Miracle-dz/UniFAR-FTUs huggingface dataset:
In vivo analysis of the stability and transport of nuclear poly(A)+ RNA

We have studied the distribution of poly(A)+ RNA in the mammalian cell nucleus and its transport through nuclear pores by fluorescence and electron microscopic in situ hybridization. Poly(A)+ RNA was detected in the nucleus as a speckled pattern which includes interchromatin granule clusters and perichromatin fibrils. When cells are fractionated by detergent and salt extraction as well as DNase I digestion, the majority of the nuclear poly(A)+ RNA was found to remain associated with the nonchromatin RNP-enriched fraction of the nucleus. After inhibition of RNA polymerase II transcription for 5-10 h, a stable population of poly(A)+ RNA remained in the nucleus and was reorganized into fewer and larger interchromatin granule clusters along with pre- mRNA splicing factors. This stable population of nuclear RNA may play an important role in nuclear function. Furthermore, we have observed that, in actively transcribing cells, the regions of poly(A)+ RNA which reached the nuclear pore complexes appeared as narrow concentrations of RNA suggesting a limited or directed pathway of movement. All of the observed nuclear pores contained poly(A)+ RNA staining suggesting that they are all capable of exporting RNA. In addition, we have directly visualized, for the first time in mammalian cells, the transport of poly(A)+ RNA through the nuclear pore complexes.
Evaluation of real time stereo vision system using web cameras

Stereo vision is a computationally expensive process that limits accurate real time performance. However, this is usually due to large resolutions in high end cameras. When low cost web cameras are exchanged for high resolution cameras, a practical real time stereo system can achieve real time performance. The accuracy of the disparity (depth) data depends strongly on the stereo camera calibration and rectification. Chessboards that have landscape orientations, which take at least 50% of the physical image size in a camera and move across the horizontal axis between sample views, give the best data for Levenberg-Marquardt iterative stereo camera calibration algorithm and Bougeut's stereo rectification algorithm to converge to an accurate result. Our research, using a 7×7 SAD window correspondence algorithm with a modern PC, generates approximately 8 frames per second with a sequential single thread programming model. The frame rate of our system provides reasonably real time response; however, the accuracy of depth data limits the number of applications. Therefore, applications that require detecting relative distances rather than absolute distances between objects, such as wheelchair navigation around buildings, could be equipped with our stereo vision system.
Spiking Irregularities of Acupuncture Electrical Signals in Spinal Dorsal

Neural system characterizes information in external stimulations by spatiotemporal encoding. When stimulated by the acupuncture, the neural system can evoke irregular electrical signals. In order to reveal the underlying mechanisms about the conduction and function of acupuncture, experiments are designed that different types of manual acupuncture (MA) manipulations and different frequencies of MA manipulations are taken at 'Zusanli' points of experiment rats, and the induced electrical signals in spinal dorsal root ganglion are detected and recorded. The concept of the inters pike interval (ISI) is used for the study of the acupuncture electrical signals. The ISI distribution is fit well by Gamma distribution, which has two parameters, one is time-dependent firing rate and the other one is a shape parameter characterizing spiking irregularities. The shape parameter is estimated as the measure of spiking irregularities and used to identify the type of MA manipulations or analysis frequency adaption of MA manipulations.
Mapping visual signal processing onto multi-core platform via algorithm/architecture co-exploration

Degree of parallelism and data communication should be investigated to achieve high performance for mapping algorithm onto multi-core platform since multi-core platform would concurrently process multiple tasks and lots of data would be transferred between storages and processors. This paper proposes a method to resolve the burden of increase on data transfer rate in parallel processing via the analysis on the dependency matrix of data flow graph. The proposed method does not bias any multi-core platform since it just considers the intrinsic characteristics of algorithm, i.e., data flow graph. This paper utilizes dependency matrix, which conveys the causality of data transfer, for quantifying data transfer rate and corresponding storage requirement; as a consequence, a feasible mapping result, which has smaller data transfer rate and acceptable storage requirement, was exploited. Furthermore, in conjunction with degree of parallelism quantification, this paper presents a comprehensive exploration on design space for mapping algorithm onto multi-core platform through dependency matrix. IBM Cell Broadband Engine is selected to be the targeted multi-core platform in this paper. Experimental results show that when six cores are used, our result can speedup 5.75x on average as compared to single-core case; in addition, by integrating the proposed method on data transfer analysis, about 46% cycles of data transfer could be saved and overall performance could be further increased to 7.51x on average in comparison with the scenario of single-core without data reuse.
A NUMA-Aware Runtime Environment for the Actor Model

