Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements

Transposable elements (TEs) allow rewiring of regulatory networks, and the recent amplification of the ISX element dispersed 77 functional but suboptimal binding sites for the dosage compensation complex to a newly formed X chromosome in Drosophila. Here we identify two linked refining mutations within ISX that interact epistatically to increase binding affinity to the dosage compensation complex. Selection has increased the frequency of this derived haplotype in the population, which is fixed at 30% of ISX insertions and polymorphic among another 41%. Sharing of this haplotype indicates that high levels of gene conversion among ISX elements allow them to ‘crowd-source’ refining mutations, and a refining mutation that occurs at any single ISX element can spread in two dimensions: horizontally across insertion sites by non-allelic gene conversion, and vertically through the population by natural selection. These results describe a novel route by which fully functional regulatory elements can arise rapidly from TEs and implicate non-allelic gene conversion as having an important role in accelerating the evolutionary fine-tuning of regulatory networks. DOI: http://dx.doi. org/10.7554/eLife.05899. 001
Dual-Geometric Neighbor Embedding for Image Super Resolution With Sparse Tensor

Neighbors embedding (NE) technology has proved its efficiency in single image super resolution (SISR). However, image patches do not strictly follow the similar structure in the low-resolution and high-resolution spaces, consequently leading to a bias to the image restoration. In this paper, considering that patches are a set of data with multiview characteristics and spatial organization, we advance a dual-geometric neighbor embedding (DGNE) approach for SISR. In DGNE, multiview features and local spatial neighbors of patches are explored to find a feature-spatial manifold embedding for images. We adopt a geometrically motivated assumption that for each patch there exists a small neighborhood in which only the patches that come from the same feature-spatial manifold, will lie approximately in a low-dimensional affine subspace formulated by sparse neighbors. In order to find the sparse neighbors, a tensor-simultaneous orthogonal matching pursuit algorithm is advanced to realize a joint sparse coding of feature-spatial image tensors. Some experiments are performed on realizing a 3X amplification of natural images, and the recovered results prove its efficiency and superiority to its counterparts.
Data mining for early disease outbreak detection

This thesis presents an early disease outbreak detection algorithm called What's Strange About Recent Events (WSARE). Unlike traditional disease outbreak detection algorithms that look for peaks in a univariate time series of health-care data, WSARE tries to improve its timeliness of detection by taking a novel multivariate approach. Current health-care data used for surveillance are no longer simply a time series of aggregate daily counts. Instead, a wealth of spatial; temporal, demographic, and symptom information is available. WSARE incorporates all of this information using a rule-based approach that compares recent health-care data against data from a baseline distribution and finds subgroups of the data whose proportions have changed the most in the recent data. In addition, health-care data also pose difficulties for surveillance algorithms because of inherent temporal trends such as seasonal effects and day of week variations. WSARE approaches this problem using a Bayesian network to produce a baseline distribution that accounts for these temporal trends. The algorithm itself incorporates a wide range of ideas, including association rules, Bayesian networks, hypothesis testing and permutation tests to produce a powerful detection algorithm that is careful to evaluate the significance of the alarms that it raises.
The Midas Touch The Effects of Interpersonal Touch on Restaurant Tipping

The present study examined the effects of two types of touch in a controlled but natural setting, a restaurant. Waitresses briefly touched customers either on the hand or the shoulder as they were returning change. Customers' reactions were assessed by a restaurant survey and a novel behavioral measure, the tip expressed as a percentage of the bill. The tipping rate for the two types of touch did not differ from each other and did not differ according to the customer's gender. Both tipping rates were significantly larger than a control, no-touch condition. There were no touch effects on ratings of the waitress, the restaurant's atmosphere, or the dining experience. It was concluded that touch effects can occur without awareness, and that males will not react more negatively to touch than females when the touch is unobtrusive or free of status and dependency connotations.
The plate tectonics of Cenozoic SE Asia and the distribution of land and sea

