Miracle-dz/UniFAR-FTUs huggingface dataset:
Dark-Field Illumination on Zero-Mode Waveguide/Microfluidic Hybrid Chip Reveals T4 Replisomal Protein Interactions

The ability of zero-mode waveguides (ZMWs) to guide light energy into subwavelength-diameter cylindrical nanoapertures has been exploited for single-molecule fluorescence studies of biomolecules at micromolar concentrations, the typical dissociation constants for biomolecular interactions. Although epi-fluorescence microscopy is now adopted for ZMW-based imaging as an alternative to the commercialized ZMW imaging platform, its suitability and performance awaits rigorous examination. Here, we present conical lens-based dark-field fluorescence microscopy in combination with a ZMW/microfluidic chip for single-molecule fluorescence imaging. We demonstrate that compared to epi-illumination, the dark-field configuration displayed diminished background and noise and enhanced signal-to-noise ratios. This signal-to-noise ratio for imaging using the dark-field setup remains essentially unperturbed by the presence of background fluorescent molecules at micromolar concentration. Our design allowed single-molecule FRET studies that revealed weak DNA–protein and protein–protein interactions found with T4 replisomal proteins.
Superlinear and Quadratic Convergence of Aane-scaling Interior-point Newton Methods for Problems with Simple Bounds without Strct Complementarity Assumption Superlinear and Quadratic Convergence of Aane-scaling Interior-point Newton Methods for Problems with Simple Bounds without Strict Complementar

A class of aane-scaling interior-point methods for bound constrained optimization problems is introduced which are locally q{superlinear or q{quadratic convergent. It is assumed that the strong second order suucient optimality conditions at the solution are satissed, but strict complementarity is not required. The methods are modiications of the aane-scaling interior-point Newton methods introduced by T. There are two modiications. One is a modiication of the scaling matrix, the other one is the use of a projection of the step to maintain strict feasibility rather than a simple scaling of the step. A comprehensive local convergence analysis is given. A simple example is presented to illustrate the pitfalls of the original approach by Coleman and Li in the degenerate case and to demonstrate the performance of the fast converging modiications developed in this paper.
Principles and promise of Fabry–Perot resonators at terahertz frequencies

Fabry–Perot resonators have tremendous potential to enhance the sensitivity of spectroscopic systems at terahertz (THz) frequencies. Increasing sensitivity will be of benefit in compensating for the relatively low power of current high resolution continuous wave THz radiation techniques, and to fully express the potential of THz spectroscopy as source power increases. Improved sensitivities, and thus scanning speeds, will allow detailed studies of the complex vibration-rotation-tunneling dynamics that large molecules show at THz wavelengths, and will be especially important in studying more elusive, transient species such as those present in planetary atmospheres and the interstellar medium. Coupling radiation into the cavity presents unique challenges at THz frequencies, however, meaning that the cavity configurations common in neighboring frequency domains cannot simply be translated. Instead, novel constructions are needed. Here we present a resonator design in which wire-grid polarizers serve as the input and output coupling mirrors. Using this configuration, Q-factors of a few times 10^5 are achieved near 0.3 THz. To aid future investigations, the parameter space that limits the quality of the cavity is explored and paths to improved performance highlighted. Lastly, the performance of polarizer cavity-based Fourier transform (FT) THz spectrometers is discussed, in particular those design optimizations that should allow for the construction of THz instrumentation that rivals and eventually surpasses the sensitivities achieved with modern FT-microwave cavity spectrometers.
Lifetime in Wireless Sensor Networks

The following paper deals with criterion used to measure communication protocol efficiency in Wireless Sensor Networks. As energy is a crucial characteristic of those networks, it is necessary to pay attention both to the energy consumption and to the distribution of energy consumption, when using communication protocols, so as to increase the lifetime of the whole network. Our aim is to present and discuss criterion designed to analyze communication protocol effectiveness. When designing, for example, communication protocols, it is really important to measure performances with a suitable metric according to our application, else it would be difficult to analyze and to improve a protocol. In this paper, we draw a list of existing criterion, and then introduce two new ones : Average Node Percentage and Monitored Interest Point Percentage. We also point out the relevance regarding the required application for each criterion.
Preventing reading difficulties in young children

1 Front Matter 2 Executive Summary 3 Part I: Introduction to Reading 4 1. Introduction 5 2. The Process of Learning to Read 6 Part II: Who Are We Talking About? 7 3. Who Has Reading Difficulties? 8 4. Predictors of Success and Failure in Reading 9 Part III: Prevention and Intervention 10 5. Preventing Reading Difficulties Before Kindergarten 11 6. Instructional Strategies for Kindergarten and the Primary Grades 12 7. Organizational Strategies for Kindergarten and the Primary Grades 13 8. Helping Children with Reading Difficulties in Grades 1 to 3 14 Part IV: Knowledge into Action 15 9. The Agents of Change 16 10. Recommendations for Practice and Research 17 References 18 Biographical Sketches 19 Index
A Wyner-Ziv video codec with horizontal and vertical sampling

