Miracle-dz/UniFAR-FTUs huggingface dataset:
Replication Termination: Containing Fork Fusion-Mediated Pathologies in Escherichia coli

Duplication of bacterial chromosomes is initiated via the assembly of two replication forks at a single defined origin. Forks proceed bi-directionally until they fuse in a specialised termination area opposite the origin. This area is flanked by polar replication fork pause sites that allow forks to enter but not to leave. The precise function of this replication fork trap has remained enigmatic, as no obvious phenotypes have been associated with its inactivation. However, the fork trap becomes a serious problem to cells if the second fork is stalled at an impediment, as replication cannot be completed, suggesting that a significant evolutionary advantage for maintaining this chromosomal arrangement must exist. Recently, we demonstrated that head-on fusion of replication forks can trigger over-replication of the chromosome. This over-replication is normally prevented by a number of proteins including RecG helicase and 3’ exonucleases. However, even in the absence of these proteins it can be safely contained within the replication fork trap, highlighting that multiple systems might be involved in coordinating replication fork fusions. Here, we discuss whether considering the problems associated with head-on replication fork fusion events helps us to better understand the important role of the replication fork trap in cellular metabolism.
NODDI and Tensor-Based Microstructural Indices as Predictors of Functional Connectivity

In Diffusion Weighted MR Imaging (DWI), the signal is affected by the biophysical properties of neuronal cells and their relative placement, as well as extra-cellular tissue compartments. Typically, microstructural indices, such as fractional anisotropy (FA) and mean diffusivity (MD), are based on a tensor model that cannot disentangle the influence of these parameters. Recently, Neurite Orientation Dispersion and Density Imaging (NODDI) has exploited multi-shell acquisition protocols to model the diffusion signal as the contribution of three tissue compartments. NODDI microstructural indices, such as intra-cellular volume fraction (ICVF) and orientation dispersion index (ODI) are directly related to neuronal density and orientation dispersion, respectively. One way of examining the neurophysiological role of these microstructural indices across neuronal fibres is to look into how they relate to brain function. Here we exploit a statistical framework based on sparse Canonical Correlation Analysis (sCCA) and randomised Lasso to identify structural connections that are highly correlated with resting-state functional connectivity measured with simultaneous EEG-fMRI. Our results reveal distinct structural fingerprints for each microstructural index that also reflect their inter-relationships.
Fabrication of Localized Surface Plasmon Resonance Fiber Probes Using Ionic Self-Assembled Gold Nanoparticles

An nm-thickness composite gold thin film consisting of gold nanoparticles and polyelectrolytes is fabricated through ionic self-assembled multilayers (ISAM) technique and is deposited on end-faces of optical fibers to construct localized surface plasmon resonance (LSPR) fiber probes. We demonstrate that the LSPR spectrum induced by ISAM gold films can be fine-tuned through the ISAM procedure. We investigate variations of reflection spectra of the probe with respect to the layer-by-layer adsorption of ISAMs onto end-faces of fibers, and study the spectral variation mechanism. Finally, we demonstrated using this fiber probe to detect the biotin-streptavidin bioconjugate pair. ISAM adsorbed on optical fibers potentially provides a simple, fast, robust, and low-cost, platform for LSPR biosensing applications.
Comparison of Word Intelligibility in Spoken and Sung Phrases

Twenty listeners were exposed to spoken and sung passages in English produced by three trained vocalists. Passages included representative words extracted from a large database of vocal lyrics, including both popular and classical repertoires. Target words were set within spoken or sung carrier phrases. Sung carrier phrases were selected from classical vocal melodies. Roughly a quarter of all words sung by an unaccompanied soloist were misheard. Sung passages showed a seven-fold decrease in intelligibility compared with their spoken counterparts. The perceptual mistakes occurring with vowels replicate previous studies showing the centralization of vowels. Significant confusions are also evident for consonants, especially voiced stops and nasals.
Generalized Architecture to Capture End to End Provenance in a System

Provenance is the metadata about the origin, context or history of data on how it came into its present state of being. Data in our context are files. The information about how the file was created and maintained can throw a lot of information on the credibility of data stored in the file. This information can be obtained by collecting the provenance of data. In this paper we propose a generalized framework to capture provenance information of files in a system and present a prototype tool which capture cut/copy/paste dependency of files in Linux X Windows as a proof of concept for our idea.
PENGARUH COMMITMENT ORGANIZATIONAL DAN (POS) TERHADAP KINERJA KARYAWAN MELALUI (OCB) PADA PT. NASMOCO KALIGAWE