The actor model is present in several mission-critical systems, such as those supporting WhatsApp and Twitter. These systems serve thousands of clients simultaneously, therefore demanding substantial computing resources usually provided by multiprocessor and multicore platforms. Non-Uniform Memory Access (NUMA) architectures account for an important share of these platforms. Yet, little or no research has been done on the suitability of the current actor runtime environments for these machines. Current runtime environments assume a flat memory space, thus not performing as well as they could. The NUMA environment presents challenges to the actor model runtime environment in fields varying from memory management to scheduling and load-balancing. In this document we analyze and characterize actor based applications to, in light of the above, propose improvements to actor runtime environments. As a proof of concept, we have applied our ideas in a real actor runtime environment, the Erlang virtual machine. This modified virtual machine uses the NUMA characteristics and the application knowledge to take better memory management, scheduling and load-balancing decisions. We have evaluated this modified runtime environment using standard benchmarks and, taking the default virtual machine as a baseline, we improved the performance of the tested applications by a factor of 2.50 on the best case while limiting our slowdown on the worst case by a factor of 1.09.
Interactive 3 D Medical Visualization : A Parallel Approach to Surface Rendering 3 D Medical Data

Using Pixel-Planes 5, a parallel multicomputer for computer graphics [Fuchs 90], we have constructed a system for visualizing volumetric medical data based on polygonal approaches to surface rendering. The goal is a medical visualization system that has intuitive navigation and exploration capabilities to present 3D clinical data using three dimensional images. To provide a natural navigation of patient data, segmentation parameters should provide user feedback at minimum rates of one update per second, and viewing direction and lighting control should respond in tenths of seconds. Our approach differs from other methods under investigation at UNC [Yoo 92] as we take advantage of the hardware graphics accelerators for polygon rendering rather than attempt direct volume rendering.
Positive and negative regulation of the composite octamer motif of the interleukin 2 enhancer by AP-1, Oct-2, and retinoic acid receptor

The differentiating agent retinoic acid (RA) has been previously reported to interfere with 12-O-tetradecanoyl-phorbol-13-acetate (TPA)/Ca(2+)-induced signals for the regulation of the -96 to -66-bp octamer motif found in the enhancer for the interleukin (IL)-2 gene, which encodes a major T lymphocyte growth factor. The IL-2 octamer motif is a composite cis-element which binds Oct-1 and Oct-2 as well as a TPA/Ca(2+)-inducible nuclear factor, previously termed octamer- associated protein (OAP40). We show here that Oct-2, despite the presence of an active transcriptional activation domain, requires TPA/Ca(2+)-induced signals to strongly transactivate the IL-2 octamer motif in Jurkat T cells. This Oct-2-dependent transactivation is inhibited by RA. The presence of an intact COOH-terminal domain of Oct- 2 contributes to both TPA/Ca(2+)-induced transactivation and the RA- mediated repression. We also show that both Fos and Jun components of the AP-1 factors participate in the OAP40 complex. Furthermore, transfected c-jun, jun-B, jun-D, c-fos, or Fos-B expression vectors partially substitute for TPA and Ca2+ and cooperate with Oct-2 for the transactivation of the combined OAP/octamer cis-element. Mutations of the genuine octamer-binding site abrogate both the binding of Oct-1 and Oct-2 and the TPA/Ca(2+)-induced transactivation of the OAP/octamer motif. OAP confers to Oct-2 responsivity to both TPA/Ca2+ and RA, since specific mutations of the AP-1/OAP-binding site significantly reduce the transactivation by Oct-2 in response to TPA and Ca2+ and abolish the inhibition by RA. Furthermore, retinoic acid receptor (RAR) alpha is able to inhibit in vitro the formation of the complex between the nuclear AP-1/OAP and its specific binding site, resulting in the interference with Oct-2-dependent cis-regulatory function of this AP-1 element. Therefore, we propose that the TPA/calcium-activated AP-1/OAP element is the main target of positive or negative regulatory signals influencing the IL-2 octamer motif, through synergism with Oct-2 and antagonism by RAR.
A Batch Join Scheme for Flash Crowd Reduction in IPTV Systems

Peer-to-peer (P2P) streaming is an effective and popular approach for large scale television multicasting over Internet. However, it is always a major challenge when thousands of peers join a popular P2P IPTV channel in a short time, so called the problem of flash crowd. When the problem occurs, a large number of users suffer from large latency in joining a channel and even get blocked. In the past, rare studies are focused on the flash crowd issue. In this paper, we identify several key factors that may cause the flash crowd problem: request congestion, stream congestion, control message, and maintenance overhead. Based on our analysis, we present a batch join scheme instead of processing new users one by one. Our batch join process also solves the problem of current join processes that only use existing active peers to serve new users. We generate a virtual sub tee based purely on a batch of new peers which is then connected to an active peer server. Simulation results demonstrate that our batch join scheme significantly mitigate the flash crowd situation. Moreover, both of the peer blocking rate and re-join times are significant reduced.
Long-Term Effects and Prognosis in Acute Heart Failure Treated with Tolvaptan: The AVCMA Trial

