Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical Relevance of resistant strains of Helicobacter pylori: a review of current data

Acquired resistance of Helicobacter pylori to metronidazole and clarithromycin has been reported, with metronidazole resistance being very common. This has an important clinical impact on dual therapies, as well as on the standard triple therapies. However, when antisecretory drug based triple therapies with amoxycillin or clarithromycin and metronidazole are used, the resistance can be overcome in up to 75% of the cases in most of the studies. Clarithromycin seems to be a better choice than amoxycillin to achieve this goal. Nevertheless, resistance to metronidazole remains a risk factor for treatment failure. The most precise information comes from studies in which minimum inhibitory concentrations (MICs) are reported as well as whether the strain is susceptible or resistant. Few data are available from clinical trials to measure the impact of clarithromycin resistance. However, such resistance seems to have a negative impact on the clinical outcome of treatment. It is of greater importance that H pylori resistance is closely monitored in the future.
Driver identification and authentication with active behavior modeling

The legitimate driver of a vehicle traditionally gains authorization to access their vehicle via tokens such as ignition keys, some modern versions of which feature RFID tags. However, this token-based approach is not capable of detecting all instances of vehicle misuse. Technology trends have allowed for affordable and efficient collection of various sensor data in real time from the vehicle, its surroundings, and devices carried by the driver, such as smartphones. In this paper, we propose to use this sensory data to actively identify and authenticate the driver of a vehicle by determining characteristics which uniquely categorize individuals' driving behavior. Our approach is capable of continuously authenticating a driver throughout a driving session, as opposed to alternative approaches which are either performed offline or as a session starts. This means our modeling approach can be used to detect mid-session driving attacks, such as carjacking, which are beyond the scope of alternative driver authentication solutions. A simulated driving environment was used to collect sensory data of driver habits including steering wheel position and pedal pressure. These features are classified using a Support Vector Machine (SVM) learning algorithm. Our pilot study with 10 human subjects shows that we can use various aspects of how a vehicle is operated to successfully identify a driver under 2.5 minutes with a 95% confidence interval and with at most one false positive per driving day.
Naïve Bayes Classifier for Arabic Word Sense Disambiguation

Word Sense Disambiguation (WSD) is the process of selecting a sense of an ambiguous word in a given context from a set of predefined senses. Sense Inventory usually comes from a dictionary or thesaurus. In Arabic, the main cause of word ambiguity is the lack of diacritics of the most digital documents so the same word can occurs with different senses. In this paper, we use the rooting algorithm with Naive Bayes Classifier to solve the ambiguity of nondiacritics words in Arabic language. Our Experimental study proves that using of rooting algorithm with Naive Bayes (NB) Classifier enhances the accuracy by 16% and also decreases the dimensionality of the training documents.
Seneschal: Classification and Analysis in Supervised Mixture-modelling

This paper describes an algorithm that is an extension of mixture-modelling to supervised clustering. It is demonstrated to be as accurate as current state-of-the-art machine learning algorithms across various data sets, and significantly more accurate than distance-based supervised clustering algorithms. Most significantly, it combines the classification itself with the calculation of rich information about the probabilities of class membership, the significance of attributes in relation to a classification, and the data space described by the data items and attributes.
Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12

IHF and HU are two heterodimeric nucleoid-associated proteins (NAP) that belong to the same protein family but interact differently with the DNA. IHF is a sequence-specific DNA-binding protein that bends the DNA by over 160°. HU is the most conserved NAP, which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. Despite their importance, the in vivo interactions of the two proteins to the DNA remain to be described at a high resolution and on a genome-wide scale. Further, the effects of these proteins on gene expression on a global scale remain contentious. Finally, the contrast between the functions of the homo- and heterodimeric forms of proteins deserves the attention of further study. Here we present a genome-scale study of HU- and IHF binding to the Escherichia coli K12 chromosome using ChIP-seq. We also perform microarray analysis of gene expression in single- and double-deletion mutants of each protein to identify their regulons. The sequence-specific binding profile of IHF encompasses ∼30% of all operons, though the expression of <10% of these is affected by its deletion suggesting combinatorial control or a molecular backup. The binding profile for HU is reflective of relatively non-specific binding to the chromosome, however, with a preference for A/T-rich DNA. The HU regulon comprises highly conserved genes including those that are essential and possibly supercoiling sensitive. Finally, by performing ChIP-seq experiments, where possible, of each subunit of IHF and HU in the absence of the other subunit, we define genome-wide maps of DNA binding of the proteins in their hetero- and homodimeric forms.
Where did I come from? Where am I going? Functional influences on visual search fixation duration