The research was motivated by the decrease in the sales division employees at PT. Nasmoco Kaligawe annually. In addition, many employees who complained about the lack of support in the organization of work, coupled with the level of employee performance in achieving sales targets fluktuatif. The aim of this research is conducted to determine the influence of commitment organizational and perceived organizational support to company performance through organizational citizenship behavior. The population is all of employees of the sales division. The sample are 60 person of employees of sales division, with sample technique used was sensus sampling. The analysis used in this research is the Path Analysis using software SPS 15.0, which previously tested the validity, reliability, correlation coefficient, simple and multiple regression analysis, the coefficient of determination, and signification test (t test and F test) first. The result of this research approved that commitment organizational (X1) and perceived organizational support (X2) partially or simultaneously can influenced organizational citizenship behavior (Y1) and employee performance (Y2). According the result of path analysis showed that organizational citizenship behavior variable is intervening variable towards employee performance in this research.
Convergent thalamic and mesencephalic projections to the anterior medial cortex in the rat

Small microelectrophoretic deposits of horseradish‐peroxidase (HRP) were placed at various loci within the gray matter of the rat's anterior medial cortex. A comparison of the patterns of retrograde cell‐labeling charted in 26 such cases confirmed earlier findings in fiber‐degeneration studies according to which the respective thalamocortical projections of the mediodorsal (MD) and anteromedial nucleus (AM) overlap each other over a wide region of the anterior medial cortex. This region of thalamocortical convergence, extending from pregenual levels caudalward as far as the anterior border of the retrosplenial cortex, corresponds almost exactly to the cortical region from which locally deposited HRP was found to be transported so as to label cells in one or both of two mesencephalic cell groups: the ventral tegmental area (AVT) dorsal and lateral to the interpeduncular nucleus, and the medial one‐quarter of the pars compacta of the substantia nigra (SNC). The reported findings suggest that the corticipetal projections of AVT and SNC are organized so that AVT projects largely to the area infraradiata of the pregenual cortex which receives its major thalamocortical projection from MD, whereas SNC‐efferents are distributed to the area infraradiata of the supracallosal cortex which receives most of its thalamocortical afferents from AM; the two mesencephalocortical projections do, however, appear to overlap each other in a region of the medial cortex immediately posterior to the level of the genu corporis callosi. HRP injected into the medial cortex of five rats pre‐treated with 6‐hydroxydopamine, a drug that produces chemical lesions of catecholamine neurons, failed to label any cells in AVT and SNC but did label numerous cells in MD and AM. This finding suggests that the ventral tegmental cells projecting to the anterior medial cortex are exclusively dopamine neurons.
MULTIPLE CFO ESTIMATION IN OFDM UNDERWATER COMMUNICATION SYSTEMS

Abstract– When channel is severely frequency selective, Orthogonal Frequency Division Multiplexing (OFDM) is a suitable candidate for high rate communications. In multipath fading channels like harsh underwater channels, due to Inter Carrier Interference (ICI) and Carrier Frequency Offset (CFO) the performance of this technique is dramatically decreased. Therefore, these effects must be alleviated to overcome the performance degradation. To do that, first the CFO’s must be estimated. In this paper, we consider an underwater channel with three sets of paths and we assume that the paths in each set have similar Doppler scale factor. For minimum transmission power, Zero Padded OFDM (ZP-OFDM) is considered. We propose a new method based on MUltiple SIgnal Classification (MUSIC) technique that facilitates the estimation of multiple CFO’s in Under Water Acoustic (UWA) channel and compare it with the derived Maximum Likelihood (ML) estimator algorithm. Simulation results show that the proposed method is robust against the received Signal to Noise Ratio (SNR) variations.
Voting based automatic exudate detection in color fundus photographs

Diabetic retinopathy is one of the leading causes of preventable blindness. Screening programs using color fundus photographs enable early diagnosis of diabetic retinopathy, which enables timely treatment of the disease. Exudate detection algorithms are important for development of automatic screening systems and in this paper we present a method for detection of exudate regions in color fundus photographs. The method combines different preprocessing and candidate extraction algorithms to increase the exudate detection accuracy. First, we form an ensemble of different candidate extraction algorithms, which are used to increase the accuracy. After extracting the potential exudate regions we apply machine learning based classification for detection of exudate regions. For experimental validation we use the DRiDB color fundus image set where the presented method achieves higher accuracy in comparison to other state-of-the art methods.
Du féodalisme au capitalisme : à propos des conséquences de la Révolution sur l'évolution de l'économie française

L'auteur rend compte des apports nouveaux, tant des ouvrages les plus recents qui se sont multiplies sur le sujet, que des colloques et rencontres scientifiques tenus a l'approche du bicentenaire. Il rappelle les positions prises et les problematiques en jeu sur le bilan negatif ou positif de la Revolution dans le domaine economique. Une analyse precise par secteurs permet d'aboutir a une conclusion beaucoup plus nuancee que certaines syntheses hâtives d'aujourd'hui.
Depression in Parkinson's disease. The impact of symptom overlap on prevalence.