Background. Diuresis is a major therapy for the reduction of congestive symptoms in acute decompensated heart failure (ADHF) patients. We previously reported the efficacy and safety of tolvaptan compared to carperitide in hospitalized patients with ADHF. There were some reports of cardio- and renal-protective effects in carperitide; therefore, the purpose of this study was to compare the long-term effects of tolvaptan and carperitide on cardiorenal function and prognosis. Methods and Results. One hundred and five ADHF patients treated with either tolvaptan or carperitide were followed after hospital discharge. Levels of plasma B-type natriuretic peptide, serum sodium, potassium, creatinine, and estimated glomerular filtration rate were measured before administration of tolvaptan or carperitide at baseline, the time of discharge, and one year after discharge. These data between tolvaptan and carperitide groups were not different one year after discharge. Kaplan-Meier survival curves demonstrated that the event-free rate regarding all events, cardiac events, all cause deaths, and rehospitalization due to worsening heart failure was not significantly different between tolvaptan and carperitide groups. Conclusions. We demonstrated that tolvaptan had similar effects on cardiac and renal function and led to a similar prognosis in the long term, compared to carperitide.
Reinventing the Contingency Wheel: Scalable Visual Analytics of Large Categorical Data

Contingency tables summarize the relations between categorical variables and arise in both scientific and business domains. Asymmetrically large two-way contingency tables pose a problem for common visualization methods. The Contingency Wheel has been recently proposed as an interactive visual method to explore and analyze such tables. However, the scalability and readability of this method are limited when dealing with large and dense tables. In this paper we present Contingency Wheel++, new visual analytics methods that overcome these major shortcomings: (1) regarding automated methods, a measure of association based on Pearson's residuals alleviates the bias of the raw residuals originally used, (2) regarding visualization methods, a frequency-based abstraction of the visual elements eliminates overlapping and makes analyzing both positive and negative associations possible, and (3) regarding the interactive exploration environment, a multi-level overview+detail interface enables exploring individual data items that are aggregated in the visualization or in the table using coordinated views. We illustrate the applicability of these new methods with a use case and show how they enable discovering and analyzing nontrivial patterns and associations in large categorical data.
An empirical analysis of the co-evolution of schema and code in database applications

Modern database applications are among the most widely used and complex software systems. They constantly evolve, responding to changes to data, database schemas, and code. It is challenging to manage these changes and ensure that everything co-evolves consistently. For example, when a database schema is modified, all the code that interacts with the database must be changed accordingly. Although database evolution and software evolution have been extensively studied in isolation, the co-evolution of schema and code has largely been unexplored. This paper presents the first comprehensive empirical analysis of the co-evolution of database schemas and code in ten popular large open-source database applications, totaling over 160K revisions. Our major findings include: 1) Database schemas evolve frequently during the application lifecycle, exhibiting a variety of change types with similar distributions across the studied applications; 2) Overall, schema changes induce significant code-level modifications, while certain change types have more impact on code than others; and 3) Co-change analyses can be viable to automate or assist with database application evolution. We have also observed that: 1) 80% of the schema changes happened in 20-30% of the tables, while nearly 40% of the tables did not change; and 2) Referential integrity constraints and stored procedures are rarely used in our studied subjects. We believe that our study reveals new insights into how database applications evolve and useful guidelines for designing assistive tools to aid their evolution.
Handling forecast errors while bidding for display advertising

Most of the online advertising today is sold via an auction, which requires the advertiser to respond with a valid bid within a fraction of a second. As such, most advertisers employ bidding agents to submit bids on their behalf. The architecture of such agents typically has (1) an offline optimization phase which incorporates the bidder's knowledge about the market and (2) an online bidding strategy which simply executes the offline strategy. The online strategy is typically highly dependent on both supply and expected price distributions, both of which are forecast using traditional machine learning methods. In this work we investigate the optimum strategy of the bidding agent when faced with incorrect forecasts. At a high level, the agent can invest resources in improving the forecasts, or can tighten the loop between successive offline optimization cycles in order to detect errors more quickly. We show analytically that the latter strategy, while simple, is extremely effective in dealing with forecast errors, and confirm this finding with experimental evaluations.
How guilt/shame proneness and coping styles are related to music performance anxiety and stress symptoms by gender