Real time simulation of visual search behavior can occur only if the control of fixation durations is sufficiently understood. Visual search studies have typically confounded pre- and post-saccadic influences on fixation duration. In the present study, pre- and post-saccadic influences on fixation durations were compared by considering saccade direction. Novel use of a gaze-contingent moving obstructer paradigm also addressed relative contributions of both influences to total fixation duration. As a function of saccade direction, pre-saccadic fixation durations exhibited a different pattern from post-saccadic fixation durations. Post-saccadic fixations were also more strongly influenced by peripheral obstruction than pre-saccadic fixation durations. This suggests that post-saccadic influences may contribute more to fixation durations than pre-saccadic influences. Together, the results demonstrate that it is insufficient to model the control of visual search fixation durations without consideration of pre- and post-saccadic influences.
Prognostic Value of miR-21 in Various Cancers: An Updating Meta-Analysis

Background Recently, more and more studies investigated the value of microRNA (miRNA) as a diagnostic or prognostic biomarker in various cancers. MiR-21 was found dysregulated in almost all types of cancers. While the prognostic role of miR-21 in many cancers has been studied, the results were not consistent. Methods We performed a meta-analysis to investigate the correlation between miR-21 and survival of general cancers by calculating pooled hazard ratios (HR) and 95% confidence intervals (CI). Results The pooled results of 63 published studies showed that elevated miR-21 was a predictor for poor survival of general carcinomas, with pooled HR of 1.91 (95%CI: 1.66–2.19) for OS, 1.42 (95% CI: 1.16–1.74) for DFS and 2.2 (95% CI: 1.64–2.96) for RFS/CSS. MiR-21 was also a prognostic biomarker in the patients who received adjuvant therapy, with pooled HR of 2.4 (95%CI: 1.18–4.9) for OS. Conclusions Our results showed that miR-21 could act as a significant biomarker in the prognosis of various cancers. Further studies are warranted before the application of the useful biomarker in the clinical.
Analysis of T cell antigen receptor (TCR) expression by human peripheral blood CD4-8- alpha/beta T cells demonstrates preferential use of several V beta genes and an invariant TCR alpha chain

CD4-CD8- (double negative [DN]) alpha/beta T cells are a largely uncharacterized subpopulation of unknown function. To investigate whether these cells are selected to recognize particular antigens or antigen-presenting molecules, DN alpha/beta T cells were purified from the peripheral blood of five normal donors and their T cell receptor (TCR) alpha and beta chains were examined. Random cloning of TCR alpha chains by single-sided polymerase chain reaction (PCR) amplification identified an invariant rearrangement between V alpha 24 and J alpha Q, with no N region diversity, which was expressed preferentially by DN alpha/beta T cells from all donors. Random cloning also identified a precise V alpha 7.2-J alpha (IGRJa14) rearrangement, with two variable amino acids encoded in the V-J junction, which was enriched in the DN alpha/beta T cell preparations from some, but not all, donors. Analysis of TCR beta chains by quantitative PCR amplification demonstrated that the expression of four V beta gene families, V beta 2, 8, 11, and 13, was markedly increased in these DN alpha/beta T cell preparations. The expression of particular TCRs by DN alpha/beta T cells from multiple donors indicates that these cells, or at least a subpopulation of cells with this phenotype, recognize a limited spectrum of antigens and suggests that they may use nonpolymorphic antigen-presenting molecules.
Determination of stress using Blood Pressure and Galvanic Skin Response

Stress is a response to mental/emotional or physical aspects that is encountered in daily life. In order to manage stress, it is required to monitor the stress levels on continuous basis. Individual physiological parameters such as Galvanic Skin Response (GSR), Heart Rate (HR), Blood Pressure (BP), ECG (Electrocardiography) and respiration activity can be used as a measure to determine stress. But, the accuracy of determination is limited by using individual parameters. Usage of multiple parameters aids in better determination of stress. A combination of parameters such as GSR and Blood Pressure further increases the accuracy. The paper signifies better detection of stress by using GSR and BP.
Methodology for Zero-moment Point Experimental Modeling in the Frequency Domain

Frequency domain methodology is applied to obtain a nominal model for the Zero-Moment Point (ZMP) stability index of a biped robot in an attempt to establish a relationship between the robot trunk trajectories and the stability margin of the contact surface of the foot (or feet) touching the supporting soil. To this end the biped robot trunk is excited with a variable frequency sinusoidal signal around several operating points. These input oscillations generate other output oscillations that can be analyzed with the help of the ZMP measurement system. The proposed ZMP modeling approach not only considers classical rigid body model uncertainties but also non-modelled robot mechanical structure vibration modes. The non-linear ZMP model is obtained following three consecutive stages: Equivalent inverted pendulum dynamics, where saturation and acceleration upper bounds are taken into account, non-modelled inverted pendulum dynamics, including non-linear effects, and low-pass dynamics defining the system cut-off frequency. The effectiveness of this method is demonstrated in practice with the SILO2 biped robot prototype, and a simple control strategy is implemented in order to validate experimentally the usefulness of the models developed.
PtdIns (3,4,5) P3 Recruitment of Myo10 Is Essential for Axon Development