In Wyner-Ziv (WZ) video coding, decoder side information (SI), among other components, takes a key role in decoding and reconstruction. In most existing WZ video coding schemes, SI is generated using motion compensated temporal interpolation (MCTI), which requires very frequent insertion of intra (key) frames in encoded bit stream or a very small group of pictures (GOP) size. This makes such methods far from practical, and enlarging GOP size is helpless to overcome this drawback as this will reduce the temporal correlation between intra frames and hence degrades the performance of MCTI. To overcome this drawback, we propose, in this paper, a WZ video codec with horizontal and vertical (HV) sampling. In the codec, a frame, before coding, is divided into four equal-sized sub-frames using an HV sampling process. Only one of the sub-frames is intra coded, while the remaining ones are WZ coded. This way, spatial correlation in an intra frame is converted to temporal correlation, while temporal correlation between adjacent frames is partly converted to spatial correlation, and SI at the decoder can always be estimated through motion estimation using the intra coded sub-frames. The tight constraint on GOP size of other WZ video coding schemes is released in the proposed WZ video codec, and hence leads to more practical WZ video coding solution.
The problems of students’ physical training individualization

Purpose: to assess physical health and biological age of 1st 2nd year girl students, depending on their physical activity, as well as to work out system of control over students’ health. Material: in the research 1st and 2nd year girl students (n=120) participated. Results: students’ busy in their working day was analyzed as well as student’s understanding of healthy life style during working day. We also paid attention to reasons of sharp weakening of students’ physical fitness and determined integral indicator of healthy life style conception as well as significance of every its component. The following concepts are introduced: physical health, including individual level of physical condition; physical fitness and physical state. We found normal level for every component of physical health and correlation between population, regional and individual norms. Conclusions: For students’ healthy life style formation it is necessary to observe norm requirements to all its components. Violation of any component’s norm results in worsening general final result.
Robust moving horizon state estimation: Application to bioprocesses

In this paper, a robust nonlinear receding-horizon observer is proposed for the estimation of cellular concentration in a bioreactor. In the presence of uncertainties on the model parameter or on the initial state of the system, this estimation problem can lead to poor estimation performance. A min-max optimization solution can be used to increase the robustness of the observer in the presence of parameter uncertainties. This solution assumes that each model parameter belongs to an interval. The paper proposes an alternative modeling for these parameters: A Gaussian model is assumed in order to take into account the correlation between parameters. As the confidence region for the parameters is now an ellipsoid, the max step in the min-max problem is replaced by more tractable statistics. Expected value has been tested for its simplicity. For robustness requirements a statistic considering the variance of the estimation has also been developed. Numerical simulations illustrate the efficiency of the proposed estimation scheme.
Information Theory and Associative Word Learning

Information theory has its roots in optimizing communication in the limited domain of a networks. However, over the years, it has been seen to have a wide range of applicability in areas like linguistics, artificial intelligence and cognitive science. ( [? ],[? ]) More recently work has examined the application of information theory to finding episode boundaries in unsegmented time series [P. Cohen, 2002 ]. Much of this work is motivated by the belief that cognitive development is served by information theory. Specifically, that learning serves to reduce the entropy of the observed world.
Global analysis of proliferation and cell cycle gene expression in the regulation of hematopoietic stem and progenitor cell fates

Knowledge of the molecular networks controlling the proliferation and fate of hematopoietic stem cells (HSC) is essential to understand their function in maintaining blood cell production during normal hematopoiesis and upon clinical transplantation. Using highly purified stem and progenitor cell populations, we define the proliferation index and status of the cell cycle machinery at discrete stages of hematopoietic differentiation and during cytokine-mediated HSC mobilization. We identify distinct sets of cell cycle proteins that specifically associate with differentiation, self-renewal, and maintenance of quiescence in HSC and progenitor cells. Moreover, we describe a striking inequality of function among in vivo cycling and quiescent HSC by demonstrating that their long-term engraftment potential resides predominantly in the G0 fraction. These data provide a direct link between HSC proliferation and function and identify discrete molecular targets in regulating HSC cell fate decisions that could have implications for both the therapeutic use of HSC and the understanding of leukemic transformation.
A penalty-based approach for contact forces computation in bipedal robots

