Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of Exponent Parameter Value for the Partition Matrix on the Performance of Fuzzy C Means Algorithm

Soft Clustering plays a very important rule on clustering real world data where a data item contributes to more than one cluster. Fuzzy logic based algorithms are always suitable for performing soft clustering tasks. Fuzzy C Means (FCM) algorithm is a very popular fuzzy logic based algorithm. In case of fuzzy logic based algorithm, the parameter like exponent for the partition matrix that we have to fix for the clustering task plays a very important rule on the performance of the algorithm. In this paper, an experimental analysis is done on FCM algorithm to observe the impact of this parameter on the performance of the algorithm.
A Simple Text Mining Approach for Ranking Pairwise Associations in Biomedical Applications

We present a simple text mining method that is easy to implement, requires minimal data collection and preparation, and is easy to use for proposing ranked associations between a list of target terms and a key phrase. We call this method KinderMiner, and apply it to two biomedical applications. The first application is to identify relevant transcription factors for cell reprogramming, and the second is to identify potential drugs for investigation in drug repositioning. We compare the results from our algorithm to existing data and state-of-the-art algorithms, demonstrating compelling results for both application areas. While we apply the algorithm here for biomedical applications, we argue that the method is generalizable to any available corpus of sufficient size.
Optically transparent membrane based on bacterial cellulose/polycaprolactone

Optically transparent membranes from bacterial cellulose (BC)/polycaprolactone (PCL) have been prepared by impregnation of PCL acetone solution into dried BC membranes. UV-Vis measurements showed an increase on transparency in BC/PCL membrane when compared with pristine BC. The good transparency of the BC/PCL can be related to the presence of BC nanofibers associated with deposit of PCL nano-sized spherulites which are smaller than the wavelength of visible light and practically free of light scattering. XRD results show that cellulose type I structure is preserved inside the BC/PCL membrane, while the mechanical properties suggested indicated that PCL acts as a plasticizer for the BC membrane. The novel BC/PCL membrane could be used for preparation of fully biocompatible flexible display and biodegradable food packaging.
Two Minimal Problems for Cameras with Radial Distortion

Epipolar geometry and relative camera pose computation for uncalibrated cameras with radial distortion has recently been formulated as a minimal problem and successfully solved in floating point arithmetics. The singularity of the fundamental matrix has been used to reduce the minimal number of points to eight. It was assumed that the cameras were not calibrated but had same distortions. In this paper we formulate two new minimal problems for estimating epipolar geometry of cameras with radial distortion. First we present a minimal algorithm for partially calibrated cameras with same radial distortion. Using the trace constraint which holds for the epipolar geometry of calibrated cameras to reduce the number of necessary points from eight to six. We demonstrate that the problem is solvable in exact rational arithmetics. Secondly, we present a minimal algorithm for uncalibrated cameras with different radial distortions. We show that the problem can be solved using nine points in two views by manipulating polynomials by a sequence of Gauss-Jordan eliminations in exact rational arithmetics. We demonstrate the algorithms on synthetic and real data.
Airway Epithelial Cells Condition Dendritic Cells to Express Multiple Immune Surveillance Genes

Increasing evidence suggests that crosstalk between airway epithelial cells (AEC) and adjacent dendritic cells (DC) tightly regulates airway mucosal DC function in steady state. AEC are known to express multiple immmuno-modulatory factors, though detailed information on how this influences human DC function remains incomplete. We recently demonstrated using an in vitro coculture model that AEC alter differentiation of monocytes into DC in a manner that inhibits expression of potentially damaging Th2 effector function. In the current study, we have extended these findings to examine other aspects of DC function. Using micro-array technology we show that multiple genes important for immune surveillance are significantly over expressed in purified AEC-conditioned DC, compared to control DC. These findings were confirmed by quantitative real time PCR or flow cytometry in an independent sample set. In particular, AEC-conditioned DC showed selective upregulation of chemokines that recruit Th1 cells, but minimal change in chemokines linked to Th2 cell recruitment. AEC-conditioned DC were also characterized by enhanced expression of complement family genes (C1QB, C2, CD59 and SERPING1), Fcγ receptor genes (FCGR1A, FCGR2A, FCGR2B and FCGR2C), signaling lymphocytic activation molecule family member 1 (SLAM), programmed death ligands 1 and 2, CD54 and CD200R1, relative to control DC. These findings suggest that AEC conditioning facilitates the capacity of DC to react to danger signals, to enhance leukocyte recruitment, especially of Th1 effector cells, and to interact with other immune cell populations while minimizing the risks of excessive inflammation leading to tissue damage.
Architectural Analysis of MATLAB/Simulink Models with Artshop

