principles to provide a proper theoretical framework to administer research tools for collection of relevant data. Both qualitative and quantitative research tools have been administered viz., interviews, observations, and survey on the target population. In order to highlight the advantages of starting English early in Pakistan and get the optimum benefits from this change, this paper provides some suggestions and recommendations. We must train and prepare the teachers and the schools so that they may cope with the new scenario, in a professional and planned way. This paper mainly focuses on highlighting the problems emerging in the new scenario to the forefront. Limited scope does not allow the researcher to provide practical solutions to the problem at length. It does, however, open areas of research for the future researches and researchers. This paper tends to engage the teachers, administrators, policy makers to focus on the complexities of TEYL to make the change in the policy a real success. The culture of the classrooms, teaching and learning could be transformed towards betterment by funding the researchers to focus on this issue. The hiring, training and evaluation of school instructors could also be impacted in this way. The paper begins with an overview of previous researches bringing out the TEYL principles on the forefront focusing on the definitions, explanations and argumentation on this theme. It then focuses on the target population viz., the teachers and students to find out the ground realities, opinions, perceptions, apprehensions and suggestions, and then moves on to give recommendations.
Method Overview of Cardiomyocytes Generation from Pluripotent Stem Cells

Pioneering preclinical studies have demonstrated that cardiomyocytes generated from pluripotent stem cells (PSC-CMs) hold tremendous potential for the treatment of tissue loss and insufficiency (such as HF and MI) that result from heart disease. PSCs stand out as the one of the most promising candidates due to their ability to differentiate into CMs. However, methods for inducing differentiation have lagged behind and are still considered controversial because of the poor capacity for CM differentiation. Here, we introduce alternative methods in various disciplines that promote cardiac differentiation and review the current efforts underway to refine techniques for regenerative purposes. Growth factors, small chemical molecules, electrical stimulation, miRs, and Nanopattered (NP) engineering techniques are emerging as efficient and reproducible options for fine-tuning of desired cardiac lineage differentiation properties and therapeutic treatments for regeneration of tissue lost as a consequence of heart disease.
Effect of Biotic and Abiotic Stress on the Development and Production of Calligonum Polygonoides Subsp.Comosum Grown in Tunisian Arid Conditions

In recent decades, pre-Saharian Tunisian consequences of desertification have gradually become a major environmental problem. We are witnessing the continuous degradation of natural vegetation, due to various human activities. These activities often lead to overgrazing, due to the decline in the size of the course (after cultivation) and increased grazing pressure, manifested by the degradation of the vegetation cover. Such quantitative and / or qualitative degradation is accompanied by irreversible changes in the flora and, therefore, plants are threatened by the dominance of numerous species of animals. To study the effects of seasonal drought and grazing on the parameters of vegetative growth and floristic diversity in canopy, several cuts were made and transects were installed in an experimental plot located in the region of El Ouara (southern Tunisia). Recovery and floristic density were measured during two seasons (fall and spring) with the use of the point quadrat method. The main results of this study show that: For physically undisturbed plants, high productions were recorded in spring and summer. However for physically disturbed plants, that is to say, cut twice, the species showed in irrigated and dry higher capacity spring regrowth (cut in February-March). In general, a significant difference of biomass (B) between the two regimes was observed in spring. Grain production was limited to spring in both water regimes. The annual / perennial ratio is more influenced by seasonal drought and the effect of grazing in the sense of a reduction of vegetation cover is more remarkable in the fall. The overall recovery of the vegetation may be considered a good indicator of the structural state of the ecosystem. Alpha and beta diversity is in turn good indicators of ecosystem structure that should be followed in similar studies.
How to Pre~lict Congruential Generators

In this paper we show how to' predict a large class of pseudorandom number generators. Namely, generators outputting a sequence of integers sO,sl,'" where Sj is computed by the k recurrence Sj == ;~1 (Xj cl>j(SO,SI, .! ,sj-l) (mod m) for integers m and (Xj, and integer functions cl>j ,j=l,.,k. Our predictors are efficient, provided that the functions cl>j are computable (over the integers) in polynomial time. These predictors have access to the elements of the sequence prior to the element being predicted, but they do not know the modulus m , nor the coefficients (Xj the generalor actually works with. This extends previous results about the predictability of such generators, In particular, w~ prove ~e predictability of multivariate polynomial generators, i.e. generators where Sj == P (Sj-tl, . , Sj_l) (mod m), for a polynomial P of fixed degree in n variables. This research was supported by grant No. 86-00301 from the Uni1ed States Israel Binational Science FOIDldation (SSP). JelUsalem, Israel. Technion Computer Science Department Technical Report CS0533 1988
Social Assistance and Informality: Examining the Link in Colombia