In the present study, the predictive values of gender, coping strategies, and guilt/shame orientation were examined in relation to music performance anxiety (MPA) and stress symptoms among university-level Turkish music students. The sample consisted of 399 participants (244 females and 155 males) who were being trained in various instruments. Independent t-test analyses revealed that females had higher scores than males on MPA, stress, helpless and submissive coping strategies, guilt, and shame orientation. Hierarchical regression analyses showed that gender, solo concert experience, helpless and self-confident coping, and shame orientation significantly predicted MPA scores. A similar analysis revealed that gender, helpless and socially supported coping, and shame significantly predicted stress scores. Since gender was a significant predictor in the preliminary regression analyses, gender-based regression analyses were performed. These analyses indicated that, for females, solo concert experience, helpless approach, and shame predicted MPA; and helpless approach and shame orientation predicted stress scores. On the other hand, for males, solo concert experience and the helpless approach appeared as the significant predictors of MPA; and only helpless approach predicted stress scores. Findings are discussed in the light of current literature and cultural characteristics.
Responses of redwood soil microbial community structure and N transformations to climate change

Soil microorganisms perform critical ecosystem functions, including decomposition, nitrogen (N) mineralization and nitrification. Soil temperature and water availability can be critical determinants of the rates of these processes as well as microbial community composition and structure. This research examined how changes in climate affect bacterial and fungal community structures and rates of N mineralization and nitrification in coast redwood forest soils. Soils were reciprocally transplanted between three redwood sites located across a latitudinal climate gradient, from near the southern extent of redwoods to near their northern extent and collected one year later at the end of the summer. A molecular community fingerprinting technique was used to examine changes in fungal and bacterial community structures, and 15N-isotope pool dilution was used to measure gross rates of N mineralization and nitrification. After one year, soil fungal and bacterial community structures in transplanted soils had changed to become more similar, but not identical, to those native to their new destination sites. Both climatic and edaphic variables were correlated with the variability in microbial community structure. While there were few significant differences in gross N mineralization rates between soil-climate combinations, gross nitrification rates were influenced by a change in climate. Rates of gross nitrification were highest in soils when located in the wetter, most northern site. While rates of gross nitrification varied widely in soils with water potentials above -0.05 MPa, rates were low in soils below -0.05 MPa. Changes in redwood climate, fog frequency and summer water availability will likely alter soil microbial community structure and rates of gross nitrification. Greater magnitude changes in climate or more than one year of exposure may be necessary to cause alterations in rates of gross N mineralization.
Manufacturing Execution System for a Subsidiary of Aerospace Manufacturing Industry

Abstract—Aerospace manufacturing requires precision tools and control systems. Integrated Manufacturing Execution System (MES) in a subsidiary of aerospace manufacturing industry initiate, guide, respond to and report on manufacturing activities as they occur from order launch to finished product by improving quality and reducing costs of the product. Products can be tracked throughout the manufacturing process using the work-in-process (WIP) tools in MES Factory Server, reducing time to complete the product. It provides product history including part traceability that meets Military Specifications and Aerospace specification requirements for the life of the product. MES fill the gap between the production planning system at the higher level and the Shop Floor at the lower level. Nowadays, MES applications have become essential to support real-time production control as well as data collection and reporting, require improving production performance. Starting with the brief background of MES, this paper provides an overview of the literature related to evolution and current position of MES that is found in various research papers. Current status of the industry under study is required an effective MES that is developed and described. This paper presents the architecture of MES for subsidiary of an aerospace manufacturing industry by analyzing the design need of an aerospace manufacturing industry and unfolding the functions of its modules. The complete MES architecture consists of MES databases having different modules functions and the MES Factory Server that allow factory managers to query and update the MES databases.
Real-Time Resolution of Self-Intersection in Dynamic Cylindrical Free-Form Deformation

This paper presents a method of self-intersection detection and resolution for dynamic cylindrical-lattice-based free-form deformation (FFD). The lattice-based approach allows efficient computation of deformation of complex geometries. But excessive deformation can cause visual anomalies such as surface infiltration and distortion. This paper derives a geometrically intuitive sufficient condition to guarantee that the FFD function is a homeomorphism and there is no self-intersection. The FFD function is defined by linear and quadratic B-Spline functions with the control points of the cylindrical lattice cell. The sufficient condition is satisfied if each trilinear function of the nine prism-shaped pentahedrons derived from the cell has a positive Jacobian determinant. The positivity is satisfied if the 12 tetrahedrons derived from the pentahedron have positive volumes. Based on the sufficient condition, the proposed method converts the self-intersection problem into a point-face collision detection and response problem suitable for dynamic simulation. The efficiency and accuracy of the self-intersection detection algorithm is analyzed and compared with a previous method. The results show that the proposed technique allows simulation of excessive deformation of tubular objects in an efficient and realistic manner.