Myosin X (Myo10) with pleckstrin homology (PH) domains is a motor protein acting in filopodium initiation and extension. However, its potential role has not been fully understood, especially in neuronal development. In the present study the preferential accumulation of Myo10 in axon tips has been revealed in primary culture of hippocampal neurons with the aid of immunofluorescence from anti-Myo10 antibody in combination with anti-Tuj1 antibody as specific marker. Knocking down Myo10 gene transcription impaired outgrowth of axon with loss of Tau-1-positive phenotype. Interestingly, inhibition of actin polymerization by cytochalasin D rescued the defect of axon outgrowth. Furthermore, ectopic expression of Myo10 with enhanced green fluorescence protein (EGFP) labeled Myo10 mutants induced multiple axon-like neurites in a motor-independent way. Mechanism studies demonstrated that the recruitment of Myo10 through its PH domain to phosphatidylinositol (3,4,5)-trisphosphate (PtdIns (3,4,5) P3) was essential for axon formation. In addition, in vivo studies confirmed that Myo10 was required for neuronal morphological transition during radial neuronal migration in the developmental neocortex.
Under Consideration for Publication in Theory and Practice of Logic Programming Loop Formulas for Description Logic Programs *

Description Logic Programs (dl-programs) proposed by Eiter et al. constitute an elegant yet powerful formalism for the integration of answer set programming with description logics, for the Semantic Web. In this paper, we generalize the notions of completion and loop formulas of logic programs to description logic programs and show that the answer sets of a dl-program can be precisely captured by the models of its completion and loop formulas. Furthermore, we propose a new, alternative semantics for dl-programs, called the canonical answer set semantics, which is defined by the models of completion that satisfy what are called canonical loop formulas. A desirable property of canonical answer sets is that they are free of circular justifications. Some properties of canonical answer sets are also explored.
Teaching how to generate complex nominal phrases used to define new concepts or describe objects

Teaching technical vocabulary is a task which requires special techniques and the use of a context. Scientific texts incorporate complex noun phrases as part of their communicative function within a concept-oriented theory. The occurrence of these combinations constitutes a common feature of the above-mentioned texts. The aim of this paper is to examine the different functions which underlie those phrases and how they generate depending on the information they convey. Based on the communicative approach, we present these nominal phrases to our students as a means to define and describe new objects and concepts. In order to produce reliable, well-formed and permissible compound nominal phrases, their complexity is analysed and the different chunks are split up to understand the way each element is added to convey new information. The semantic relationships between all the different elements, which are dependent upon the function these items perform within the complex phrase, are also studied.
Intrusion Detection System using Self Organizing Map: A Survey

Due to usage of computer every field, Network Security is the major concerned in today’s scenario. Every year the number of users and speed of network is increasing, along with it online fraud or security threats are also increasing. Every day a new attack is generated to harm the system or network. It is necessary to protect the system or networks from various threats by using Intrusion Detection System which can detect “known” as well as “unknown” attack and generate alerts if any unusual behavior in the traffic. There are various approaches for IDS, but in this paper, survey is focused on IDS using Self Organizing Map. SOM is unsupervised, fast conversion and automatic clustering algorithm which is able to handle novelty detection. The main objective of the survey is to find and address the current challenges of SOM. Our survey shows that the existing IDS based on SOM have poor detection rate for U2R and R2L attacks. To improve it, proper normalization technique should be used. During the survey we also found that HSOM and GHSOM are advance model of SOM which have their own unique feature for better performance of IDS. GHSOM is efficient due to its low computation time. This survey is beneficial to design and develop efficient SOM based IDS having less computation time and better detection rate.
C II* Absorption in Damped Lyα Systems. I. Star Formation Rates in a Two-Phase Medium

We describe a technique that for the first time measures star formation rates (SFRs) in damped Lyα systems (DLAs) directly. We assume that massive stars form in DLAs and that the far-ultraviolet (FUV) radiation they emit heats the gas by the grain photoelectric mechanism. We infer the heating rate by equating it to the cooling rate measured by the strength of C II* λ1335. 7 absorption. Since the heating rate is proportional to the product of the dust-to-gas ratio, the grain photoelectric heating efficiency, and the SFR per unit area, , we can deduce for DLAs in which the cooling rate and dust-to-gas ratio have been measured. We consider models in which the dust consists of carbonaceous grains and silicate grains. We present two-phase models in which the cold neutral medium (CNM) and warm neutral medium (WNM) are in pressure equilibrium. In the CNM model the line of sight passes through CNM and WNM gas, while in the WNM model the line of sight passes only through WNM gas. Since the grain photoelectric heating efficiency is at least an order of magnitude higher in the CNM than in the WNM, most of the C II* absorption arises in the CNM in the CNM model. We use the measured C II* absorption lines to derive for a sample of ≈30 DLAs in which κ has been inferred from element depletion patterns. We show that the inferred corresponds to an average over the star-forming volume of the DLA rather than to local star formation along the line of sight. We obtain the average and show that = 10-2.2 M☉ yr-1 kpc-2 for the CNM solution and = 10-1.3 M☉ yr-1 kpc-2 for the WNM solution. Interestingly, the SFR per unit area in the CNM solution is similar to that measured in the Milky Way interstellar medium.
PS1-10jh CONTINUES TO FOLLOW THE FALLBACK ACCRETION RATE OF A TIDALLY DISRUPTED STAR

