Miracle-dz/UniFAR-FTUs huggingface dataset:
KIF5B-ALK, a Novel Fusion Oncokinase Identified by an Immunohistochemistry-based Diagnostic System for ALK-positive Lung Cancer

Purpose: EML4-ALK is a transforming fusion tyrosine kinase, several isoforms of which have been identified in lung cancer. Immunohistochemical detection of EML4-ALK has proved difficult, however, likely as a result of low transcriptional activity conferred by the promoter-enhancer region of EML4. The sensitivity of EML4-ALK detection by immunohistochemistry should be increased adequately. Experimental Design: We developed an intercalated antibody-enhanced polymer (iAEP) method that incorporates an intercalating antibody between the primary antibody to ALK and the dextran polymer-based detection reagents. Results: Our iAEP method discriminated between tumors positive or negative for EML4-ALK in a test set of specimens. Four tumors were also found to be positive for ALK in an archive of lung adenocarcinoma (n = 130) and another 4 among fresh cases analyzed in a diagnostic laboratory. These 8 tumors were found to include 1 with EML4-ALK variant 1, 1 with variant 2, 3 with variant 3, and 2 with previously unidentified variants (designated variants 6 and 7). Inverse reverse transcription-PCR analysis revealed that the remaining tumor harbored a novel fusion in which intron 24 of KIF5B was ligated to intron 19 of ALK. Multiplex reverse transcription-PCR analysis of additional archival tumor specimens identified another case of lung adenocarcinoma positive for KIF5B-ALK. Conclusions: The iAEP method should prove suitable for immunohistochemical screening of tumors positive for ALK or ALK fusion proteins among pathologic archives. Coupling of PCR-based detection to the iAEP method should further facilitate the rapid identification of novel ALK fusion genes such as KIF5B-ALK.
Evolutionary computing for optimizing type-2 fuzzy systems in intelligent control of non-linear dynamic plants

We describe in this paper the use of evolutionary computing techniques for optimizing the design of intelligent controllers. Genetic algorithms can be used to optimize the topology of a fuzzy system for control. We are considering type-2 fuzzy logic for intelligent control and as a consequence the task of designing the fuzzy system is more difficult. We use hierarchical genetic algorithms because the problem of fuzzy system optimization requires a hierarchical chromosome for representing the information about membership functions and parameters.
Minimization and Reliability Analyses of Attack Graphs

Abstract : An attack graph is a succinct representation of all paths through a system that end in a state where an intruder has successfully achieved his goal. Today Red Teams determine the vulnerability of networked systems by drawing gigantic attack graphs by hand. Constructing attack graphs by hand is tedious, error-prone, and impractical for large systems. By viewing an attack as a violation of a safety property, we can use model checking to produce attack graphs automatically: a successful path from the intruder's viewpoint is a counterexample produced by the model checker. In this paper we present an algorithm for generating attack graphs using model checking. Security analysts use attack graphs for detection, defense, and forensics. In this paper we present a minimization technique that allows analysts to decide which minimal set of security measures would guarantee the safety of the system. We provide a formal characterization of this problem: we prove that it is polynomially equivalent to the minimum hitting set problem and we present a greedy algorithm with provable bounds. We also present a reliability technique that allows analysts to perform a simple cost-benefit analysis depending on the likelihoods of attacks. By interpreting attack graphs as Markov Decision Processes we can use a standard MDP value iteration algorithm to compute the probabilities of intruder success for each attack the graph. We illustrate our work in the context of a small example that includes models of a firewall and an intrusion detection system.
Document Clustering: A Review

As the internet is exploding with huge volume of text documents, the need of grouping similar documents together for versatile applications have hold the attention of researchers in this area. Document clustering can facilitate the tasks of document organization and web browsing, search engine results, corpus summarization, documents classification, information retrieval and filtering. However several attempts have been made to develop efficient document clustering algorithms but most of the clustering methods suffer from challenges in dealing with problems of high dimensionality, scalability, accuracy and meaningful cluster labels. This paper intends to provide a brief summary over methods studied and current state of documents clustering research, including basic traditional methods as well as advanced fuzzy based, GA, PSO, HS oriented techniques etc. Also document representation model and its challenges, dimensionality reduction mechanisms, issues in document clustering, and cluster quality evaluation criteria are discussed.
Effects of dialyser and dialysate on the acute phase reaction in clinical bicarbonate dialysis.

