Miracle-dz/UniFAR-FTUs huggingface dataset:
Traffic Aware Power Saving Protocol in Multi-hop Mobile Ad-Hoc Networks

This paper presents an optimization of PSM to improve its energy conservation. According to PSM, time is divided into beacon intervals. At the beginning of each beacon interval, all stations must be awake during a specific period called ATIM window to be able to send and receive synchronization messages and announcements of buffered data frames. PSM specifies that a station having sent or received an announcement or having sent a beacon must remain awake during the entire beacon interval. This may lead to wasting energy specially at light traffic loads where stations should conserve the most. We propose an enhancement called the Traffic Aware Power Saving Mode (TA-PSM) to solve this problem by allowing nodes to enter the doze state when they are no more involved in data delivery even if they have already sent a beacon, an ATIM or an ATIM-ACK. Our objective is to reduce the energy consumption without any throttling to throughput. Extensive simulations based on fixed and dynamic topologies showed that TA-PSM provides a much better energy conservation and a lower power consumption per delivered data frame.
An Ontological Approach to Secure MANET Management

Mobile ad hoc networks (MANETs) rely on dynamic configuration decisions to efficiently operate in a rapidly changing environment of limited resources. The ability of a MANET to make decisions that accurately reflect the real environment depends on the quality of the input to those decisions. However, collecting and processing of the multitudinous factors related to the operation of a MANET is a significant challenge. Equally significant in current approaches to dynamic MANET management is the lack of consideration given to security factors. We show how our ontology of MANET attributes including device security and performance characteristics can be leveraged to efficiently and effectively make dynamic configuration decisions for managing a MANET.
Mismatch Repair Status Is a Predictive Factor of Tumour Response to 5-Fluorouracil and Irinotecan Chemotherapy in Patients with Advanced Colorectal Cancer

Background and Aims: To determine the association between DNA mismatch repair (MMR) protein expression and response to chemotherapy in patients with advanced colorectal cancer (CRC). Methods: Using immunohistochemistry, tumour expression of 2 MMR genes, hMLH1 and hMSH2, was assessed in 86 patients with advanced CRC, who were treated with either irinotecan alone or in combination with 5-flurouracil/folinic acid. Results: Weak/negative staining in the tumours was associated with the presence of metastases at diagnosis (p = 0.026) and with the time for metastases to appear (p = 0.0001). An objective response to treatment was observed in 32/56 (57%) patients who had tumours with negative/weak MMR protein expression (p = 0.001), compared to 17% of patients with tumours with moderate/strong expression. Those who had tumours with weak/absent expression of either hMLH1 or hMSH2 who received the combination therapy were more likely to show an objective response (p = 0.0001). Conclusion: Advanced CRC patients whose tumours have deficient MMR demonstrate a shorter time to metastasis than those with normal hMLH1/hMSH2 expression. Patients with MMR-deficient tumours are also more likely to benefit from combination chemotherapy (irinotecan plus 5-flurouracil/folinic acid).
A novel technique for the scanned color image descreening

A quality of scanned color image is often hampered due the way images are printed. Usually electrophotographic printer prints the images by using halftoning technique wherein images are printed as a matrix of dots. This gives the illusion as images are printed as a perfect picture but behind the scene they are actually matrix of dots. So there is no problem as far as printed copies are considered, the real problem arise when such copies undergo scanning process. Scanned copies thus are affected by screen like artifacts and moiré patterns. The technique when applied on such images will produce clear scanned images. Technique consists of first separating the color image planes and then applying image redundancy based denoising algorithm to remove printing noise and to attenuate distortions. Then features such as screen frequency and local gradient are extracted to filter the image. This will remove halftone patterns in the scanned image. Finally edge preserving filtering is done to improve the sharpness of edges. Thus quality of resulting image will be better than the original image.
Point Cloud Noise and Outlier Removal for Image-Based 3D Reconstruction