A water well pump assembly designed for operation within a well casing and embodying a pump cylinder having the usual foot valve and traveling plunger valve, together with a novel head valve which is disposed at the upper end of the cylinder above the plunger valve and which functions when an excess quantity of air enters the cylinder through the foot valve to prevent the hydrostatic column of liquid in the liquid outlet pipe above the plunger from following the latter during its downstroke. By such an arrangement, the resultant partial vacuum which is established by downward movement of the plunger causes the foot valve to become seated and the traveling valve to become unseated so that upward movement of the plunger causes unseating of the head valve and passage of the excess air upwardly into the liquid outlet pipe. Continued reciprocation of the plunger causes the pump assembly to function in the manner of a gas pump until such time as the excess air is discharged from the cylinder, after which the pump assembly resumes its function as a water pump.
Feedback Control of Rayleigh Convection in Viscoelastic Maxwell Fluids

Control of Rayleigh convection in a viscoelastic Maxwell fluid is addressed here by considering a feedback from shadowgraphic visualizations. Here, a theoretical approach is made to the problem of the onset of convective motion through a source term in the lower thermal boundary condition. A numerical Galerkin technique is then used to study the linear hydrodynamic stability. Small relaxation times are considered for Prandtl numbers 1 and 10. Interesting results for the Rayleigh, the wavenumber, and the frequency of oscillations are presented along with discussion on the physical mechanism. In short, the linear hydrodynamic stability analysis states that suppression of convection may be favored.
Nonlinear dynamic response of reciprocating compressor system with rub-impact fault caused by subsidence

In this paper, a nonlinear dynamic model of the single-stage reciprocating compressor system with a rub-impact fault caused by subsidence is developed, considering the piston rod flexibility. Meanwhile, different rub-impact scenarios of the crosshead including no corner, a single corner, two opposite corners, and two adjacent corners of the crosshead impacting on the slide, are considered in this model. Numerical simulation results show that the subsidence, time-varying load, and piston rod flexibility have significant effects on the vibration response of the reciprocating compressor system with rub-impact, where the larger the subsidence and time-varying load, the more intense the vibration response. Moreover, compared to the rigid piston rod, the flexible piston rod causes the system to generate stronger shock. In the rub-impact, the crosshead appeared in three different motion modes: noncontact; permanent contact; and collision – and most of the collisions occur in the form of two adjacent corners impacting on the slide. In addition, strange attractors are observed in the phase space trajectories, and the existence of chaotic behavior is verified using the Poincaré section method and maximum Lyapunov exponent method.
AWARENESS OF HEALTH RISKS AS A RESULT OF CONSUMPTION OF RAW MILK IN ARUSHA CITY AND MERU DISTRICT, TANZANIA

A cross-sectional study was conducted in Arusha city and Meru District Council, Tanzania, from October to December 2012, to assess the awareness of smallholder dairy farmers, milk vendors and milk retailers to milk quality and health risks associated with raw milk consumption. A total of 105 respondents were interviewed and milk samples collected for laboratory analysis. Laboratory assessment included physical and microbial quality using standard procedures and antibiotic residues using Delvotest. Questionnaire results indicated high level of awareness that consumption of raw milk could predispose consumers to health hazards. Among the health problems specified included tuberculosis and brucellosis. Nevertheless, majority of respondents used raw unboiled soured milk as fermented milk for sale. Plastic containers were commonly used for storage and transportation of milk. Milk pH below 6.6 was 35.2% and specific gravity below 1.028 g/ml was 13.3%. Mean Total Viable Count (TVC) of milk from vendors was higher than that from retailers and smallholder dairy farmers. Generally, 64.8% of milk samples assessed had higher TVC than the maximum recommended level of 2.0 x10 5 cfu/ml (East Africa Community standards). Commonly isolated bacteria were Staphylococcus aureus, E.coli, Pseudomonas spp. and Corynebacterium spp. All smallholder dairy farmers were aware of drug residues in milk and 97.1% complied with drug withdrawal periods. This possibly led to all milk samples analysed to be free from antibiotic residues. It is concluded that the level of awareness to milk quality is high, although practices associated with milking and post harvest handling practices along the value chain predisposes milk to microbial contamination. It is therefore recommended that public education should be given to all stakeholders in dairy industry on milking and post harvest handling of milk to minimize the likely losses due to rejection of spoiled milk and milk-borne dangers which may occur due to consumption of contaminated milk.
Dark Matter and Dark Energy: A Physicist’s Perspective

