Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Analysis of Calcium Spikes upon Activation of Serotonin1A and Purinergic Receptors

Calcium signaling represents one of the most important signaling cascades in cells and regulates diverse processes such as exocytosis, muscle contraction and relaxation, gene expression and cell growth. G protein-coupled receptors (GPCRs) are the most important family of receptors that activate calcium signaling. Since calcium signaling regulates a large number of physiological responses, it is intriguing that how changes in cytosolic calcium levels by a wide range of stimuli lead to signal-specific physiological responses in the cellular interior. In order to address this issue, we have analyzed temporal calcium profiles induced by two GPCRs, the serotonin1A and purinergic receptors. In this work, we have described a set of parameters for the analysis of calcium transients that could provide novel insight into mechanisms responsible for maintaining signal specificity by shaping calcium transients. An interesting feature of calcium signaling that has emerged from our analysis is that the profile of individual transients in a calcium response could play an important role in maintaining downstream signal specificity. In summary, our analysis offers a novel approach to identify differences in calcium response patterns induced by various stimuli.
The efficacy and safety of high-intensity focused ultrasound ablation of benign thyroid nodules

High-intensity focused ultrasound (HIFU) is a promising form of thermal ablation of benign thyroid nodules, but evidence supporting its use is scarce. The present review evaluated the efficacy and safety of single-session HIFU treatment of benign thyroid nodules. As reported in the literature, the extent of nodule shrinkage following treatment ranged from 48.8% to 68.8%. Like other forms of ablation, the shrinkage rate was greatest in the first 3-6 months, and the best responders were patients with small (≤10 mL) nodules. Complications were uncommon, but temporary vocal cord palsy occurred in 3%-4% of patients, and was related to the distance between the HIFU beam and the recurrent laryngeal nerve. Despite being safe and efficacious, a larger-scale prospective trial is required.
Impact of nutritional stress on drug susceptibility and biofilm structures of Burkholderia pseudomallei and Burkholderia thailandensis grown in static and microfluidic systems

Burkholderia pseudomallei is the causative agent of melioidosis and regarded as a bioterrorism threat. It can adapt to the nutrient-limited environment as the bacteria can survive in triple distilled water for 16 years. Moreover, B. pseudomallei exhibits intrinsic resistance to diverse groups of antibiotics in particular while growing in biofilms. Recently, nutrient-limited condition influenced both biofilm formation and ceftazidime (CAZ) tolerance of B. pseudomallei were found. However, there is no information about how nutrient-limitation together with antibiotics used in melioidosis treatment affects the structure of the biofilm produced by B. pseudomallei. Moreover, no comparative study to investigate the biofilm architectures of B. pseudomallei and the related B. thailandensis under different nutrient concentrations has been reported. Therefore, this study aims to provide new information on the effects of four antibiotics used in melioidosis treatment, viz. ceftazidime (CAZ), imipenem (IMI), meropenem (MEM) and doxycycline (DOX) on biofilm architecture of B. pseudomallei and B. thailandensis with different nutrient concentrations under static and flow conditions using confocal laser scanning microscopy. Impact of nutritional stress on drug susceptibility of B. pseudomallei and B. thailandensis grown planktonically or as biofilm was also evaluated. The findings of this study indicate that nutrient-limited environment enhanced survival of B. pseudomallei in biofilm after exposure to the tested antibiotics. The shedding planktonic B. pseudomallei and B. thailandensis were also found to have increased CAZ tolerance in nutrient-limited environment. However, killing activities of MEM and IMI were stronger than CAZ and DOX on B. pseudomallei and B. thailandensis both in planktonic cells and in 2-day old biofilm. In addition, MEM and IMI were able to inhibit B. pseudomallei and B. thailandensis biofilm formation to a larger extend compared to CAZ and DOX. Differences in biofilm architecture were observed for biofilms grown under static and flow conditions. Under static conditions, biofilms grown in full strength modified Vogel and Bonner’s medium (MVBM) showed honeycomb-like architecture while a knitted-like structure was observed under limited nutrient condition (0.1×MVBM). Under flow conditions, biofilms grown in MVBM showed a multilayer structure while merely dispersed bacteria were found when grown in 0.1×MVBM. Altogether, this study provides more insight on the effect of four antibiotics against B. pseudomallei and B. thailandensis in biofilm under different nutrient and flow conditions. Since biofilm formation is believed to be involved in disease relapse, MEM and IMI may be better therapeutic options than CAZ for melioidosis treatment.
UV-B phototherapy clears psoriasis through local effects.