The reported prevalence of depression concomitant with Parkinson's disease varies greatly in the literature, which may partly be explained by symptom overlap. To determine the impact of symptom overlap on the prevalence, the authors tested 100 Parkinson's disease patients for major depression (DSM-III-R) with both a standard, inclusive method and a diagnostic-etiologic, exclusive method. The authors found that the prevalence detected with the inclusive method (23%) decreased when the exclusive method was used (13%), which was mainly caused by lower scores on the item "loss of interest. " The study's findings give empirical support for the relevance of the new category in DSM-IV "mood disorder due to a general medical condition. "
Constraint and opportunity in genome innovation

The development of rigorous molecular taxonomy pioneered by Carl Woese has freed evolution science to explore numerous cellular activities that lead to genome change in evolution. These activities include symbiogenesis, inter- and intracellular horizontal DNA transfer, incorporation of DNA from infectious agents, and natural genetic engineering, especially the activity of mobile elements. This article reviews documented examples of all these processes and proposes experiments to extend our understanding of cell-mediated genome change.
E-cadherin in gastric carcinomas: Relations with histological parameters and its prognostic value.

PURPOSE Gastric cancer (GC) is still one of the most common malignancies with the majority of the tumors being diagnosed at advanced stage. The need for identification of prognostic and early detection biomarkers is thus compulsory. E-cadherin is one of the emerging biomarkers that is currently evaluated in the literature in the frame of epithelial-mesenchymal transition (EMT). Our aim was to study the expression of E-cadherin in the various histological subtypes of GC and to evaluate its prognostic value. METHODS This historical cohort survey was performed on gastric tumors obtained from 66 (46 men and 20 women) patients with documented gastric adenocarcinoma who underwent total or partial gastrectomy and regional lymphadenectomy from 2003 till 2011. Features such as tumor size, depth of invasion, grade and histological subtype, lymphovascular space invasion and regional lymph nodes involvement were also evaluated. Immunohistochemistry (IHC) was used for assessing the expression of E-cadherin with a semi-quantitative model. RESULTS The correlation of E-cadherin tissue expression with patient overall survival (OS) or disease-free survival (DFS) was not statistically significant, as well as with gender, T stage, N stage, TNM stage, grade, positive lymph nodes ratio or lymphovascular invasion. CONCLUSIONS 73.0% of the evaluated tumors showed abnormal E-cadherin expression in IHC, but the correlation of E-cadherin tissue expression with patient OS or DFS was not statistically significant. Literature stands equivocal about the association between E-cadherin gene mutation, and histopathology and tumor invasiveness. Our results further strengthen the need of larger studies to fully elucidate the predictive role of E-cadherin in the natural history of GC.
On Pulse Position Modulation and Its Application to PLLs for Spur Reduction

Randomizing the positions of charge pump current pulses in a PLL breaks their periodicity and redistributes the reference spurs into broadband noise. Closed form expressions for the power spectral density (PSD) of pulse position modulated (PPM) signals are derived and intuitive explanations for the results are given. The redistributed noise has a high-pass shape and does not affect the close in phase noise of the PLL. PPM using a uniformly distributed i.i. d. sequence completely removes the spurs and provides a first-order shaping of redistributed noise. Higher order shaping and reduction of redistributed noise at intermediate offset frequencies are possible using PPM with a high-pass shaped modulating sequence and pulse repetition. Circuit implementations of these techniques are given and their nonidealities are discussed. Simulation results from a 1 GHz PLL operating from a reference frequency of 20 MHz and a bandwidth of 1 MHz confirm the results of the analysis and viability of the proposed techniques. In the presence of nonidealities spurs can be reduced by at least 13 dB without any trimming of the delays in the PPM circuits and by 25 dB after trimming the delays to within 5% of the nominal value.
A comparison of three standard methods of identifying mast cells in endobronchial biopsies in normal and asthmatic subjects

Reported mast‐cell counts in endobronchial biopsies from asthmatic subjects are conflicting, with different methodologies often being used. This study compared three standard methods of counting mast cells in endobronchial biopsies from asthmatic and normal subjects. Endobronchial biopsies were obtained from atopic asthmatic subjects (n= 17), atopic nonasthmatic subjects (n=6), and nonatopic nonasthmatic control subjects (n=5). After overnight fixation in Carnoy's fixative, mast cells were stained by the short and long toluidine blue methods and antitryptase immunohistochemistry and were counted by light microscopy. Method comparison was made according to Bland & Altman. The limits of agreement were unacceptable for each of the comparisons, suggesting that the methods are not interchangeable. Coefficients of repeatability were excellent, and not different for the individual techniques. These results suggest that some of the reported differences in mast‐cell numbers in endobronchial biopsies in asthma may be due to the staining method used, making direct comparisons between studies invalid. Agreement on a standard method is required for counting mast cells in bronchial biopsies, and we recommend the immunohistochemical method, since fixation is less critical and the resultant tissue sections facilitate clear, accurate, and rapid counts.
Character Networks and Centrality

