Miracle-dz/UniFAR-FTUs huggingface dataset:
Phosphatidylethanolamine recognition promotes enteropathogenic E. coli and enterohemorrhagic E. coli host cell attachment.

Using both solid phase and liposome aggregation assays, we screened a variety of glycolipids and phospholipids and found that EHEC and EPEC bind specifically and in a dose-dependent manner to PE. This binding was consistently observed whether the lipid was immobilized on a thin layer chromatography plate, in a microtitre well or incorporated into a unilamellar vesicle suspended in aqueous solution. There was no evidence of binding to other phospholipids such as phosphatidylcholine (PC) or phosphatidylserine (PS). Bacterial binding to two epithelial cell lines also correlated with the level of outer leaflet PE and was reduced following preincubation with anti-PE. The PE-binding phenotype of EPEC appeared to correlate with the bundle-forming pilus (bfp) genotype of a number of clinical isolates. These results provide evidence of a receptor role for PE in the adhesion of EHEC and EPEC to host cells.
Platelet Internalization in Early Thrombogenesis

Activated platelets rapidly internalize ligand-alpha(IIb)beta 3 complexes and particulates. The platelets sequester these primarily to the surface-connected canalicular system (SCCS), alpha-granules or evaginated surfaces. This occurs swiftly as activation initiates shape change, internal transformation, and secretion out of the platelet SCCS. The transmembrane signaling mechanism for internalization is through the platelet submembranous, detergent-resistant, cytochalasin B-resistant cytoskeletal filaments, not cytoplasmic actin filaments. This work proposes the model that platelet internalization responses contribute in the retraction of clots and participate in vivo in thrombus development at sites of coronary artery injury. In isometric clot retraction, the retracting platelets show internalization of fibrinogen-gold and fibrin while spreading on the polymerizing fibrin strands. The combination of platelet internalization (retracting) with evagination (spreading) on fibrin strands appear to approximate and organize nearby platelets into the developing thrombi. Ex vivo findings are similar under flowing conditions on denuded rabbit aortic endothelium with fibrinogen-gold markers. Early thrombi developing in vivo at sites of congenital coronary artery lesions in perinatal piglets show fibrin strands internalized into the SCCS of platelets. A thrombogenesis model is proposed that shows that platelet internalization responses anchor fibrin and approximate platelets, thus enhancing thrombus development and retraction.
Application of genetic algorithms to robot kinematics calibration

Position and orientation accuracy of an end-effector is affected by the precision of kinematics parameters of the robot manipulator. Thus, good precision requires good knowledge of robot physical parameter values. However, this condition can be difficult to meet in practice. Hence, calibration techniques can be devised in order to improve the robot accuracy through estimation of these particular parameters. In this article, the genetic algorithm is used to calibrate the robot kinematics accuracy. A kinematics model is formulated and conducted as an optimisation problem for ABB Irb 6000 robot manipulator. The objective is to analyse and evaluate the performance of the GA in optimising such robot kinematics accuracy. In this algorithm, small changes in the kinematics parameters values represent the parent and offspring population and the end-effector error represents the fitness functions. A numerical example has been used to demonstrate the convergence and effectiveness of the given model.
Design and performance analysis of a directly-coupled solar photovoltaic irrigation pump system at Gaibandha, Bangladesh

Due to climate change and high price of fossil fuel, demand of electricity for irrigation need is increasing. Harnessing solar power to meet this increasing demand can be a good solution. In this paper, we have shown the design and performance analysis of a directly coupled solar photovoltaic (PV) motor-pump system operating at Gaibandha, Bangladesh. Three 1kW DC series motor coupled with pumps were powered by photovoltaic panels of 2kWp. The motor pumps were directly connected without any converter. All of the components of the system were available and bought from the local market. With average insolation, the system can lift 1,20,000 to 1,72,000 lit/day. We have calculated the efficiency of the motor-pumps at different time of the day. Finally, we have calculated the simple payback period of the system. We found the system to be viable technically and economically.
New disseminated intravascular coagulation score: A useful tool to predict mortality in comparison with Acute Physiology and Chronic Health Evaluation II and Logistic Organ Dysfunction scores