This paper presents evidence on the labor market effects of social assistance programs in the short and medium run. We evaluate the impacts of a Conditional Cash Transfer program (Familias en Accion) on informality in Colombia. We exploit an exogenous shock linked to cash transfer benefits that the government provides to poor people to evaluate the effect of these benefits on informality. We argue that being a beneficiary of social programs may create perverse incentives that drive people towards informality through a substitution effect. Survey data of “Familias en Accion” program was used to identify whether the program had any effect on workers’ labor decisions concerning participation (or the lack thereof) in the informal labor market in Colombia after one and four years after its implementation. We apply matching algorithms and difference-in-differences estimations to evaluate the effect of the program. We find that a worker’s informality condition may be affected by receiving CCT income and by the structure of the colombian health system.
EVS 28 KINTEX , Korea , May 3-6 , 2015 Investigating factors affecting electric vehicles adoption : an aggregated panel data analysis over U . S . states

Increasing the usage of electric vehicles has been proposed as a policy to decrease aggregate fuel consumption and greenhouse gas (GHG) emissions in an effort to mitigate the causes of climate change. In order to increase the attraction of electric vehicles for consumers, governments have employed a number of incentives. In this study, the relationship between shares of electric vehicle and the presence of government incentives as well as other influential socio-economic factors were examined. The methodology of this study is based on a crosssectional/time-series (panel) analysis. The developed model is an aggregated binomial logit share model that estimates the modal split between EV and conventional vehicles for different U.S. states from 2003 to 2011. The model was estimated using different panel data methods and the results were compared. The results demonstrated that electricity prices were negatively associated with EV use while, urban roads and government incentives were positively correlated with states’ electric vehicle market share. Sensitivity analysis suggested that of these factors, electricity price affects electric vehicle adoption rate the most. According to the sensitivity analysis of electric vehicle adoption rate, state of Vermont has the most sensitivity with respect to electricity price and New Jersey is the most sensitive state with respect to urban roads and incentives. Moreover, the time trend model analysis found that the electric vehicle adoption has been increasing over time, which is consistent with diffusion of new technology theory.
Estimation of Block-Toeplitz Covariance Matrices

We consider the problem of estimating structured covarimws using maximum-likelihood methodology. The structured covariance matrices of interest here are block-Toeplitz matrices and Toeplitz-block-Toeplitz matrices. These arise naturally in wideband array processing, and in narrowband array processing with rectangular arrays. An EM algorithm for estimating a blockToeplitz matrix is derived based on an embedding in a larger block-circulant matrix. An EM algorithm for estimating a Toeplitz-block-Toeplitz matrix is derived based on an embedding in a larger circulant-blockcidant matrix.
Effects of long-term starvation and refeeding on fatty acid metabolism-related gene expressions in the liver of zebrafish , Danio rerio

Ayşe ÖLMEZ, Mehtap BAYIR, Chunfang WANG, Abdulkadir BAYIR* Department of Aquaculture and Fisheries, Almus Vocational College, Gaziosmanpaşa University, Almus, Tokat, Turkey Department of Agricultural Biotechnology, Faculty of Agriculture, Atatürk University, Erzurum, Turkey The College of Fisheries, Huazhong Agricultural University, Wuhan, P. R. China Department of Aquaculture, Faculty of Fisheries, Atatürk University, Erzurum, Turkey
Influence of Amazon and Orinoco offshore surface water plumes on oligotrophic bacterioplankton diversity in the west tropical Atlantic

The Amazon and Orinoco River low-salinity plumes extend > 200 km eastwards into the west tropical Atlantic Ocean and Caribbean Sea; combined, they have the greatest discharge of fresh water and suspended sediments to oceans worldwide. However, their impacts upon bacterioplankton assemblages have not been previously described. We investigated bacterioplankton assemblage composition using a sensitive DNA fingerprinting technique - automated rRNA intergenic spacer analysis (ARISA)-over vertical profiles from surface waters to 1200 m depth. Bacterioplankton fingerprint richness and diversity were lowest immediately below the plume at 40 m, but at all other depths were statistically indistinguishable. Surface water bacterial production was significantly and negatively correlated with salinity (r = -0.805, p 1% of fingerprint total amplified DNA fluorescence) OTUs in plume, intermediate plume and oceanic conditions. The inconsistency of total assemblage composition within surface plume waters demonstrates that assemblage composition is not tied directly to salinity but possibly to rapid microbial cycling and mixing of assemblages within small water masses. Moreover, our results demonstrate that the Amazon and Orinoco River offshore plumes have significant effects upon surface and underlying water bacterioplankton production in adjacent tropical waters.