Point sets generated by image-based 3D reconstruction techniques are often much noisier than those obtained using active techniques like laser scanning. Therefore, they pose greater challenges to the subsequent surface reconstruction (meshing) stage. We present a simple and effective method for removing noise and outliers from such point sets. Our algorithm uses the input images and corresponding depth maps to remove pixels which are geometrically or photometrically inconsistent with the colored surface implied by the input. This allows standard surface reconstruction methods (such as Poisson surface reconstruction) to perform less smoothing and thus achieve higher quality surfaces with more features. Our algorithm is efficient, easy to implement, and robust to varying amounts of noise. We demonstrate the benefits of our algorithm in combination with a variety of state-of-the-art depth and surface reconstruction methods.
Monadic second order logic on graphs with local cardinality constraints

We introduce the class of MSO-LCC problems, which are problems of the following form. Given a graph <i>G</i> and for each vertex <i>v</i> of <i>G</i> a set α(<i>v</i>) of non-negative integers. Is there a set <i>S</i> of vertices or edges of <i>G</i> such that, (1) <i>S</i> satisfies a fixed property expressible in monadic second order logic, and (2) for each vertex <i>v</i> of <i>G</i> the number of vertices/edges in <i>S</i> adjacent/incident with <i>v</i> belongs to the set α(<i>v</i>)? We demonstrate that several hard combinatorial problems such as Lovász's General Factor Problem can be naturally formulated as MSO-LCC problems. Our main result is the polynomial-time tractability of MSO-LCC problems for graphs of bounded treewidth. We obtain this result by means of a tree-automata approach. By way of contrast we show that a more general class of MSO-LCC problems, where cardinality constraints are applied to second-order variables that are arbitrarily quantified, does not admit polynomial-time tractability for graphs of bounded treewidth unless P=NP.
Observing the determinants of the psychotherapeutic process in depressive disorders. A clinical case study within a psychodynamic approach

This paper focuses on the relationship between depressive disorders, personality configurations, and mental functioning. A one-year treatment of a young man with the diagnosis of Depression is presented: the clinical and empirical points of view are described in depth through an assessment at the beginning and at one year after of an oriented psychodynamic psychotherapy. SCID I and II and HAMRS were administered to the patient in assessment phase. In the same phase he filled in BDI-II, and DEQ; the psychotherapist completed SWAP-200. These clinician instruments were used again after 1 year of the treatment. The PDM point of view is also presented. All sessions are audiotaped: 12 verbatim transcripts were coded with the Defense Mechanisms Rating Scale and CCRT. The results show a decrease in depressive symptoms, a change in some personality configurations, but a substantial invariance of the introjective profile, and a modification in mental functioning.
The bread and butter of statistical analysis “t-test”: Uses and misuses

Statistical tests are very important in biomedical research.1 Several factors play a role in selecting the most appropriate statistical test.2 The misuse or inaccurate use of a statistical test may navigate the research in the wrong direction, and hence incorrect conclusions. Because it is probably the most commonly used statistical test, Student’s t-test is considered “the bread and butter” of statistical analysis. The William Gossett test “Student’s t-test” is easy to use, however, it is also misused.3 There are three types of the t-test, which are used for comparing either a single mean or two population means (Table-I). Each t-test can be used under specific conditions and criteria.
Structural analysis of an eIF3 subcomplex reveals conserved interactions required for a stable and proper translation pre-initiation complex assembly

Translation initiation factor eIF3 acts as the key orchestrator of the canonical initiation pathway in eukaryotes, yet its structure is greatly unexplored. We report the 2.2 Å resolution crystal structure of the complex between the yeast seven-bladed β-propeller eIF3i/TIF34 and a C-terminal α-helix of eIF3b/PRT1, which reveals universally conserved interactions. Mutating these interactions displays severe growth defects and eliminates association of eIF3i/TIF34 and strikingly also eIF3g/TIF35 with eIF3 and 40S subunits in vivo. Unexpectedly, 40S-association of the remaining eIF3 subcomplex and eIF5 is likewise destabilized resulting in formation of aberrant pre-initiation complexes (PICs) containing eIF2 and eIF1, which critically compromises scanning arrest on mRNA at its AUG start codon suggesting that the contacts between mRNA and ribosomal decoding site are impaired. Remarkably, overexpression of eIF3g/TIF35 suppresses the leaky scanning and growth defects most probably by preventing these aberrant PICs to form. Leaky scanning is also partially suppressed by eIF1, one of the key regulators of AUG recognition, and its mutant sui1G107R but the mechanism differs. We conclude that the C-terminus of eIF3b/PRT1 orchestrates co-operative recruitment of eIF3i/TIF34 and eIF3g/TIF35 to the 40S subunit for a stable and proper assembly of 48S pre-initiation complexes necessary for stringent AUG recognition on mRNAs.
Genome-Wide Analysis of the Cyclin Gene Family in Tomato