BACKGROUND In chronic haemodialysis (HD), morbidity may result from repetitive induction of the acute phase response, caused by a bioincompatible dialysis membrane and/or contaminated dialysate. In the present study, cytokine release (interleukin-6, IL-6) and subsequent production of acute phase proteins (C-reactive protein, CRP and secretory phospholipase A(2), sPLA(2)) were assessed to investigate whether the HD-induced acute phase reaction depends mainly on the type of membrane or on the sterility of the dialysate. METHODS In 11 patients, IL-6, CRP and sPLA(2) levels were assessed in blood samples drawn before (t(0)), at the end (t(180)) and 24 h after the start of HD (t(1440)). All patients were dialysed on Cuprammonium (CU) and Polysulphon (PS) dialysers and seven patients underwent an additional HD session on CU plus a dialysate filter (CUf). RESULTS IL-6 levels were increased significantly at t(180) compared with t(0) (P<0.02) with both CU and CUf. At t(1440), IL-6 levels had returned to baseline. In contrast, marked fluctuations did not occur during HD with PS. At t(180), IL-6 was significantly greater with CU and CUf devices, than with PS (P<0.02). Following HD with CU and CUf, a significant increase in CRP was observed at t(1440), compared with postdialysis values (P</=0.05). In addition, sPLA(2) values were markedly increased at t(1440), compared with t(180), but only significant in the case of CU (P=0.01). IL-6 levels at t(180) were significantly correlated with CRP (r=0.50, P<0.01) and sPLA(2) (r=0.47, P=0.01) values at t(1440). During HD with PS membranes, neither CRP nor sPLA(2) values were markedly changed. CONCLUSIONS In contrast to PS, both CU and CUf resulted in elevated IL-6 plasma levels at the end of HD, compared with t(0), which correlated with increased CRP and sPLA(2) values 24 h later. Therefore, the type of membrane, rather than the bacterial quality of the dialysate, seems to be responsible for the induction of the acute phase response during clinical bicarbonate HD.
Knowledge Representation , Tags , Metadata CONNECTING THE DOTS : MUSIC METADATA GENERATION , SCHEMAS AND APPLICATIONS

With the ever-increasing amount of digitized music becoming available, metadata is a key driver for different music related application domains. A service that combines different metadata sources should be aware of the existence of different schemas to store and exchange music metadata. The user of a metadata provider could benefit from knowledge about the metadata needs for different music application domains. In this paper, we present how we can compare the expressiveness and richness of a metadata schema for an application. To cope with different levels of granularity in metadata fields we defined clusters of semantically related metadata fields. Similarly, application domains were defined to tackle the fine-grained functionality space in music applications. Next is shown to what extent music application domains and metadata schemas make use of the metadata field clusters. Finally, we link the metadata schemas with the application domains. A decision table is presented that assists the user of a metadata provider in choosing the right metadata schema for his application.
Is Health Care an Individual Necessity? Evidence from Social Security Notch

This paper exploits Social Security legislation changes to identify the causal effect of Social Security income on out-of-pocket medical expenditures of the elderly. Using household level consumption data from the 1986-1994 Consumer Expenditure Survey and an instrumental variables strategy, the empirical results show that the estimated income elasticities of out-of pocket total medical costs, medical service expenses, and prescription drug expenses are about 0.55, 0.49, and 0.87, respectively. The estimated elasticities increase substantially and are statistically significant for elderly individuals with less than a high school education. The corresponding income elasticities are 1.69, 2.14, and 1.38, respectively. These findings are in contrast to existing studies and provide empirical evidence that health care expenditures are highly income sensitive among the low-educated elderly.
Rapid caspase‐3 activation during apoptosis revealed using fluorescence‐resonance energy transfer

Caspase‐3 is a crucial component of the apoptotic machinery in many cell types. Here, we report the timescale of caspase‐3 activation in single living cells undergoing apoptosis. This was achieved by measuring the extent of fluorescence resonance energy transfer within a recombinant substrate containing cyan fluorescent protein (CFP) linked by a short peptide possessing the caspase‐3 cleavage sequence, DEVD, to yellow fluorescent protein (YFP; i.e. CFP–DEVD–YFP). We demonstrate that, once initiated, the activation of caspase‐3 is a very rapid process, taking 5 min or less to reach completion. Furthermore, this process occurs almost simultaneously with a depolarization of the mitochondrial membrane potential. These events occur just prior to the characteristic morphological changes associated with apoptosis. Our results clearly demonstrate that, once initiated, the commitment of cells to apoptosis is a remarkably rapid event when visualized at the single cell level.
Pedestrian Detection by Using a Spatio-Temporal Histogram of Oriented Gradients

In this paper, we propose a pedestrian detection algorithm based on both appearance and motion features to achieve high detection accuracy when applied to complex scenes. Here, a pedestrian's appearance is described by a histogram of oriented spatial gradients, and his/her motion is represented by another histogram of temporal gradients computed from successive frames. Since pedestrians typically exhibit not only their human shapes but also unique human movements generated by their arms and legs, the proposed algorithm is particularly powerful in discriminating a pedestrian from a cluttered situation, where some background regions may appear to have human shapes, but their motion differs from human movement. Unlike the algorithm based on a co-occurrence feature descriptor where significant generalization errors may arise owing to the lack of extensive training samples to cover feature variations, the proposed algorithm describes the shape and motion as unique features. These features enable us to train a pedestrian detector in the form of a spatio-temporal histogram of oriented gradients using the AdaBoost algorithm with a relatively small training dataset, while still achieving excellent detection performance. We have confirmed the effectiveness of the proposed algorithm through experiments on several public datasets.
Copyright Violation on the Internet: Extent and Approaches to Detection and Deterrence

