Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Correlated Breakpoints in Cancer

During oncogenesis the loss of caretaker genes leads to chromosomal instability: chromosomes mispair during anaphase, and may undergo nonhomologous recombination, or break during telophase. This instability leads to changes in the copy number of genes, changes in their expression patterns, and can construct novel genes through fusion or truncation. Array comparative genome hybridization (aCGH) [6] is a high-throughput technique used to assess these copy-number variants. aCGH assesses these deviations from the normal genome through the use of short probing sequences that are represented uniquely in the human genome. These probes are hybridized to fluorescently tagged experimental genomic DNA and fluorescently tagged reference DNA. The score for each probe is given as log2(E/R), where E is the luminosity of the experimental sample, and R is the luminosity of the reference. The log2 ratio of the luminosities of the sample and reference is a noisy estimate of the relative copy number of genomic material in the experimental sample as compared to the reference. Probes hybridized to regions of normal copy number have a log2 ratio close to zero, while gains are positive and areas of loss are negative. While there is no computational impediment to attempting to correlate the measurements at individual aCGH probes there is a statistical barrier. The number of possible probe pairings is quadratic in the number of probes, and the number of possible combinations is exponential in the number of probes. Modern arrays contain upwards of several million probes. Due to multiple hypothesis testing, an attempt to näıvely test the correlation between all pairs in a 244, 000 probe array would necessitate correcting each p-value by a factor of 5.95 ∗ 1010. To reduce the the number of hypotheses tested we rely on the notion of breakpoints. A breakpoint is a point on a chromosome that is the terminus of some gross structural change. Intervals are a related structure which are
An Adaptive Traffic Allocation Algorithm in MANET

A dynamic traffic allocation algorithm based on packet delay and hops in Mobile Ad hoc networks is proposed. The algorithm is based on the minimization product of delay and the number of hops in each path and adjusts the traffic adaptively so as to make load-balanced which optimizes network resource utilization. Simulation demonstrated that the algorithm could dynamically balance the traffic allocation between paths. The aim of the minimum utilization of resource in mobile Ad hoc networks can be achieved.
A privacy-preserving algorithm for distributed constraint optimization

Distributed constraint optimization problems enable the representation of many combinatorial problems that are distributed by nature. An important motivation for such problems is to preserve the privacy of the participating agents during the solving process. The present paper introduces a novel privacy-preserving algorithm for this purpose. The proposed algorithm requires a secure solution of several multiparty computation problems. Consequently, appropriate novel secure protocols are devised and analyzed.
Differential Effects of Eicosapentaenoic Acid and Docosahexaenoic Acid on Vascular Reactivity of the Forearm Microcirculation in Hyperlipidemic, Overweight Men

BackgroundRecent evidence supports differential effects of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), the 2 major &ohgr;3 fatty acids of marine origin, on blood pressure in humans and vascular reactivity in adult spontaneously hypertensive rats. We investigated possible differences in the effects of purified EPA or DHA on forearm vascular reactivity in overweight hyperlipidemic men that might contribute to the blood pressure–lowering effects of fish oils. Methods and ResultsWith a double-blind, placebo-controlled trial of parallel design, 59 overweight, mildly hyperlipidemic men were randomized to receive 4 g/d purified EPA, DHA, or olive oil (placebo) capsules while continuing their usual diets for 6 weeks. Forearm blood flow (FBF) was measured with venous occlusion, strain-gauge plethysmography during the sequential intra-arterial administration of acetylcholine (7.5, 15, and 30 &mgr;g/min), sodium nitroprusside (1.5, 3, and 10 &mgr;g/min), norepinephrine (10, 20, and 40 ng/min), a single-dose infusion of NG-monomethyl-l-arginine (L-NMMA) (1 mg/min), and coinfusion of acetylcholine (7.5, 15, and 30 &mgr;g/min) and L-NMMA. Forty of the 56 subjects who completed the study underwent FBF measurements. Plasma phospholipid EPA levels increased significantly (P <0.0001) after supplementation with EPA, and DHA composition increased with DHA supplementation (P <0.0001). Relative to placebo, DHA, but not EPA, supplementation significantly improved FBF in response to acetylcholine infusion (P =0.040) and coinfusion of acetylcholine with L-NMMA (P =0.040). Infusion of L-NMMA alone showed no group differences. DHA significantly enhanced dilatory responses to sodium nitroprusside (P <0.0001) and attenuated constrictor responses to norepinephrine (P =0.017). ConclusionsRelative to placebo, DHA, but not EPA, enhances vasodilator mechanisms and attenuates constrictor responses in the forearm microcirculation. Improvements in endothelium-independent mechanisms appear to be predominant and may contribute to the selective blood pressure–lowering effect observed with DHA compared with EPA in humans.
Building and Exploring Semantic Equivalences Resources