For physicists, recent developments in astrophysics and cosmology present exciting challenges. We are conducting “experiments” in energy regimes some of which will be probed by accelerators in the near future, and others which are inevitably the subject of more speculative theoretical investigations. Dark matter is an area where we have hope of making discoveries both with accelerator experiments and dedicated searches. Inflation and dark energy lie in regimes where presently our only hope for a fundamental understanding lies in string theory. Physics summary talk of the conference The Dark Universe: Matter, Energy and Gravity, Space Telescope Institute, April 2001
Supporting views in object-oriented databases

In contrast to base relations, views are typically not stored permanently, but rather computed on demand. Queries to view relations are modified by query substitution so as to operate on the underlying base relations. Therefore, any update to a base relation propagates automatically to all views defined over it. Conversely, view relations can not be updated freely, since it is often ambiguous how to trace view updates back to updates of base tuples. Typically, only views containing the key of their (one) underlying base relation can be updated.
Public Bikesharing in North America during a Period of Rapid Expansion: Understanding Business Models, Industry Trends, and User Impacts

This study evaluates public bikesharing in North America, reviewing the change in travel behavior exhibited by members of different programs in the context of their business models and operational environment. Twenty-three interviews were conducted with IT-based bikesharing organizations in the United States, Canada, and Mexico in 2013. The authors also conducted two kinds of surveys with bikesharing users, an online member survey and an on-street survey. Results show that bikesharing is causing a diverse array of modal shifts within the different cities surveyed. Bikesharing was found to reduce the number of respondents using the bus in four of the five cities. The survey also found that bikesharing reduced respondents driving by large margins in all cities. The appendix examines bikesharing rebalancing through an analysis of the Hubway bikesharing system in Boston
Ultra metal-poor stars: improved atmospheric parameters and NLTE abundances of magnesium and calcium

The most metal-poor stars are the oldest objects, they provide a unique opportunity to study the earliest epoch of the Galaxy formation and individual nucleosynthesis events. These stars should be investigated with a scrupulous care, taking into account all available photometric, spectroscopic, and astrometric informations. We determined atmospheric parameters for 17 ultra metal-poor (UMP) stars, using an extensive method based on colour-Teff calibrations, isochrones, Gaia DR2 trigonometric parallaxes, and non-local thermodynamic equilibrium (NLTE) analysis of the Ca i/Ca ii ionization equilibrium and the Balmer line wings. We updated the model atom of Ca i- ii by including recent quantum-mechanical rate coefficients for the Ca i + H i and Ca ii + H i inelastic collisions. For any line of Ca i and Ca ii in our sample stars, the changes in collisional data result in a shift of smaller than 0.05 dex in the NLTE abundance. We determined magnesium and calcium NLTE and LTE abundances of our sample stars. For 10 stars, we found close-to-solar [Ca/Mg] NLTE abundance ratios. In the remaining stars, magnesium and calcium abundances do not follow each other, such that [Ca/Mg] varies between −3.15 and + 0.36, suggesting a contribution to stellar Mg and Ca abundances from a small number of supernova explosions with different properties. The obtained atmospheric parameters will be used in the forthcoming paper to determine NLTE abundances of chemical elements observed in spectra of the UMP stars.
LTE Signal Transmission Over a Linearized Analog Photonic Link With High Fidelity