Objective:To compare the performance of a coagulation score—the new scoring system for diagnosing disseminated intravascular coagulation (DIC)—with the Acute Physiology and Chronic Health Evaluation (APACHE) II and Logistic Organ Dysfunction score in mortality prediction. Design:Single-center retrospective study. Setting:Medical intensive care unit of the University of Munich. Patients:A total of 797 patients admitted to the intensive care unit between January 1, 1996, and January 1, 2001. Methods:A retrospective analysis of all patients was done if the coagulation variables d-dimer, platelet count, fibrinogen, and prothrombin index were available within the first 12 hrs after admission. Patients with missing values, fibrinolytic therapy, or unknown survival status were excluded from analysis. As a marker of fibrin generation, d-dimer was measured and integrated into the scoring system for DIC together with prothrombin time, fibrinogen, and platelet count. A coagulation score was calculated in analogy with the scoring system for DIC in patients not typically developing DIC. Measurements and Results:Overall, the mean result of the scoring system for DIC was 2.2 points. An increasing scoring system for DIC was associated with increasing mortality in patients with serious infections. Use of the scoring system for DIC in addition to the APACHE II score helps to predict mortality better than the APACHE II score alone, especially in patients with infections. The Cox regression analysis showed that the DIC and APACHE II scores correlated independently with survival time with a greater effect of the DIC score than the APACHE II or the Logistic Organ Dysfunction score. Similar results were obtained using the coagulation score in patients with cardiocirculatory diseases. Conclusion:Our retrospective data suggest that a combination of the APACHE II score and the scoring system for DIC predicts mortality in critically ill patients with available variables better than the APACHE II score alone. This effect is most pronounced among patients with active infection. These results of our retrospective analysis have to be confirmed in a prospective study.
Three-Dimensional Distribution of UBF and Nopp140 in Relationship to Ribosomal DNA Transcription During Mouse Preimplantation Development1

ABSTRACT The nucleolus is a dynamic nuclear compartment that is mostly involved in ribosome subunit biogenesis; however, it may also play a role in many other biological processes, such as stress response and the cell cycle. Mainly using electron microscopy, several studies have tried to decipher how active nucleoli are set up during early development in mice. In this study, we analyzed nucleologenesis during mouse early embryonic development using 3D-immunofluorescent detection of UBF and Nopp140, two proteins associated with different nucleolar compartments. UBF is a transcription factor that helps maintain the euchromatic state of ribosomal genes; Nopp140 is a phosphoprotein that has been implicated in pre-rRNA processing. First, using detailed image analyses and the in situ proximity ligation assay technique, we demonstrate that UBF and Nopp140 dynamic redistribution between the two-cell and blastocyst stages (time of implantation) is correlated with morphological and structural modifications that occur in embryonic nucleolar compartments. Our results also support the hypothesis that nucleoli develop at the periphery of nucleolar precursor bodies. Finally, we show that the RNA polymerase I inhibitor CX-5461: 1) disrupts transcriptional activity, 2) alters preimplantation development, and 3) leads to a complete reorganization of UBF and Nopp140 distribution. Altogether, our results underscore that highly dynamic changes are occurring in the nucleoli of embryos and confirm a close link between ribosomal gene transcription and nucleologenesis during the early stages of development.
Effect of cell seeding concentration on the quality of tissue engineered constructs loaded with adult human articular chondrocytes