A character network represents relations between characters from a text; the relations are based on text proximity, shared scenes/events, quoted speech, etc. Our project sketches a theoretical framework for character network analysis, bringing together narratology, both close and distant reading approaches, and social network analysis. It is in line with recent attempts to automatise the extraction of literary social networks (Elson, 2012; Sack, 2013) and other studies stressing the importance of character- systems (Woloch, 2003; Moretti, 2011). The method we use to build the network is direct and simple. First, we extract co-occurrences from a book index, without the need for text analysis. We then describe the narrative roles of the characters, which we deduce from their respective positions in the network, i.e. the discourse. As a case study, we use the autobiographical novel Les Confessions by Jean-Jacques Rousseau. We start by identifying co-occurrences of characters in the book index of our edition (Slatkine, 2012). Subsequently, we compute four types of centrality: degree, closeness, betweenness, eigenvector. We then use these measures to propose a typology of narrative roles for the characters. We show that the two parts of Les Confessions, written years apart, are structured around mirroring central figures that bear similar centrality scores. The first part revolves around the mentor of Rousseau; a figure of openness. The second part centres on a group of schemers, depicting a period of deep paranoia. We also highlight characters with intermediary roles: they provide narrative links between the societies in the life of the author. The method we detail in this complete case study of character network analysis can be applied to any work documented by an index.
Face recognition using spatially smoothed discriminant structure-preserved projections

Abstract. Recently, structure-preserved projections (SPP) were proposed as a local matching-based algorithm for face recognition. Compared with other methods, the main advantage of SPP is that it can preserve the configural structure of subpatterns in each face image. However, the SPP algorithm ignores the information among samples from different classes, which may weaken its recognition performances. Moreover, the relationships of nearby pixels in the subpattern are also neglected in SPP. In order to address these limitations, a new algorithm termed spatially smoothed discriminant structure-preserved projections (SS-DSPP) is proposed. SS-DSPP takes advantage of the class information to characterize the discrimination structure of subpatterns from different classes, and a new spatially smooth constraint is also derived to preserve the intrinsic two-dimensional structure of each subpattern. The feasibility and effectiveness of the proposed algorithm are evaluated on four standard face databases (Yale, extended YaleB, CMU PIE, and AR). Experimental results demonstrate that our SS-DSPP outperforms the original SPP and several state-of-the-art algorithms.
Observer-Based Robust Control of Uncertain Fuzzy Models with Pole Placement Constraints

Practical systems are often modelled by nonlinear dynamics. Controlling nonlinear systems are still open problems due to their complexity nature. This problem becomes more complex when the system parameters are uncertain. To control such systems, we may use the linearization technique around a given operating point and then employ the known methods of linear control theory. This approach is successful when the operating point of the system is restricted to a certain region. Unfortunately, in practice this approach will not work for some physical systems with a time-varying operating point. The fuzzy model proposed by Takagi-Sugeno (T-S) is an alternative that can be used in this case. It has been proved that T-S fuzzy models can effectively approximate any continuous nonlinear systems by a set of local linear dynamics with their linguistic description. This fuzzy dynamic model is a convex combination of several linear models. It is described by fuzzy rules of the type If-Then that represent local input output models for a nonlinear system. The overall system model is obtained by “blending” these linear models through nonlinear fuzzy membership functions. For more details on this topic, we refer the reader to (Tanaka & al 1998 and Wand & al, 1995) and the references therein. The stability analysis and the synthesis of controllers and observers for nonlinear systems described by T-S fuzzy models have been the subject of many research works in recent years. The fuzzy controller is often designed under the well-known procedure: Parallel Distributed Compensation (PDC). In presence of parametric uncertainties in T-S fuzzy models, it is necessary to consider the robust stability in order to guarantee both the stability and the robustness with respect to the latter. These may include modelling error, parameter perturbations, external disturbances, and fuzzy approximation errors. So far, there have been some attempts in the area of uncertain nonlinear systems based on the T-S fuzzy models in the literature. The most of these existing works assume that all the system states are measured. However, in many control systems and real applications, these are not always available. Several authors have recently proposed observer based robust controller design methods considering the fact that in real control problems the full state information is not always available. In the case without uncertainties, we apply the separation property to design the observer-based controller: the observer synthesis is designed so that its dynamics are fast and we independently design the controller by imposing slower dynamics. Recently, much effort has been devoted to observer-based control for T-S fuzzy models. (Tanaka & al, 1998) have studied the fuzzy observer design for T-S fuzzy control systems. Nonetheless, in