This research uses data collected from a university campus network via Deep Packet Inspection (DPI) monitoring and from the largest public BitTorrent tracker to characterize the extent of unauthorized transfers of copyrighted content using Peer-to-Peer (P2P) and to evaluate the effectiveness and limitations of DPI in detection of such activity, both to provide a perspective of how much copyright infringement happens using P2P and to inform those seeking to deploy DPI technology. Use of P2P and transfers of copyrighted content were widespread on campus. In Spring 2008, 40% of students living on campus were detected using a P2P protocol, 70% of which were observed attempting to transfer copyrighted material. In late 2010, we estimate that over 800 million copies of content were transferred globally using BitTorrent per day, with an estimated number of transferred songs 13.1 times greater than worldwide sales of songs, and estimated number of transferred movies 6.8 times greater than worldwide box-office sales and 16.4 times greater than U.S. DVD and Blu-ray sales. Most transfers were from a small number of very popular titles that were widely available for sale. We found no evidence that use of P2P to transfer content without violating copyright was common both on campus and global BitTorrent. This indicates that copyright law is violated frequently using P2P, and while we cannot quantify how P2P transfers translate to lost sales, it is reasonable to assume some sales are lost due to P2P. Focusing on effectiveness of DPI, after a couple weeks of monitoring DPI found up to 80% of detected P2P users attempting to transfer copyrighted content. In the short term, DPI could be effective to assess which network users transfer copyrighted content using P2P given some weeks of monitoring. However, limitations such as not being able to detect users of encrypted P2P can reduce DPIʼs effectiveness in the long term. Using behavioral classifiers that we implemented and that can detect encrypted BitTorrent from traffic summaries, we found students shifting from unencrypted to encrypted BitTorrent in the 2007-2008 academic year. If this trend continues, effectiveness of DPI for enforcement can be significantly hindered
A new experimental model of cigarette smoke-induced emphysema in Wistar rats*, **

OBJECTIVE: To describe a new murine model of cigarette smoke-induced emphysema. METHODS: Twenty-four male Wistar rats were divided into two groups: the cigarette smoke group, comprising 12 rats exposed to smoke from 12 commercial filter cigarettes three times a day (a total of 36 cigarettes per day) every day for 30 weeks; and the control group, comprising 12 rats exposed to room air three times a day every day for 30 weeks. Lung function was assessed by mechanical ventilation, and emphysema was morphometrically assessed by measurement of the mean linear intercept (Lm). RESULTS: The mean weight gain was significantly (approximately ten times) lower in the cigarette smoke group than in the control group. The Lm was 25.0% higher in the cigarette smoke group. There was a trend toward worsening of lung function parameters in the cigarette smoke group. CONCLUSIONS: The new murine model of cigarette smoke-induced emphysema and the methodology employed in the present study are effective and reproducible, representing a promising and economically viable option for use in studies investigating the pathophysiology of and therapeutic approaches to COPD.
Psychological well-being and workplace relations gaps on generational differences

This research is done to gain a picture of relationships and communications between staffs and higher-ups, problems that arise in workplace, the problem-solving connected with the generational differences and effects on psychological well-being. Gaps in work relation due to generational differences is not managed well, will indirectly affect the workplace condition and how each individuals do the work. The findings from this research are (1) Individuals can overcome differences between generations if they are able to manage their psychological well-being (2) Gap can occur in the relationship between staffs and higher-ups caused by individual differences in mindset, the value of work embraced, and the way individuals do work, which is affected by differences in the character of each generation (3) The ability to manage psychological well-being can overcome the differences in generations between staffs and higher-ups, namely each must have empathy to be able to understand each other's thoughts, and have the same goal, which is to advance and develop the organization through thinking, ideas and innovations.
Simulation of T-Wave Alternans and its Relation to the Duration of Ventricular Action Potentials Disturbance

The aim of the study was to simulate T-wave alternans (TWA) magnitude distribution maps on the body surface employing ECGSIM program and then to compare obtained results with data measured from patients. The toolbox for ECGSIM program was developed for TWA simulation. Graphical representation of spatial distribution of TWA magnitude was implemented. Body surface maps of TWA were simulated for different locations of the disturbances on the heart. Simulated data were compared with recordings from patients and similarities were found. Preliminary study shows that ECGSIM program can be used for approximate location of action potential disturbances in the heart cells.
Vehicle Flow Detection Based on Machine Vision

Vehicle flow detection is the key technology of intelligence traffic system. In order to overcome the shortcomings of traditional detection method which with low detection precision and is difficult to install and maintenance, a method, based on machine vision, which combines adjacent frame difference and background frame difference is proposed, besides, another method of vehicles count by vertical projection is also proposed. The simulation results show that the proposed vehicle detection algorithm not only can achieve high detection accuracy, but also is very simple and fast.
da Vinci decoded: does da Vinci stereopsis rely on disparity?