Cyclins play important roles in cell division and cell expansion. They also interact with cyclin-dependent kinases to control cell cycle progression in plants. Our genome-wide analysis identified 52 expressed cyclin genes in tomato. Phylogenetic analysis of the deduced amino sequences of tomato and Arabidopsis cyclin genes divided them into 10 types, A-, B-, C-, D-, H-, L-, T-, U-, SDS- and J18. Pfam analysis indicated that most tomato cyclins contain a cyclin-N domain. C-, H- and J18 types only contain a cyclin-C domain, and U-type cyclins contain another potential cyclin domain. All of the cyclin genes are distributed throughout the tomato genome except for chromosome 8, and 30 of them were found to be segmentally duplicated; they are found on the duplicate segments of chromosome 1, 2, 3, 4, 5, 6, 10, 11 and 12, suggesting that tomato cyclin genes experienced a mass of segmental duplication. Quantitative real-time polymerase chain reaction analysis indicates that the expression patterns of tomato cyclin genes were significantly different in vegetative and reproductive stages. Transcription of most cyclin genes can be enhanced or repressed by exogenous application of gibberellin, which implies that gibberellin maybe a direct regulator of cyclin genes. The study presented here may be useful as a guide for further functional research on tomato cyclins.
Heat shock proteins and high mobility group box 1 protein lack cytokine function

In search of the etiology and pathophysiology for autoimmune and chronic inflammatory diseases, many molecules have been identified as endogenous damage‐associated molecules with proinflammatory cytokine functions that may be responsible for the sterile inflammation leading to tissue injuries observed in these disorders. HSPs and HMGB1 are intracellular molecular chaperones for peptides and DNAs, respectively. They are released extracellularly upon cellular injury or activation. In vitro studies revealed that HSPs and HMGB1 were capable of inducing the release of proinflammatory cytokines by monocytes and macrophages and the activation and maturation of DCs. These cytokine effects were reported to be mediated by TLR2 and TLR4 signal transduction pathways. Thus, they were called endogenous ligands of TLR2 and TLR4 and might serve as danger signals, alarmins, or damage‐associated molecules to the host immune system. It has been suggested that HSPs provide a link between innate and adaptive immune systems, and HMGB1 functions at the cross‐road between innate and adaptive immunity. However, recent evidence suggests that highly purified HSPs and HMGB1, although retaining their biological activities, do not have cytokine effects. Thus, HSPs and HMGB1 do not meet the definition of endogenous ligands of TLRs, danger signals, alarmins, or damage‐associated molecules. In contrast, HSPs and HMGB1 are found to bind a number of pathogen‐associated molecules, such as LPS and bacterial lipopeptides, and enhance the cytokine effects of these molecules. The significance of these cytokine‐enhancing effects of HSPs and HMGB1 needs further investigation.
Extended Pairwise Potentials

Inference in Markov Random Fields can be cast as the minimization of a potential function that is typically composed of unary and pairwise terms. The pairwise potentials measure the cost of assigning labels to two neighboring pixels and are often in the form of differences between labels, rather than of their separate values. We generalize this formulation to allow pairwise potentials to depend on both label differences AND their separate values. We also show that the minimization can be computed efficiently by using an extended version of the generalized distance transform in the belief propagation algorithm. We show that the generalized potential function may be useful in applications such as image restoration and labeling where fine grained control is desirable.
The Ccr4-Pop2-NOT mRNA Deadenylase Contributes to Septin Organization in Saccharomyces cerevisiae