Many aspects of the process of in vitro differentiation of chondrocytes in three‐dimensional (3D) scaffolds need to be further investigated. Chitosan scaffolds were produced by freeze‐drying 3% w/v 90% DDA chitosan gels. The effect of the cell seeding concentration was evaluated by culturing human adult chondrocytes in chitosan scaffolds After the first passage, cells were seeded into chitosan scaffolds with a diameter of 8 mm. The final cell seeding concentration per cm3 of chitosan scaffold was: Group A, 3 × 106; Group B, 6 × 106; Group C, 12 × 106; and Group D, 25 × 106 cells. After 14 and 28 days in 3D culture, the constructs were assesed for collagen, glucosaminoglycans and DNA content. The mechanical properties of the constructs were determined using a dynamic oscillatory shear test. The histological aspect of the constructs was evaluated using the Bern score. The collagen and GAG concentration increased, varying the cell seeding concentration. There was a significant increase in proteoglycan and hydroxyproline production between groups C and D. The sulphated GAG content increased significantly in the group D as compared to the other groups. The mechanical properties of the different constructs increased over time, from 9.6 G′/kPa at 14 days of 3D culture to 14.6 G′/kPa at 28 days under the same culture conditions. In this study we were able to determine that concentrations of 12–25 million cells/cm2 are needed to increase the matrix production and mechanical properties of human adult chondrocytes under static conditions. Copyright © 2008 John Wiley & Sons, Ltd.
Beta-Band Oscillations Represent Auditory Beat and Its Metrical Hierarchy in Perception and Imagery

Dancing to music involves synchronized movements, which can be at the basic beat level or higher hierarchical metrical levels, as in a march (groups of two basic beats, one–two–one–two …) or waltz (groups of three basic beats, one–two–three–one–two–three …). Our previous human magnetoencephalography studies revealed that the subjective sense of meter influences auditory evoked responses phase locked to the stimulus. Moreover, the timing of metronome clicks was represented in periodic modulation of induced (non-phase locked) β-band (13–30 Hz) oscillation in bilateral auditory and sensorimotor cortices. Here, we further examine whether acoustically accented and subjectively imagined metric processing in march and waltz contexts during listening to isochronous beats were reflected in neuromagnetic β-band activity recorded from young adult musicians. First, we replicated previous findings of beat-related β-power decrease at 200 ms after the beat followed by a predictive increase toward the onset of the next beat. Second, we showed that the β decrease was significantly influenced by the metrical structure, as reflected by differences across beat type for both perception and imagery conditions. Specifically, the β-power decrease associated with imagined downbeats (the count “one”) was larger than that for both the upbeat (preceding the count “one”) in the march, and for the middle beat in the waltz. Moreover, beamformer source analysis for the whole brain volume revealed that the metric contrasts involved auditory and sensorimotor cortices; frontal, parietal, and inferior temporal lobes; and cerebellum. We suggest that the observed β-band activities reflect a translation of timing information to auditory–motor coordination. SIGNIFICANCE STATEMENT With magnetoencephalography, we examined β-band oscillatory activities around 20 Hz while participants listened to metronome beats and imagined musical meters such as a march and waltz. We demonstrated that β-band event-related desynchronization in the auditory cortex differentiates between beat positions, specifically between downbeats and the following beat. This is the first demonstration of β-band oscillations related to hierarchical and internalized timing information. Moreover, the meter representation in the β oscillations was widespread across the brain, including sensorimotor and premotor cortices, parietal lobe, and cerebellum. The results extend current understanding of the role of β oscillations in neural processing of predictive timing.
Dynamic studies of gadolinium uptake in brain tumors using inversion‐recovery echo‐planar imaging

Echo‐planar imaging has been used to observe the dynamics of Gd‐DTPA uptake in brain tumors. It has been possible to examine both vascular uptake and diffusion across the blood‐brain barrier in a single experiment, by using the IR‐MBEST echo‐planar sequence which combines a high temporal resolution (approximately 3 s) with strong T1 weighting. To model the uptake it is necessary to know the arterial concentration of Gd‐DTPA; in this study the signal in the sagittal sinus was measured to avoid the need to take repeated blood samples. The time constant for transfer across the blood‐brain barrier was measured to be between 20 and 1050 s for different tumors. The results of the modeling correlated with the results of other assessments of tumor vascularity.
A model of foregut activity in the blowfly Phormia regina Meigen. II. Peristalsis in the crop duct during the crop-emptying process.