Computation of contact forces is essential for the simulation of mechanical systems with unilateral constraints, like bipedal robots. Most methods are based on the rigid body assumption. They can be categorized into constraint-based and penalty-based approaches. In the former, contact forces are computed by solving an optimization problem based on linear or nonlinear complementarity conditions. Unfortunately, these methods cannot be directly applied to articulated systems described in generalized coordinates. In the second approach, spring-damper models are used to minimize interpenetration between the surfaces in contact. The main criticism to penalty approaches are parameter tunning, static friction handling, and the difficulties to treat multiple simultaneous unilateral contacts. In this work we present a new compliant approach based on input-output feedback linearization. The main advantages of the proposed approach are, the spring-damper parameters are independent of the parameters of the system (i.e masses, inertias), no a priori-defined velocity thresholds are required to distinguish between dynamic and static friction, multiple simultaneous unilateral contacts are naturally handled. The proposition has been succesfully applied to the simulation of a 3D bipedal walking robot.
Healing from historical trauma for persons of African ancestry in the United States: an African centered psychology approach to wellness

This critical analysis of the literature explores the potential of African-centered psychology to address the sequelae of historical trauma in the 21st century persons of African ancestry in the United States. African American face significant health and wellness challenges including socioeconomic disparities, interpersonal violence, substance abuse, psycho-spiritual distress, and physical health issues. The literature questions the validity of mainstream psychological science to effectively conceptualize and treat persons of African ancestry, and calls for the identification of specific, culturally relevant interventions to increase physical and psychological wellness. The concept of historical trauma helps to explain the psycho-spiritual distress experienced by many persons of African ancestry in the United States, including internalized oppression, as the sequelae of unhealed wounds relates to enslavement and colonization, through the destruction of culture, language and religion, and imposition of non-inclusive systems of education, government and law. An African-centered psychology approach may alleviate suffering related to historical trauma. This dissertation further integrates the literature on the historical trauma response with the literature on African-centered psychology. Wellness goals for persons of African ancestry are identified in the literature of scholars, researchers, practitioners, activists, and community members. Concepts and strategies from an African-centered psychology framework are then explored for their potential to help illuminate challenges, address needs, and support goals, in alignment with cultural values and work currently being done in this field. Implications in the areas of epistemology, research, clinical practice, practitioner training, and public acknowledgement are explored in depth, and recommendations for incorporating African centered strategies in therapeutic interventions are made. This dissertation also identifies its own theoretical and methodological limitations, and proposes areas for future investigation.
Real-time streaming and robust streaming H.264/AVC video

With the increasingly extensive applications for the new emerging video coding standard, H.264/AVC, it becomes more and more important that we transport H.264/AVC video over MPEG-2 system by exploiting all the existing large amount of the infrastructure of MPEG-2 systems. In this paper, we propose two solutions for it. The key technologies are as follows: firstly we use an H.264/AVC video as an elementary stream of an MPEG-2 system and multiplex it into a TS (transport stream), then extend the T-STD (transport stream-system target decoder) of MPEG-2 standard, so as to transport MPEG-2 TS through Internet and decode it in the client. Ordinarily, the decoded elementary stream should come from a container (a system layer encapsulation including a compression layer), such as AVI. However, we take MPEG-2 TS as a container herein. We encapsulate the H.264/AVC elementary stream into this container in the server, and extract the H.264/AVC video from it to be decoded and be represented. If we use the UDP (user datagram protocol) as a transport protocol, the streaming process will be a real-time one. The experiment result shows that we get a good result, with less than 5% frames whose PSNR<40 dB. We can even get a robust streaming by using the HTTP/TCP (hyper-text transport protocol/transport control protocol) as a transport protocol. All the streaming solutions that we proposed in this paper can also be used for mobile video.
Rapid Diagnosis of Pulmonary and Extrapulmonary Tuberculosis in HIV-Infected Patients. Comparison of LED Fluorescent Microscopy and the GeneXpert MTB/RIF Assay in a District Hospital in India

HIV-related tuberculosis is difficult to diagnose and is associated with high morbidity and mortality. Recently, the World Health Organization has endorsed the GeneXpert MTB/RIF (Xpert) assay for the diagnosis of pulmonary tuberculosis in HIV-infected patients from developing countries, but information about the use of Xpert for the diagnosis of extrapulmonary tuberculosis is scarce. In this study, we compared the performance of light-emitting diode (LED) auramine fluorescent microscopy and the Xpert assay for the diagnosis of tuberculosis in HIV infected patients in a district hospital of India. Although at higher cost, Xpert outperformed LED fluorescent microscopy in all type of specimens, especially in cerebrospinal fluid where the number of positive results was increased 11 times. Pleural fluid, ascitic fluid, pus, and stool specimens also yielded positive results with the Xpert assay. When collecting two additional early-morning sputum samples, the increase of the number of positive results with the Xpert assay was lower than previously reported for HIV infected patients. Rifampicin resistance was observed in 2.2% of the cases. The results of this study show that the Xpert assay can dramatically improve the rapid diagnosis of tuberculous meningitis and other types of extrapulmonary tuberculosis of HIV infected patients.
A conversation with Professor Bo Zhang