This paper introduces the artshop model repository framework which, among others, includes methods to analyse the structure and quality of the architecture of model-based software developed with The Mathwork's Matlab-Simulink/Stateflow. The framework supports the import of MATLAB-Simulink/Stateflow models and is able to synchronize imported models with their initial sources. Imported model data can be queried, inspected, analyzed and enriched with meta-information like associations or additional documentation. Analyses provided by artshop include duplicate detection, model slicing, various coupling and cohesion metrics and user-defined conformity checks for MATLAB/Simulink models.
The Estimation of Chaotic Signal Initial Value

Chaotic signal has abroad applications in communication. Most such applications require an accurate estimation of initial values of actual chaotic sequence from a noisy signal so as to recover the Chaotic signal to realize the correct receiving in the terminial. Some algorithms are currently available which are limited to ideal situations with very high signal-to-noise ratios(SNR’s). This paper presents a modified minimum mean squares estimate algorithm to estimate the initial condition of a chaotic signal in a wide range of SNR’s down to -3dB. Take the logistic map as an example, we have simulated and validated the new method.
A novel diplexer-based receiver for simultaneous wireless information and power transfer

Simultaneous wireless information and power transfer (SWIPT) is an appealing research area because both information and energy can be delivered to wireless devices simultaneously. In this paper, we propose a novel diplexer-based receiver that can utilize both the baseband and the doubling frequency signals after the mixer. The baseband signals are used for information decoding (ID) and the doubling frequency signals are converted to direct current for energy harvesting (EH). We then analyze the signal in the receiver and find that the power of the EH part is equal to that of the ID part. Therefore, the diplexer-based receiver can be used as a power splitter with a power splitting (PS) factor of value 0.5. Moreover, we show that joint design of the classical PS scheme and the diplexer-based scheme can further improve the performance. The simulation results demonstrate the advantage of our new design.
Regulation of Arbuscular Mycorrhization by Carbon. The Symbiotic Interaction Cannot Be Improved by Increased Carbon Availability Accomplished by Root-Specifically Enhanced Invertase Activity[W]

The mutualistic interaction in arbuscular mycorrhiza (AM) is characterized by an exchange of mineral nutrients and carbon. The major benefit of AM, which is the supply of phosphate to the plant, and the stimulation of mycorrhization by low phosphate fertilization has been well studied. However, less is known about the regulatory function of carbon availability on AM formation. Here the effect of enhanced levels of hexoses in the root, the main form of carbohydrate used by the fungus, on AM formation was analyzed. Modulation of the root carbohydrate status was performed by expressing genes encoding a yeast (Saccharomyces cerevisiae)-derived invertase, which was directed to different subcellular locations. Using tobacco (Nicotiana tabacum) alc∷cwINV plants, the yeast invertase was induced in the whole root system or in root parts. Despite increased hexose levels in these roots, we did not detect any effect on the colonization with Glomus intraradices analyzed by assessment of fungal structures and the level of fungus-specific palmitvaccenic acid, indicative for the fungal carbon supply, or the plant phosphate content. Roots of Medicago truncatula, transformed to express genes encoding an apoplast-, cytosol-, or vacuolar-located yeast-derived invertase, had increased hexose-to-sucrose ratios compared to β-glucuronidase-transformed roots. However, transformations with the invertase genes did not affect mycorrhization. These data suggest the carbohydrate supply in AM cannot be improved by root-specifically increased hexose levels, implying that under normal conditions sufficient carbon is available in mycorrhizal roots. In contrast, tobacco rolC∷ppa plants with defective phloem loading and tobacco pyk10∷InvInh plants with decreased acid invertase activity in roots exhibited a diminished mycorrhization.
A Description of Tunable Machine Translation Evaluation Systems in WMT13 Metrics Task

This paper is to describe our machine translation evaluation systems used for participation in the WMT13 shared Metrics Task. In the Metrics task, we submitted two automatic MT evaluation systems nLEPOR_baseline and LEPOR_v3. 1. nLEPOR_baseline is an n-gram based language independent MT evaluation metric employing the factors of modified sentence length penalty, position difference penalty, n-gram precision and n-gram recall. nLEPOR_baseline measures the similarity of the system output translations and the reference translations only on word sequences. LEPOR_v3. 1 is a new version of LEPOR metric using the mathematical harmonic mean to group the factors and employing some linguistic features, such as the part-of-speech information. The evaluation results of WMT13 show LEPOR_v3. 1 yields the highest averagescore 0.86 with human judgments at systemlevel using Pearson correlation criterion on English-to-other (FR, DE, ES, CS, RU) language pairs.
Restructuring unit tests with TestSurgeon

The software engineering community has produced great techniques for software maintainability, however, less effort is dedicated to have unit tests modular and extensible. TestSurgeon is a profiler for unit tests which collects information from tests execution. It proposes a metric for similarity between tests and provides a visualization to help developers restructure their unit tests.
The Neurospora Circadian System