Language resources that include semantic equivalences at word level are common, and its usefulness is well established in text processing applications, as in the case of search. Named entities also play an important role for text based applications, but are not usually covered by the previously mentioned resources. The present work describes the WES base, Wikipedia Entity Synonym base, a freely available resource based on the Wikipedia. The WES base was built for the Portuguese Language, with the same format of another freely available thesaurus for the same language, the TeP base, which allows integration of equivalences both at word level and entity level. The resource has been built in a language independent way, so that it can be extended to different languages. The WES base was used in a Question Answering system, enhancing significantly its performance.
New results in optimal quadratic supply rates

This paper concerns studying dissipativity of a system with supply rates that depend on one or more parameters. We show that suitable choice of supply rate turns out to make dissipativity equivalent to traditional gain/phase margin conditions for stability. Further, the well-known circle criterion corresponds to a different supply rate, and here optimizing the supply rate is nothing but finding the largest circle such that circle criterion implies absolute stability for time-varying nonlinearities. L¿-control is another example of dissipativity with respect to a relevant supply rate, and here we show that, in fact, improper L¿-controllers are easily dealt with using our approach (unlike the standard state space methods). We formulate and prove necessary and sufficient conditions for L¿-control, and then conclude that optimal controllers always exist (under suboptimal solvability conditions).
Efficient tiling for an ODE discrete integration program: redundant tasks instead of trapezoidal shaped-tiles

In this paper, we present an efficient and simple solution to the parallelization of discrete integration programs of ordinary differential equations (ODE). The main technique used is known as loop tiling. To avoid the overhead due to code complexity and border effects, we introduce redundant tasks and we use non parallelepiped tiles. Thanks both to cache reuse (? 4:3) and coarse granularity (? 24:5), the speedup using 25 processors over the non-tiled sequential implementation is larger than 106.We also present the draft of a fuzzy methodology to optimize the tile size and we illustrate it using real measurements for the communication cost and the execution time. In particular, we observe that the model of communication latencies over a Myrinet network is not as simple as is usually reported.
The Acute-Phase Proteins Serum Amyloid A and C Reactive Protein in Transudates and Exudates

The distinction between exudates and transudates is very important in the patient management. Here we evaluate whether the acute-phase protein serum amyloid A (SAA), in comparison with C reactive protein (CRP) and total protein (TP), can be useful in this discrimination. CRP, SAA, and TP were determined in 36 exudate samples (27 pleural and 9 ascitic) and in 12 transudates (9 pleural and 3 ascitic). CRP, SAA, and TP were measured. SAA present in the exudate corresponded to 10% of the amount found in serum, that is, the exudate/serum ratio (E/S) was 0.10 ± 0.13. For comparison, the exudate/serum ratio for CRP and TP was 0.39 ± 0.37 and 0.68 ± 0.15, respectively. There was a strong positive correlation between serum and exudate SAA concentration (r = 0.764;p < 0.0001). The concentration of SAA in transudates was low and did not overlap with that found in exudates (0.02-0.21 versus 0.8–360.5 g/mL). SAA in pleural and ascitic exudates results mainly from leakage of the serum protein via the inflamed membrane. A comparison of the E/S ratio of SAA and CRP points SAA as a very good marker in discriminating between exudates and transudates.
Sequential parameter estimation for ﬂuid-structure problems. Application to hemodynamics