The effects of the mechanical properties of the crop-duct musculature on the production of pressure increase in the crop duct by peristalsis are examined by the application of the model of Thomson and Holling to a mechanical analogue of the crop duct. Behavior of the crop-duct model in terms of the initiation of both peristalsis and reverse peristalsis reflects the observed behaviour of the crop duct of Phormia regina. Although the properties of the peristaltic wave such as amplitude, wavelength, and velocity vary in a complex manner with crop-duct volume, and also with the distance which the peristaltic wave has travelled, the structure of the model accurately reflects these variations.
An Evaluation Framework for Cross-Platform Mobile App Development Tools: A case analysis of Adobe PhoneGap framework

The 'App economy' is a highly lucrative and competitive market for independent software vendors as it potentially offers an easy highway to reach millions of users. However, the mobile application landscape is scattered and an application developer has to publish the software for several different platforms to be able to serve a majority of smartphone users. Therefore, a bunch of cross-development tools have been offered to simplify this workload. In this paper, we present an evaluation framework for comparing different cross-development tools. We use this framework to evaluate Adobe PhoneGap tool against native development in Android and Windows Phone platforms. The results of a case study reveal that while the cross-platform technique was easy to use, the appearance and usability of the app was mediocre at its best. The business impacts of these are also discussed.
On Estimation in Relative Survival

Summary Estimation of relative survival has become the first and the most basic step when reporting cancer survival statistics. Standard estimators are in routine use by all cancer registries. However, it has been recently noted that these estimators do not provide information on cancer mortality that is independent of the national general population mortality. Thus they are not suitable for comparison between countries. Furthermore, the commonly used interpretation of the relative survival curve is vague and misleading. The present article attempts to remedy these basic problems. The population quantities of the traditional estimators are carefully described and their interpretation discussed. We then propose a new estimator of net survival probability that enables the desired comparability between countries. The new estimator requires no modeling and is accompanied with a straightforward variance estimate. The methods are described on real as well as simulated data.
DECREASED EFFECT OF GLUCANTIME IN CUTANEOUS LEISHMANIASIS COMPLICATED WITH SECONDARY BACTERIAL INFECTION

Background: Glucantime is regarded as the first-line treatment of cutaneous leishmaniasis (CL); however, failure to treatment is a problem in many cases. Aim: The aim was to evaluate the therapeutic effect of glucantime in CL complicated with secondary bacterial infection compared to uncomplicated lesions. Methods: This experimental study was performed in Skin Diseases and Leishmaniasis Research Center, Isfahan, Iran. A total of 161 patients enrolled in the study had CL confirmed by positive smear of lesions. All the patients were treated with systemic glucantime for 3 weeks and followed for 2 months. Response to treatment was defined as loss of infiltration, reepithelization, and negative smear. Depending on the results of bacterial cultures, the lesions were divided into two groups and the efficacy of glucantime was compared. Results: A total of 123 patients (76.4%) were negative, and 38 patients (23.6%) were positive for secondary bacterial infection. In groups with negative bacterial culture response to treatment was 65% (80 patients) and in the other positive group, it was 31.6% (12 patients), with a difference (χ2 = 13.77, P < 0.01). Conclusion: Therapeutic effect of glucantime showed a decrease in CL lesions with secondary bacterial infection. Therefore, in the cases of unresponsiveness to treatment, the lesions should be evaluated for bacterial infection, before repeating the treatment.
comprehensive review : Krill Herd algorithm ( KH ) and its pplications saju

Krill Herd (KH) algorithm is a class of nature-inspired algorithm, which simulates the herding behavior of krill individuals. It has been successfully utilized to tackle many optimization problems in different domains and found to be very efficient. As a result, the studies has expanded significantly in the last 3 years. This paper presents the extensive (not exhaustive) review of KH algorithm in the area of applicavailable online 26 August 2016
Implementation and Performance Evaluation of Intrusion Detection and Response System