The eukaryotic filamentous fungus Neurospora crassa has proven to be a durable and dependable model system for the analysis of the cellular and molecular bases of circadian rhythms. Pioneering genetic analyses identified clock genes, and beginning with the cloning of frequency (frq), work over the past 2 decades has revealed the molecular basis of a core circadian clock feedback loop that has illuminated our understanding of circadian oscillators in microbes, plants, and animals. In this transcription/translation-based feedback loop, a heterodimer of the White Collar-1 (WC-1) and WC-2 proteins acts both as the circadian photoreceptor and, in the dark, as a transcription factor that promotes the expression of the frq gene. FRQ dimerizes and feeds back to block the activity of its activators (making a negative feedback loop), as well as feeding forward to promote the synthesis of its activator, WC-1. Phosphorylation of FRQ by several kinases leads to its ubiquitination and turnover, releasing the WC-1/WC-2 dimer to reactivate frq expression and restart the circadian cycle. Light resetting of the clock can be understood through the rapid light induction of frq expression and temperature resetting through the influence of elevated temperaturesin driving higher levels of FRQ. Several FRQ- and WC-independent, noncircadian FRQ-less oscillators (FLOs) have been described, each of which appears to regulate aspects of Neurospora growth or development. Overall, the FRQ/white collar complex feedback loop appears to coordinate the circadian system through its activity to regulate downstream-target clock-controlled genes, either directly or via regulation of driven FLOs.
Testing the Efficacy of Global Biodiversity Hotspots for Insect Conservation: The Case of South African Katydids

The use of endemism and vascular plants only for biodiversity hotspot delineation has long been contested. Few studies have focused on the efficacy of global biodiversity hotspots for the conservation of insects, an important, abundant, and often ignored component of biodiversity. We aimed to test five alternative diversity measures for hotspot delineation and examine the efficacy of biodiversity hotspots for conserving a non-typical target organism, South African katydids. Using a 1° fishnet grid, we delineated katydid hotspots in two ways: (1) count-based: grid cells in the top 10% of total, endemic, threatened and/or sensitive species richness; vs. (2) score-based: grid cells with a mean value in the top 10% on a scoring system which scored each species on the basis of its IUCN Red List threat status, distribution, mobility and trophic level. We then compared katydid hotspots with each other and with recognized biodiversity hotspots. Grid cells within biodiversity hotspots had significantly higher count-based and score-based diversity than non-hotspot grid cells. There was a significant association between the three types of hotspots. Of the count-based measures, endemic species richness was the best surrogate for the others. However, the score-based measure out-performed all count-based diversity measures. Species richness was the least successful surrogate of all. The strong performance of the score-based method for hotspot prediction emphasizes the importance of including species’ natural history information for conservation decision-making, and is easily adaptable to other organisms. Furthermore, these results add empirical support for the efficacy of biodiversity hotspots in conserving non-target organisms.
Lossless Intra Coding in HEVC with 3-tap Filters

This paper presents a pixel-by-pixel spatial prediction method for lossless intra coding within High Efficiency Video Coding (HEVC). A well-known previous pixel-by-pixel spatial prediction method uses only two neighboring pixels for prediction, based on the angular projection idea borrowed from block-based intra prediction in lossy coding. This paper explores a method which uses three neighboring pixels for prediction according to a two-dimensional correlation model, and the used neighbor pixels and prediction weights change depending on intra mode. To find the best prediction weights for each intra mode, a two-stage offline optimization algorithm is used and a number of implementation aspects are discussed to simplify the proposed prediction method. The proposed method is implemented in the HEVC reference software and experimental results show that the explored 3-tap filtering method can achieve an average 11.34% bitrate reduction over the default lossless intra coding in HEVC. The proposed method also decreases average decoding time by 12.7% while it increases average encoding time by 9.7%
An Association-Based Unified Framework for Mining Features and Opinion Words

Mining features and opinion words is essential for fine-grained opinion analysis of customer reviews. It is observed that semantic dependencies naturally exist between features and opinion words, even among features or opinion words themselves. In this article, we employ a corpus statistics association measure to quantify the pairwise word dependencies and propose a generalized association-based unified framework to identify features, including explicit and implicit features, and opinion words from reviews. We first extract explicit features and opinion words via an association-based bootstrapping method (ABOOT). ABOOT starts with a small list of annotated feature seeds and then iteratively recognizes a large number of domain-specific features and opinion words by discovering the corpus statistics association between each pair of words on a given review domain. Two instances of this ABOOT method are evaluated based on two particular association models, likelihood ratio tests (LRTs) and latent semantic analysis (LSA). Next, we introduce a natural extension to identify implicit features by employing the recognized known semantic correlations between features and opinion words. Experimental results illustrate the benefits of the proposed association-based methods for identifying features and opinion words versus benchmark methods.
BASIC: BCR assembly from single cells