: We present a robust and computationally eﬃcient parameter estimation strategy for ﬂuid-structure interaction problems. The method is based on a ﬁltering algorithm restricted to the parameter space, known as the reduced order Unscented Kalman Filter [23]. It does not require any adjoint or tangent problems. In addition, it can easily be run in parallel, which is of great interest in ﬂuid-structure problems where the computational cost of the forward simulation is already a challenge in itself. We illustrate our methodology with the estimation of the artery wall stiﬀness from the wall displacement measurements – as they could be extracted from medical imaging – in a three-dimensional idealized abdominal aortic aneurysm. We also show preliminary results about the estimation of the proximal Windkessel resistance, which is an important parameter for setting appropriate ﬂuid boundary conditions.
RMETC: A reduction method to eSPKI trust certificate

To use the trust certificate is a suitable method for the principal to enjoy the service supply in different ubiquitous environments security. But these trust certificates cannot be used directly in different ubiquitous environments because the lack of ensure directly. Therefore, the suitable reduction method is necessary. In this paper, a new reduction method to eSPKI trust certificate that is based on D-S evidence theory and extended SPKI/SDSI, named RMETC, is presented. The example scenario given in the paper shows us that how to use RMETC to solve the security service supply problem in different ubiquitous computing environments.
Some Technical Aspects about Aligning Near Languages

IULA at UPF has developed an aligner that benefits from corpus processing results to produce an accurate and robust alignment, even with noisy parallel corpora. It compares lemmata and part-of-speech tags of analysed texts but it has two main characteristics. First, apparently it only works for near languages and second it requires morphological taggers for the compared languages. These two characteristics prevent this technique from being used for any pair of languages. Whevener it its applicable, a high quality of results is achieved.
CMOS LNA and mixer components for 2GHz applications in 0.18-µm CMOS

This paper describes a low noise variable gain amplifier (LNA) and a mixer for a WCDMA front-end receiver based on a direct architecture in 0.18-µm CMOS. The LNA provides a 50O input impedance and utilizes a tuned load to provide high selectivity. The LNA achieves a maximum small signal gain of 16.8 dB and a minimum gain of 4.6 dB with good input return loss. In the high gain and the low gain modes, the NFs are 0.83 dB and 2.8 dB, respectively. The LNA's IIP3 in the high gain mode is 2.1 dBm. The mixer achieves a conversion gain of 16 dB and a double side band (DSB) NF of 13.8 dB. The mixer's IIP3 is 12.12 dBm. The achieved low noise figure, gain and overall IIP3 fulfill the specifications for a UMTS LNA and mixer design. The LNA and the mixer, respectively, consume 4 mA and 5 mA of current from a 1.8-V power supply.
QoS Management in Broadband IEEE 802 . 16 Based Networks

This paper presents a performance analysis of different scheduling techniques for the provision of QoS in Fixed Broadband Wireless Access Networks (BWA). The performance is based on the MAC protocol proposed for the IEEE 802.16 standard and focuses on the uplink channel, which if the limiting factor of BWA networks and is critical in the delivery of services to individual users on demand. Although the IEEE 802.16 standard had proposed several QoS techniques for various types of applications, they do not suggest how to schedule traffic to fulfill timing critical services such as compresed/uncompresed voice, audio and video streams. We have derived a novel scheduling algorithm that combines Round Robin, Early Deadline First and Prioritization, to perfect match VBR-like and CBR-like traffic for IEEE 802.16 based networks. Simulation results show that real-time services can be supported with very low access delays even during congestion periods. Index Terms − Fixed BWA, IEEE 802.16, QoS, Performance Analysis, Voice over IP, Scheduling algorithms, WImax.
Pap smear screening for small cell carcinoma of the uterine cervix: a case series and review of the literature