This paper presents a concept and an implementation of a linearized analog photonic link for wideband wireless communication that yields improved adjacent channel leakage ratio (ACLR). The link consists of two parallel Mach–Zehnder modulators (MZMs) driven by two lasers, and a modified uni-traveling-carrier photodetector capable of outputting high RF power when assisted by an erbium-doped fiber amplifier. The third-order intermodulation (IMD3) attributed to the MZM transfer function is suppressed by asymmetric RF and optical feeding that impose a π-phase difference between the signals in the two MZM channels. Long-Term Evolution (LTE) signals of various bandwidths are used to validate this broadband linearization approach experimentally. It is demonstrated that with this approach the first ACLR (ACLR1) can be improved by 19.2 dB for a 10-MHz LTE signal and 18.1 dB for a 20-MHz LTE signal at the cost of approximately 2-dB link gain penalty.
Modelling and analysis of business process reengineering

Business process design and business process reengineering (BPR) depend crucially on linking production procedures and organizational services to business goals and objectives. There is currently very little formula support for this kind of reasoning as analytical tasks are usually carried out informally and individual design decisions are hard to relate to business objectives. If BPR is carried out without understanding the way it is done, then the most likely outcome would be continuing less-than-satisfactory current practice and automating outdated processes. This kind of practice misses opportunities for innovation and rationalization. The modelling and analysis of business processes along with business strategies and organizational structures are essential to study the implications of BPR. In this paper, an attempt has been made to study the modelling, analysis and tools/techniques used for modelling of BPR with the help of a survey on the recently (1993-2000) employed methods and tools used for BPR modelling and analysis. A framework for modelling and analysis, and guidelines for the selection of tools/techniques of business process reengineering are presented.
Nitrogen Availability Alters Species Photosynthetic Responses to Elevated Atmospheric CO2.

xiv Chapter 1: Introduction 1 1.1. MOTIVATION 1 1.2. LITERATURE REVIEW 3 1.2.1. Effects of elevated CO2 on photosynthesis and plant growth 3 1.2.1.1. Photosynthesis 3 1.2.1.2. Plant growth and biomass accumulation 6 1.2.1.3. Carbon uptake and storage at larger scales 7 1.2.2. Effects of N fertilization on photosynthesis and plant growth 9 1.2.3. Interactions between elevated CO2 and N fertilization: the role of N in plants grown in elevated CO2 12 1.2.3.1. C-N interactions at the point of CO2 capture 12 1.2.3.2. C-N interactions at the whole plant level: biomass accumulation and plant productivity 14 1.2.3.3. C-N interactions at the ecosystem level: C sequestration and storage 15 1.3. GENERAL RESEARCH HYPOTHESES 18 1.4. SITE DESCRIPTION 20 1.5. BRIEF OVERVIEW OF THE FREE-AIR CO2 ENRICHMENT (FACE) DESIGN 20 1.6. GENERAL RESEARCH APPROACH 22 1.6. 1. Measurement protocol 22 1.6. 2. Statistical approach 24 1.6. 3. Modeling 24 1.7. REFERENCES 26 Chapter 2: Elevated CO2 concentration affects leaf photosynthesis-nitrogen relationships in Pinus taeda over nine years in Free-Air CO2 Enrichment (FACE) 37 2.1. SUMMARY 37 2.2. INTRODUCTION 38 2.3. METHODS 40 2.3.1. Photosynthetic measurements 41 2.3.2. Statistical analyses 42 2.4. RESULTS 44 2.5. DISCUSSION 53 2.6. CONCLUSIONS 56 2.7. REFERENCES 57
Tracking control of nonlinear systems with improved performance via transformational approach

In this work, we present a transformation‐based adaptive control design, for uncertain strict‐feedback nonlinear systems, to achieve given performance specifications in terms of convergence rate/time, overshoot, steady‐state (zero‐error) precision, in addition to the primary stability requirement. For the case with no uncertainty and known control coefficient, by introducing a time‐varying scaling function and an error‐dependent transformation, we develop a control strategy that is able to achieve exponential and uniform convergence of the tracking error and at the same time maintain the output tracking overshoot to be as small as desired without the need for trajectory initialization resetting. For the case with nonparametric uncertainties and unknown control directions, by employing an additional time‐varying scaling function together with a self‐tuning Nussbaum function, we develop a control scheme that not only secures asymptotic tracking but also guarantees finite time transient process in that the tracking error, prior to converging to zero, is regulated into a prespecified residual set within a prescribed time. Both theoretical analysis and numerical simulations verify the effectiveness and benefits of the proposed method.
Biophysical approach of neuronal shapes