In the 11 international joint conference on artificial intelligence (IJCAI’89), in 1989, Piatetsky-Shapiro and colleagues led a seminar on knowledge discovery in databases, which signaled the coming of age for the field of data mining. Soon after, in 1993, data mining research officially begun by first being supported by the National Natural Science Foundation of China (NSFC). This was viewed as the beginning of data mining research in China. Thus, China was among the pioneers in data mining research given that the time gap was only 4 years. Afterwards, major research activities on both fundamental research and practical applications can be found in many research institutions and universities, including Tsinghua University, Peking University, Institute of Computing Technology in Chinese Academy of Science, Nanjing University, and many others. In these institutions, applications of data mining cover a broad range of areas including finance, business, transportation, medicine, energy, etc. However, before the 21 century, due to the shortage of data, China’s KDD research was still limited in terms of theoretical depth and types of applications. This period can be considered a warm-up period, in which Chinese researchers were learning and following international major KDD research directions.
Engineering applied to Manufacturing Problems

Optimization approaches have traditionally been viewed as tools for solving manufacturing problems, the optimization approach is not suitable for many problems arising in modern manufacturing systems due to their complexity and involvement of qualitative factors. In this paper we use a tool of software engineering applied to manufacturing problems. We use the Heuristics Lab software to determine and analyze the solution obtained for Manufacturing Problems.
Smart Transformations: The Evolution of Choice Principles

Evolutionary game theory classically investigates which behavioral patterns are evolutionarily successful in a single game. More recently, a number of contributions have studied the evolution of preferences instead: which subjective conceptualizations of a game’s payoffs give rise to evolutionarily successful behavior in a single game. Here, we want to extend this existing approach even further by asking: which general patterns of subjective conceptualizations of payoff functions are evolutionarily successful across a class of games. In other words, we will look at evolutionary competition of payoff transformations in “meta-games”, obtained from averaging over payoffs of single games. Focusing for a start on the class of 2 × 2 symmetric games, we show that regret minimization can outperform payoff maximization if agents resort to a security strategy in case of radical uncertainty.
2 Detecting noninterfering executions

We present an information flow monitoring mechanism for sequ ential programs. The monitor executes a program on standard data that are tagged with labels indicat ing their security level. We formalize the monitoring mechanism as a big-step operational semantics that inte grates a static information flow analysis to gather information flow properties of non-executed branches of the program. Using the information flow monitoring mechanism, it is then possible to partition the set of all exe cutions in two sets. The first one contains executions whichare safeand the other one contains executions which may be unsafe . Based on this information, we show that, by resetting the value of some output variables, it is p ossible to alter the behavior of executions belonging to the second set in order to ensure the confidentiality of sec ret data.
Review and evaluation of the proposed wireless mesh routing protocols

Wireless mesh networks (WMNs) have emerged as a key technology for next-generation wireless networking. Because of their advantages over other wireless networks, WMNs are undergoing rapid progress and many exciting applications. Although WMNs can be built up based on existing technologies, field trials and experiments with existing WMNs prove that the performance of WMNs is still far below expectations. Therefore, several challenging research were made to develop and improve the performance. This paper presents networking routing protocols proposed for WMNs. Performance analysis is shown, performance metrics considered are routing over head and packet delivery ratio. An evaluation summary was presented.
Automatic tumor detection in automated 3-D breast ultrasound using local phase information

Tumor localization in automated whole breast ultrasound (ABUS) images is an important and challenging task in a computer-aided detection (CAD) system. In this study, a completely automatic tumor detection method using the local phase information was proposed to accurately locate the tumor in ABUS images, thus accelerate the segmenting process. The phase in the max-energy orientation (PMO) image of the preprocessed ABUS image was acquired and binarized as well as the preprocessed image and the composed image obtained from the sum of the preprocessed image and the PMO image. Then morphologic postprocessing was performed to remove non-tumor regions and a region selection algorithm was used to get the tumor region from these three binary 3-D images and generate the volume of interests (VOI). The performance of the method was evaluated using a dataset of 40 cases and the sensitivity achieved 75% and 100% with false positives per volume of 0.25 and 2, respectively. Besides, the average precision rate and average recall rate of the detected VOI were 92.4% and 20.1%. The results proved that the proposed method could deal with various breast tumors and accurately locate the tumor.