Objective Small cell carcinoma of the uterine cervix (SMCC) is extremely rare, and an aggressive disease that proliferates rapidly. It was often reported that the diagnostic accuracy of cytologic smears in diagnosing SMCC was low. This is a report of the Severance Hospital experience with the patients suffering from SMCC. Methods Twenty-seven patients with small cell carcinoma of the uterine cervix were diagnosed and treated at the Severance Hospital from November 1991 to January 2010. The data were analyzed retrospectively, based on the available charts and pathology reports. Various fields, such as chief complaints and symptoms present at first clinic visit, age, International Federation of Obstetrics and Gynecology (FIGO) clinical stage, treatment modality, the 5-year overall survival rate, and recurrence rate were investigated. Results Among the 27 patients diagnosed with small cell carcinoma of the uterine cervix, 18 of them (66.7%) presented with symptoms, including vaginal bleeding, at the first clinic visit, and the remaining 9 patients (33.3%) showed abnormal Pap smear screening in the process of their routine health check-up. The median age of the patients was 54 years (range, 24 to 77 years). FIGO stage IIB was the most common stage (11 of 27 patients). The 5-year overall survival rate of 21 patients, who could be followed up, was 57.2%. Six patients showed recurrence after remission, and the mean disease free interval of them was 9.2 months (range, 6 to 11 months). Abnormal Pap smear screening results of 9 patients was investigated, and the diagnostic accuracy of the cytologic findings was 22.2%. Conclusion Our study was consistent with the concept that Pap smear screening might not be helpful in early diagnosis of SMCC considering its low diagnostic accuracy. Further large-scale multicenter prospective studies are definitely needed in order to produce abundant information about optimal therapy and diagnosis.
Investigating recognition of children's speech

Recognition of children's speech was investigated by considering a phone recognition task. Two baseline systems were trained, one for children and one for adults, by exploiting two Italian speech databases. Under matching conditions, for training and recognition performed with data from the same population group, the phone recognition accuracy was 77.30% and 79.43% for children and adults, respectively. It was found that, for many children, recognition results were as good as for adults. However, a higher variability in phone recognition accuracy across speakers was observed for children than for adults. Vocal tract length normalization, under matched and mismatched training and testing conditions, was also investigated. For both adults and children, a performance improvement, with respect to the baseline systems, was observed.
Control of Acid Resistance inEscherichia coli

ABSTRACT Acid resistance (AR) in Escherichia coli is defined as the ability to withstand an acid challenge of pH 2.5 or less and is a trait generally restricted to stationary-phase cells. Earlier reports described three AR systems in E. coli. In the present study, the genetics and control of these three systems have been more clearly defined. Expression of the first AR system (designated the oxidative or glucose-repressed AR system) was previously shown to require the alternative sigma factor RpoS. Consistent with glucose repression, this system also proved to be dependent in many situations on the cyclic AMP receptor protein. The second AR system required the addition of arginine during pH 2.5 acid challenge, the structural gene for arginine decarboxylase (adiA), and the regulatorcysB, confirming earlier reports. The third AR system required glutamate for protection at pH 2.5, one of two genes encoding glutamate decarboxylase (gadA or gadB), and the gene encoding the putative glutamate:γ-aminobutyric acid antiporter (gadC). Only one of the two glutamate decarboxylases was needed for protection at pH 2.5. However, survival at pH 2 required both glutamate decarboxylase isozymes. Stationary phase and acid pH regulation of the gad genes proved separable. Stationary-phase induction of gadA and gadBrequired the alternative sigma factor ςS encoded byrpoS. However, acid induction of these enzymes, which was demonstrated to occur in exponential- and stationary-phase cells, proved to be ςS independent. Neither gad gene required the presence of volatile fatty acids for induction. The data also indicate that AR via the amino acid decarboxylase systems requires more than an inducible decarboxylase and antiporter. Another surprising finding was that the ςS-dependent oxidative system, originally thought to be acid induced, actually proved to be induced following entry into stationary phase regardless of the pH. However, an inhibitor produced at pH 8 somehow interferes with the activity of this system, giving the illusion of acid induction. The results also revealed that the AR system affording the most effective protection at pH 2 in complex medium (either Luria-Bertani broth or brain heart infusion broth plus 0.4% glucose) is the glutamate-dependent GAD system. Thus, E. coli possesses three overlapping acid survival systems whose various levels of control and differing requirements for activity ensure that at least one system will be available to protect the stationary-phase cell under naturally occurring acidic environments.
Comparison between the auditory lateralization ability of normal hearing elderly and youth with filtered noise