In yeast, assembly of the septins at the cell cortex is required for a series of key cell cycle events: bud-site selection, the morphogenesis and mitotic exit checkpoints, and cytokinesis. Here we establish that the Ccr4-Pop2-NOT mRNA deadenylase contributes to septin organization. mRNAs encoding regulators of septin assembly (Ccd42, Cdc24, Rga1, Rga2, Bem3, Gin4, Cla4, and Elm1) presented with short poly(A) tails at steady state in wild-type (wt) cells, suggesting their translation could be restricted by deadenylation. Deadenylation of septin regulators was dependent on the major cellular mRNA deadenylase Ccr4-Pop2-NOT, whereas the alternative deadenylase Pan2 played a minor role. Consistent with deadenylation of septin regulators being important for function, deletion of deadenylase subunits CCR4 or POP2, but not PAN2, resulted in septin morphology defects (e.g., ectopic bud-localized septin rings), particularly upon activation of the Cdc28-inhibitory kinase Swe1. Aberrant septin staining was also observed in the deadenylase-dead ccr4-1 mutant, demonstrating the deadenylase activity of Ccr4-Pop2 is required. Moreover, ccr4Δ, pop2Δ, and ccr4-1 mutants showed aberrant cell morphology previously observed in septin assembly mutants and exhibited genetic interactions with mutations that compromise septin assembly (shs1Δ, cla4Δ, elm1Δ, and gin4Δ). Mutations in the Not subunits of Ccr4-Pop2-NOT, which are thought to predominantly function in transcriptional control, also resulted in septin organization defects. Therefore, both mRNA deadenylase and transcriptional functions of Ccr4-Pop2-NOT contribute to septin organization in yeast.
Pilot based synchronization in OFDM systems using maximum likelihood estimation

Orthogonal frequency division multiplexing (OFDM) based communication systems are very efficient in combating inter-symbol interference (ISI) in frequency-selective channels. However, carrier frequency offset (CFO) severely affects system performance by destroying the orthogonality between the OFDM subcarriers. In this paper, we estimate the CFO in a block OFDM system using maximum-likelihood estimation (MLE) and pilot subcarriers. Through simulations, we then show the deleterious effect of the CFO on the bit error rate (BER) and subsequently, the performance improvement after CFO compensation.
Event-Driven User-Centric Middleware for Energy-Efficient Buildings and Public Spaces

In this paper, the design of an event-driven user-centric middleware for monitoring and managing energy consumption in public buildings and spaces is presented. The main purpose is to increase energy efficiency in buildings and public spaces, thus reducing consumption. To achieve this, the proposed service-oriented middleware has been designed to be event based, also exploiting the user behavior patterns of people who live and work in buildings. Furthermore, it allows an easy integration of heterogeneous technologies in order to enable a hardware-independent interoperability between them. Moreover, a heating ventilation and air conditioning (HVAC) control strategy has been developed, and the whole infrastructure has been deployed in a real-world case study consisting of a historical building. Finally, the results will be presented and discussed.
Convex Combination of Two Recursive Least Squares-type Algorithms for Adaptive Whitening

The recursive least squares (RLS)-type whitening algorithm is shown to be a useful solution for improving the convergence rate of the least mean square (LMS)-type whitening algorithm, but the RLStype algorithm with a constant forgetting factor requires a tradeoff between the convergence speed and steady-state misadjustment. By using a convex combination of two RLS algorithms with different forgetting factor, we present an effective method to solve the tradeoff problem of the RLS-type whitening algorithm. Firstly, two RLS-type whitening algorithms with different forgetting factor are convex combined in a reasonable manner to put together the best properties of them. Then, a mixing parameter is introduced to adjust the proportion of the two RLS algorithms, and the adaptive updating rule of the mixing parameter is obtained based on the stochastic gradient of the cost function. Finally, the weight transfer procedure and momentum term technique are developed to further improve the convergence performance of the convex combination algorithm. Since two RLS algorithms with different forgetting factor are applied and the best properties of them are acquired, the proposed combination algorithm work more efficiently than the existing adaptive whitening algorithms, as is verified by computer simulations in both stationary and non-stationary environments.
Revisiting the dissociation between singing and speaking in expressive aphasia.