We present late-time observations of the tidal disruption event candidate PS1-10jh. UV and optical imaging with Hubble Space Telescope/WFC3 localize the transient to be coincident with the host galaxy nucleus to an accuracy of 0.023 arcsec, corresponding to 66 pc. The UV flux in the F225W filter, measured 3.35 rest-frame years after the peak of the nuclear flare, is consistent with a decline that continues to follow a t−5/3 power-law with no spectral evolution. Late epochs of optical spectroscopy obtained with MMT ∼ 2 and 4 years after the peak, enable a clean subtraction of the host galaxy from the early spectra, revealing broad helium emission lines on top of a hot continuum, and placing stringent upper limits on the presence of hydrogen line emission. We do not measure Balmer Hδ absorption in the host galaxy that is strong enough to be indicative of a rare, post-starburst “E+A” galaxy as reported by Arcavi et al. The light curve of PS1-10jh over a baseline of 3.5 years is best modeled by fallback accretion of a tidally disrupted star. Its strong broad helium emission relative to hydrogen (He iiλ4686/Hα > 5) could be indicative of either the hydrogen-poor chemical composition of the disrupted star, or certain conditions in the tidal debris of a solar-composition star in the presence of an optically thick, extended reprocessing envelope.
Non-functioning pancreatic neuroendocrine tumor accompanied with multiple liver metastases: remorseful case and literature review.

CONTEXT Pancreatic neuroendocrine tumor (P-NET) is a rare and slow-growing tumor. Unfortunately, there is no clear consensus on the role and timing of surgery for primary tumor and liver metastases, although current reports refer to liver surgery including LT for unresectable liver metastases. CASE REPORT A thirty-nine-year-old man was diagnosed with nonfunctioning pancreatic neuroendocrine tumor (P-NET) in the pancreatic head, with multiple liver metastases. The tumor was 2.5 cm in diameter and he was asymptomatic. Small but multiple metastases were detected in the liver, and no extrahepatic metastases were observed. We initially intended to control the liver metastases before resection of the primary tumor. To begin with, transarterial chemoembolization (TACE) and transcatheter arterial infusion (TAI) were repeated. Thereafter, systemic chemotherapy and biotherapy were introduced according to follow-up assessments. Unfortunately, imaging assessment at about 10 months later revealed that liver metastases were partially enlarged, although some were successfully treated. Therefore, these therapies were switched to other regimens, and TACE/TAI, systemic chemotherapies and biotherapies were repeated. Although liver metastases seemed to be stable for a while, the primary tumor was enlarged even after therapy. At 3.5 years after initial diagnosis, the primary tumor became symptomatic (pain and jaundice). Liver metastases enlarged and massive swelling of the para-aortic lymph nodes was observed. Thereafter, palliative therapy was the main course of action. He died at 4.3 years after initial diagnosis. CONCLUSION Our young patient could have been a candidate for initial surgery for primary tumor and might have had a chance of subsequent liver transplantation for unresectable metastases. Surgeons still face questions in deciding the best surgical scenario in patients with P-NET with liver metastases.
A Randomized Greedy Method for Rectangular-Pattern Fill Problems

In this paper, a class of problems of physical-design optimization with rectangular shapes is presented. Efficient solutions for this class of optimization problems are needed for rectangular metal fill/negative-fill insertion during postrouting optimization. These problems are also shown to be closely related to the problem of floorplanning with rectangular macrocells. The solution must satisfy certain constraints for minimum and maximum pattern densities within a moving rectangular window while optimizing a given objective function such as the area or the aspect ratio of the resultant bounding box. It is shown in this paper that the general class of such problems defined with a gridless formulation is at least NP-hard. This proof, with minor modifications, also extends to the formulation in the gridded domain. A greedy randomized algorithm for one of our problems in the gridded domain is proposed, along with a proof that this algorithm can achieve the given objective with a very high probability while satisfying the constraints. Experimental results based on an implementation of our algorithm are provided and are shown to agree with our theoretical proof.