Background and Aim: Aging affects the audi­tory lateralization function that is achieved thr­ough processing binaural cues. One of the most important benefits of this process, along with getting informed of sound location, is increasing signal to noise ratio and improvement of speech comprehension in crowded environments, which is one of the most common hearing complaints in the elderly. This study aimed to compare the performance of the lateralization function under the headphone conditions between the elderly and the youth, with a filtered noise stimulus. Methods: This study was performed between 22 elderly aged 60−80 and 22 young people aged 20−30. The auditory threshold was less than 25 dB HL in 250 to 4000 Hz frequencies in both groups. By applying a time delay of −880 to +880 microsecond and the intensity differe­nce of −10 to +10 dB between the two ears, and with high-pass and low-pass noise stimulus, the lateralization function was examined. For descr­iption of the lateralization function, scatter diag­ram and in order to compare the results, paired t-test and independent t-test were used. Results: Findings showed that the elderly's err­ors were increased in all tests compared to those of the youth group. There was a significant difference (p < 0.05) between the two groups in lateralization by time clues with low-pass and high-pass noise. Conclusion: Results confirm the impairment of the lateralization and processing of binaural cues in the elderly differently.
Incentive and Service Differentiation in P2P Networks: A Game Theoretic Approach

Conventional peer-to-peer (P2P) networks do not provide service differentiation and incentive for users. Therefore, users can easily obtain information without themselves contributing any information or service to a P2P community. This leads to the well known free-riding problem. Consequently, most of the information requests are directed towards a small number of P2P nodes which are willing to share information or provide service, causing the "tragedy of the commons. " The aim of this paper is to provide service differentiation in a P2P network based on the amount of services each node has provided to the network community. Since the differentiation is based on nodes' prior contributions, the nodes are encouraged to share information/services with each other. We first introduce a resource distribution mechanism for all the information sharing nodes. The mechanism is distributed in nature, has linear time complexity, and guarantees Pareto-optimal resource allocation. Second, we model the whole resource request/distribution process as a competition game between the competing nodes. We show that this game has a Nash equilibrium. To realize the game, we propose a protocol in which the competing nodes can interact with the information providing node to reach Nash equilibrium efficiently and dynamically. We also present a generalized incentive mechanism for nodes having heterogeneous utility functions. Convergence analysis of the competition game is carried out. Examples are used to illustrate that the incentive protocol provides service differentiation and can induce productive resource sharing by rational network nodes. Lastly, the incentive protocol is adaptive to node arrival and departure events, and to different forms of network congestion
Underdetermined DOA estimation of multi-path signals based on ICA and sparse reconstruction

This paper proposes a method for estimating the direction of arrival (DOA) of multi-path signals for an underdetermined case, where the number of incident signals exceeds the number of sensors. Some DOA estimation methods have already been proposed for multi-path signals. However, most of them cannot be used for an underdetermined case. To deal with this problem, we propose a novel DOA estimation method which combines independent component analysis (ICA) and sparse reconstruction algorithm. It can estimate DOA of M ×(M - 1) incident signals when the number of sensors is M. The simulation results demonstrate the promising performance of the proposed algorithm compared to several state of the art methods.
Visualizing the effects of scale and geography in multivariate comparison

Our research investigates the sensitivities and complexities of visualizing multivariate data over multiple scales with the consideration of local geography. We investigate this in the context of creating geodemographic classifications, where multivariate comparison for the variable selection process is an important, yet time-consuming and intensive process. We propose a visual interactive approach which allows skewed variables and those with strong correlations to be quickly identified and investigated and the geography of multi-scale correlation to be explored. Our objective is to present comprehensive documentation of the parameter space prior to the development of the visualization tools to help explore it.