The thesis deals with the control and the measurement of neuronal shapes, "control" by using adhesive micropatterns allowing to constrain cells shape in two dimensions, "measurement" by using either interferometry or fluorescence measurements in confined spaces to gain knowledge on cell dry mass and volume.The biological question at the heart of this thesis is the regulation by the neuron of its various morphological characteristics such as length, volume, in association with the establishment of the axo-dendritic polarity. These aspects are developed and deepened in the course of this thesis on experimental but also theoretical (coll. Nir Gov, Weizmann Institute) point of views.This multidisciplinary thesis topic thus builds on biological aspects and physical instrumentation.
Dynamic Call Center Routing Policies Using Call Waiting and Agent Idle Times

We study call routing policies for call centers with multiple call types and multiple agent groups. We introduce new weight-based routing policies where each pair (call type, agent group) is given a matching priority defined as an affine combination of the longest waiting time for that call type and the longest idle time or the number of idle agents in that agent group. The coefficients in this combination are parameters to be optimized. This type of policy is more flexible than traditional ones found in practice, and it performs better in many situations. We consider objective functions that account for the service levels, the abandonment ratios, and the fairness of occupancy across agent groups. We select the parameters of all considered policies via simulation-based optimization heuristics. This requires only the availability of a simulation model of the call center, which can be much more detailed and realistic than the models used elsewhere in the literature to study the optimality of certain types of routing rules. We offer a first numerical study of realistic routing rules that takes into account the complexity of real-life call centers.
Correlation Between Body Mass Index and Fibroadenoma

Introduction Among all benign conditions, the fibroadenoma is the most common lesion worldwide as well as in Pakistan. Clinicians often face the dilemma of whether to remove the mass or to monitor it by means of periodic follow-up examinations. Although the removal of these lesions is a definitive solution, surgery may involve unnecessary excision of benign lesions and unbecoming cosmesis. Body mass index (BMI) is a known risk factor for the development of breast cancer.However, the relationship between BMI and benign breast diseases is still unclear. Some studies showed that increased BMI is a risk factor for benign breast diseases; however, a large number of studies showed that a decrease in BMI is the risk factor for benign breast diseases. Material and methods This was a descriptive cross-sectional study conducted at the Department of General Surgery, Pakistan Institute of Medical Sciences (PIMS), Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan. All patients fulfilling inclusion criteria were assessed in the breast clinic of PIMS. A final diagnosis of fibroadenoma was made after a triple assessment. Weight in kilograms and height in meters were measured. All the information was recorded in a specifically designed proforma accordingly by the postgraduate trainee. BMI was calculated by the formula: BMI=Weight in kgs/height in meters. Other variables that were noted include patients' age, gender, contact number, and hospital visit. The data were analyzed using SPSS version 21 (IBM Corp., Armonk, NY, US). Results The BMI of study patients was 21.8 ± 1.3, ranging from 19 to 24.9. Out of 300 patients presenting with benign breast disease, 60 (20%) had a fibroadenoma while 240 (80%) had other benign breast diseases. Out of 136 patients with high BMI, 42 (30.8%) had a fibroadenoma while out of 74 patients with low BMI, eight (10.8%) had a fibroadenoma; however, out of 90 patients with normal BMI, 10 (11.1%) had a fibroadenoma. Our study population showed an increased risk of fibroadenoma formation in the adolescent age group with an OR value of 8.54 (CI 4.38-16.63, P<0.001). There were also additional statistical correlations between higher BMI and the site of the lesion being the upper outer quadrant of the breast (t= 4.326 P<0.01). There was no significant correlation of BMI with size and increased number of lesions (P=0.280 and P=0.175). Conclusion High BMI seems to be a substantial risk factor for the development of a fibroadenoma, particularly in young adolescent females.