In conventional stereopsis, the depth between two objects is computed based on the retinal disparity in the position of matching points in the two eyes. When an object is occluded by another object in the scene, so that it is visible only in one eye, its retinal disparity cannot be computed. Nakayama and Shimojo (1990) found that a precept of quantitative depth between the two objects could still be established for such stimuli and proposed that this precept is based on the constraints imposed by occlusion geometry. They named this and other occlusion-based depth phenomena "da Vinci stereopsis. " Subsequent research found quantitative depth based on occlusion geometry in several other classes of stimuli grouped under the term da Vinci stereopsis. However, Nakayama and Shimojo's findings were later brought into question by Gillam, Cook, and Blackburn (2003), who suggested that quantitative depth in their stimuli was perceived based on conventional disparity. In order to understand whether da Vinci stereopsis relies on one type of mechanism or whether its function is stimulus dependent we examine the nature and source of depth in the class of stimuli used by Nakayama and Shimojo (1990). We use three different psychophysical and computational methods to show that the most likely source for depth in these stimuli is occlusion geometry. Based on these experiments and previous data we discuss the potential mechanisms responsible for processing depth from monocular features in da Vinci stereopsis.
Throughput Analysis in Cooperative Sensing Networks over Imperfect Reporting Channel

Spectrum sensing is an essential functionality that enables cognitive radios (CR) to detect spectral holes and to opportunistically use under-utilized frequency bands without causing harmful interference to primary users. In this paper, we study the fundamental tradeoff between sensing capability and achievable throughput of CR users. By assuming the reporting channel is a binary symmetric channel (BSC) with an error probability, the problem of throughput tradeoff is investigated and the relationship between the throughput, the sensing time and the number of cognitive radios is researched. By simulation we can know that the throughput becomes a single peak function with the increasing number of cognitive radios and that the performance of cooperative spectrum sensing is limited by the probability of reporting errors.
Size-dependent changes in wood chemical traits: a comparison of neotropical saplings and large trees

We have a fundamental and applied understanding of how differences in the wood chemistry of trees affects the durability of wood products. By comparison, relatively little is known about the ecological causes and consequences of species differences in wood chemistry; even less is known about how or why wood chemistry differs within species, across trees of different sizes. In this study we find strong and consistent differences in wood chemistry of saplings and canopy trees, in several tropical hardwood species. These differences point to the importance of pathogens and tree biomechanics as evolutionary causes of size-dependent changes in wood chemistry.
Salivary glucose concentration exhibits threshold kinetics in normal-weight, overweight, and obese children

Background Metabolic syndrome in childhood predicts the development of cardiovascular disease and type 2 diabetes (T2D) in adulthood. Testing for features of metabolic syndrome, such as fasting plasma glucose concentration, requires blood sampling which can be difficult in children. Here we evaluated salivary glucose concentration as a surrogate measurement for plasma glucose concentration in 11-year-old US children. Methods Children from Portland, Maine, and Cambridge, Massachusetts, with a mean age of 10.6±0.2 years provided 6-hour fasting samples of both blood and whole saliva. Salivary glucose levels were measured with a high-sensitivity assay (sensitivity =0.002 mg/dL). Plasma glucose levels were determined by a commercial clinical laboratory. Blood pressure, salivary flow rate, height, and weight were also measured. Results Of the 65 children enrolled, there were two underweight children (3.1%), 30 normal-weight children (46.2%), 12 overweight children (18.4%), and 21 obese children (32.3%). The mean overall glucose concentrations were 0.11±0.02 mg/dL in saliva and 86.3±0.8 mg/dL in plasma, and these did not differ significantly by body–weight groups. By regression analysis, the plasma concentration equaled 13.5 times the saliva concentration, with a threshold level of 84.8 mg/dL. Salivary glucose values less than threshold plasma concentration were essentially zero. Diagnostic analysis indicated a positive predictive value of 50%, a negative predictive value of 90%, and a sensitivity and specificity both of approximately 75%. The salivary glucose concentration did not vary with saliva flow rate. Conclusion Taking into account the threshold response characteristics of the salivary glucose concentration response, these results suggest that testing salivary glucose levels may be useful as a screening assay for high fasting plasma glucose levels. The low false positive value is important to assure a low fraction of missed diagnoses.