Modern intrusion detection systems (IDS) are deployed in high-speed networks. Thus, they must be able to process a large amount of data in real time. This raises the issue of performance and required an evaluation of these IDS. We present in this paper an evaluation approach, based on a series of tests. The aim is to measure the performance of the components of an IDS and their effects on the entire system, as well as to study the effect of the characteristics of the deployment environment on the operation of the IDS. So, we have implemented the IDS SNORT on machines with different technical characteristics and we have designed a network to generate a set of experiments to measure the performances obtained in the case of a deployment in high-speed networks . These experiments consist in injecting various traffic loads, characterized by different transmission times, packet numbers, packet sizes and bandwidths, and then analyzing, for each situation, the processing performed on the packets. Our experiments have revealed the weaknesses of the IDS in a precise way. Mainly, the inability to process multiple packets and the propensity to deposit, without analysis, packets in high-speed networks with heavy traffic. Our work also determined the effect of a component on the entire system and the effect of hardware characteristics on the performance of an IDS. keywords – Intrusion Detection System, SNORT, Performance Evaluation, Traffic, Packet Dropped.
Similarity weighted sparse representation for classification

In this paper, we propose a novel sparse representation method for classification called similarity weighted sparse representation (SWSR). The similarity weighted ℓ1-norm minimization, where the weighted matrix is constructed by incorporating the similarity information between the test sample and the entire training samples, is presented as an alternative to ℓ0-norm minimization to seek the optimal sparse representation for the test sample in SWSR. The sparse solution of SWSR encodes more discriminative information than other competing alternatives to ℓ0-norm minimization, so it is more suitable for classification. The experimental results on publicly available face databases demonstrate the efficacy of the proposed method.
Probabilistic Robust Control

A novel approach based on probability and randomization recently emerged to synergize with the standard deterministic methods for robust control. This philosophy and body of techniques, known under the generic name of "probabilistic robust control," is here introduced and reviewed in a tutorial perspective, with focus on design techniques based on the interaction of uncertainty randomization and convex optimization.
The Neisseria gonorrhoeae population in Sweden during 2005—phenotypes, genotypes and antibiotic resistance

In Sweden, the gonorrhoea incidence has significantly increased since an all‐time low in 1996. We aimed to phenotypically and genotypically characterise N. gonorrhoeae isolates (n=180) transmitted in Sweden during 2005. All isolates were susceptible to cefixime, ceftriaxone, and spectinomycin. However, 2%, 50% and 75% displayed intermediate susceptibility or resistance to azithromycin, ciprofloxacin and ampicillin, respectively. The isolates were assigned to 28 different serovars using Genetic Systems monoclonal antibodies (Mabs) (discriminatory index, 91.0%) and 46 different serovars using Pharmacia Mabs (index, 94.4%). Furthermore, they displayed 95 porB sequences (index, 97.8%) and 95 N. gonorrhoeae multiantigen sequence typing (NG‐MAST) sequence types (STs) (index, 98.0%). 51 (54%) of these STs have not been previously described. 14 ST clusters, comprising between 3 and 15 isolates, were identified that indicate the existence of several transmission chains. The high number of unique STs (n=63) may be associated with import of strains from abroad, local emergence of new STs, incomplete epidemiological surveillance, and/or suboptimal diagnostics, including contact tracing. Overall, the Swedish N. gonorrhoeae population was remarkably diversified. Comprehensive knowledge regarding transmission, phenotypes (including antibiotic resistance), but also in many cases highly discriminative and precise genotypic characteristics of the N. gonorrhoeae strains circulating in our societies, is crucial.
Exploring multiple feature combination strategies with a recurrent neural network architecture for off-line handwriting recognition

The BLSTM-CTC is a novel recurrent neural network architecture that has outperformed previous state of the art algorithms in tasks such as speech recognition or handwriting recognition. It has the ability to process long term dependencies in temporal signals in order to label unsegmented data. This paper describes different ways of combining features using a BLSTM-CTC architecture. Not only do we explore the low level combination (feature space combination) but we also explore high level combination (decoding combination) and mid-level (internal system representation combination). The results are compared on the RIMES word database. Our results show that the low level combination works best, thanks to the powerful data modeling of the LSTM neurons.