Motivation: The B‐cell receptor enables individual B cells to identify diverse antigens, including bacterial and viral proteins. While advances in RNA‐sequencing (RNA‐seq) have enabled high throughput profiling of transcript expression in single cells, the unique task of assembling the full‐length heavy and light chain sequences from single cell RNA‐seq (scRNA‐seq) in B cells has been largely unstudied. Results: We developed a new software tool, BASIC, which allows investigators to use scRNA‐seq for assembling BCR sequences at single‐cell resolution. To demonstrate the utility of our software, we subjected nearly 200 single human B cells to scRNA‐seq, assembled the full‐length heavy and the light chains, and experimentally confirmed these results by using single‐cell primer‐based nested PCRs and Sanger sequencing. Availability and Implementation: http://ttic.uchicago. edu/˜aakhan/BASIC Contact: aakhan@ttic.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Towards an integrated framework for querying collection of heterogeneous data

Keywords queries on various data models have been studied in the past. Regardless of the nature of target data, a keyword query poses a common problem: the difficulty in determining a suitable retrieval unit. In this paper, we discuss this problem in a new scenario that assumes several different types of data being stored and queried in a unified framework. A hypothetical general query model that borrows the ideas of our previous model designed for XML and linear video data is presented. We then state the requirements and challenges to realize such a model.
Optimal Cutoff Levels of More Sensitive Cardiac Troponin Assays for the Early Diagnosis of Myocardial Infarction in Patients With Renal Dysfunction

Background— It is unknown whether more sensitive cardiac troponin (cTn) assays maintain their clinical utility in patients with renal dysfunction. Moreover, their optimal cutoff levels in this vulnerable patient population have not previously been defined. Methods and Results— In this multicenter study, we examined the clinical utility of 7 more sensitive cTn assays (3 sensitive and 4 high-sensitivity cTn assays) in patients presenting with symptoms suggestive of acute myocardial infarction. Among 2813 unselected patients, 447 (16%) had renal dysfunction (defined as Modification of Diet in Renal Disease–estimated glomerular filtration rate <60 mL·min−1·1.73 m−2). The final diagnosis was centrally adjudicated by 2 independent cardiologists using all available information, including coronary angiography and serial levels of high-sensitivity cTnT. Acute myocardial infarction was the final diagnosis in 36% of all patients with renal dysfunction. Among patients with renal dysfunction and elevated baseline cTn levels (≥99th percentile), acute myocardial infarction was the most common diagnosis for all assays (range, 45%–80%). In patients with renal dysfunction, diagnostic accuracy at presentation, quantified by the area under the receiver-operator characteristic curve, was 0.87 to 0.89 with no significant differences between the 7 more sensitive cTn assays and further increased to 0.91 to 0.95 at 3 hours. Overall, the area under the receiver-operator characteristic curve in patients with renal dysfunction was only slightly lower than in patients with normal renal function. The optimal receiver-operator characteristic curve–derived cTn cutoff levels in patients with renal dysfunction were significantly higher compared with those in patients with normal renal function (factor, 1.9–3.4). Conclusions— More sensitive cTn assays maintain high diagnostic accuracy in patients with renal dysfunction. To ensure the best possible clinical use, assay-specific optimal cutoff levels, which are higher in patients with renal dysfunction, should be considered. Clinical Trial Registration— URL: http://www.clinicaltrials. gov. Unique identifier: NCT00470587.
Faster Complex SoC Design by Virtual Prototyping

Development of complex System on Chip (SoC) for modern communication systems has become more and more challenging. A designer has to bridge the gap between the requirements of the system at algorithmic level and its cycle true hardware description; the latter being synthesized for an Application Specific Integrated Circuit. This development requires numerous sub-steps, i.e., several intermediate descriptions on dierent
Sport Facilities as a Broadcast Studio for Human Extensibility? Geographic Information System-Based Diagrams of a High- and Low-Identified Sport Fan

This exploratory research investigation focused on the concept of human extensibility and sought to introduce the topic to the sport management literature. The purpose of this inquiry on human extensibility centered on attempting to better understand how professionalized sport facilities embrace communication technology to help virtual and remote spectators become extensible agents. The space-time path of both a high and low-identified sport fan was tracked through the creation of a Geographic Information System (GIS) based model to help explain the extensibility phenomenon. The GIS-based diagrams were established with the help of data collected from a space-time diary, video camera, and participant interviews. Professionalized sport facilities enjoy the space and ability to incorporate highly technical structures within their confines to help improve human extensibility, however, people must possess the resources (i.e., time and money), desire, and knowledge to exploit the technology. The researcher sugg.