We investigated the production of sung and spoken utterances in a non-fluent patient, C.C. , who had a severe expressive aphasia following a right-hemisphere stroke, but whose language comprehension and memory were relatively preserved. In experiment 1, C.C. repeated familiar song excerpts under four different conditions: spoken lyrics, sung lyrics on original melody, lyrics sung on new but familiar melody and melody sung to a neutral syllable "la". In experiment 2, C.C. repeated novel song excerpts under three different conditions: spoken lyrics, sung lyrics and sung-to-la melody. The mean number of words produced under the spoken and sung conditions did not differ significantly in either experiment. The mean number of notes produced was not different either in the sung-to-la and sung conditions, but was higher than the words produced, hence showing a dissociation between C.C. 's musical and verbal productions. Therefore, our findings do not support the claim that singing helps word production in non-fluent aphasic patients. Rather, they are consistent with the idea that verbal production, be it sung or spoken, result from the operation of same mechanisms.
Human and murine T‐cell responses to allelic forms of a malaria circumsporozoite protein epitope support a polyvalent vaccine strategy

Mouse models and a recent vaccine trial have indicated the importance of T‐cell immunity to the circumsporozoite protein (CSP) of malaria sporozoites. One of the major impediments for the development of a CSP‐based vaccine is that human T‐cell epitopes, identified on the CSP, span regions of significant point mutational polymorphism. Studies with human and mouse T‐cell clones have indicated that this polymorphism affects T‐cell cross‐reactivity to Th2R and Th3R, the two most polymorphic and immunodominant epitopes. We extend this observation with polyclonal human T‐cell lines, from 11 donors, raised to known variants of Th2R. These lines showed limited but variable cross‐reactivity with the heterologous peptides. T cells from B10.A4(R) (I‐Ak) mice immunized with each of 18 natural variants of Th2R indicated a similar, limited, cross‐reactivity. I‐Ak competition assays showed that a number of peptides were unable to bind because of a single polymorphic residue. In both the human and mouse assays, analysis of the sequences of immunogenic cross‐reactive and non‐cross‐reactive peptides suggested that the individual polymorphic residues affect the three‐dimensional conformation of the peptide within the major histocompatibility complex (MHC) groove in an, as yet, unpredictable way. These observations argue that design of an epitope able to generate broad cross‐reactivity is, to date, not possible. However, despite the limited cross‐reactivity of the individual human T‐cell lines, most of the donors had T‐cell repertoires capable of recognizing all or nearly all of the variants tested, which supports a strategy using a multivalent vaccine.
Performance Evaluation of Yahoo! S4: A First Look

Processing large data sets has been dominated recently by the map/reduce programming model [1], originally proposed by Google and widely adopted through the Apache Hadoop1 implementation. Over the years, developers have identified weaknesses of processing data sets in batches as in MapReduce and have proposed alternatives. One such alternative is continuous processing of data streams. This is particularly suitable for applications in online analytics, monitoring, financial data processing and fraud detection that require timely processing of data, making the delay introduced by batch processing highly undesirable. This processing paradigm has led to the development of systems such as Yahoo! S4 [2] and Twitter Storm.2 Yahoo! S4 is a general-purpose, distributed and scalable platform that allows programmers to easily develop applications for processing continuous unbounded streams of data. As these frameworks are quite young and new, there is a need to understand their performance for real time applications and find out the existing issues in terms of scalability, execution time and fault tolerance. We did an empirical evaluation of one application on Yahoo! S4 and focused on the performance in terms of scalability, lost events and fault tolerance. Findings of our analyses can be helpful towards understanding the challenges in developing stream-based data intensive computing tools and thus providing a guideline for the future development.