OBJECTIVE To determine if UV-B phototherapy clears psoriasis through systemic effects. DESIGN Randomized, within-subject comparison of change in psoriasis in 3 plaques in patients attending for whole-body UV-B therapy. Change in patients' psoriasis plaques covered during UV-B treatment was compared with plaques in an untreated control group. SETTING University hospital phototherapy unit. PATIENTS The study population comprised 17 patients with chronic plaque psoriasis treated with UV-B and 24 psoriasis control patients awaiting UV-B phototherapy. INTERVENTIONS Treatment with a standard 3-times weekly narrowband TL-01 UV-B regimen. Three similar plaques were randomly allocated to be covered every treatment, covered for 2 of 3 weekly treatments, and exposed to local UV-B every treatment. Similar plaques were selected in control patients (awaiting but not yet started UV-B therapy). Severity of psoriasis plaques was assessed using a scaling, erythema, and induration (SEI) scoring system. MAIN OUTCOME MEASURES Change in SEI score of the selected plaques over the complete treatment course for UV-B-treated patients and change over 3 weeks in SEI score of plaques covered during UV-B treatment compared with that of plaques in controls. RESULTS There was a significant (P<.001) difference in how much the SEI score changed in the 3 plaques in UV-B-treated patients. It fell by a mean of 7.6 for uncovered plaques compared with 3.2 for plaques covered during each UV-B exposure (95% confidence interval for difference, 3.0 to 5.8). In patients awaiting UV-B, SEI score of plaques fell by a mean of 0.4 over 3 weeks, compared with a mean fall of 1.4 for covered plaques in UV-B-treated patients (95% confidence interval for difference in means, 0.1 to 2.0). CONCLUSIONS If UV-B therapy has any systemic effect capable of improving psoriasis, this effect is small and unlikely to be of clinical importance. It is insufficient to alter interpretation of findings of within-subject comparative phototherapy studies. UV-B phototherapy works for chronic plaque psoriasis through local effects.
Monthly Flow Estimation Using Elman Neural Networks

Keywords: Time series estimation, Flow Estimation, Elman Neural Networks Abstract: This paper investigates the application of partially recurrent artificial neural networks (ANN) in the flow estimation for Sao Francisco River that feeds the hydroelectric power plant of Sobradinho. An Elman neural network was used suitably arranged to receive samples of the flow time series data available for Sao Francisco River shifted by one month. For that, the neural network input had a delay loop that included several sets of inputs separated in periods of five years monthly shifted. The considered neural network had three hidden layers. There is a feedback between the output and the input of the first hidden layer that enables the neural network to present temporal capabilities useful in tracking time variations. The data used in the application concern to the measured Sao Francisco river flow time series from 1931 to 1996, in a total of 65 years from what 60 were used for training and 5 for testing. The obtained results indicate that the Elman neural network is suitable to estimate the river flow for 5 year periods monthly. The average estimation error was less than 0.2 %
A MEDIATOR FOR E-BUSINESS Sven Apel , Gunter

Partner Relationship Management Systems are implemented in many companies to improve the relations to important partners along the value-chain. The goal is to differentiate themselves from competitors and their products. That leads to different types of relationships between customers, suppliers and other market-participants. Some of these types require a mediator, that connects the partners, if a direct connection is impossible. This article introduces the ideas of Partner Relationship Management within E-Business, and proposes a system called Mediator, which is able to tie together business partners in a distributed environment. This article presents the two parts of the mediator (communication system and information system) as well as their key technologies (an agent-based system based on a Peer-to-Peer network).
Majorization-minimization mixture model determination in image segmentation

A new Bayesian model for image segmentation based on a Gaussian mixture model is proposed. The model structure allows the automatic determination of the number of segments while ensuring spatial smoothness of the final output. This is achieved by defining two separate mixture weight sets: the first set of weights is spatially variant and incorporates an MRF edge-preserving smoothing prior; the second set of weights is governed by a Dirichlet prior in order to prune unnecessary mixture components. The model is trained using variational inference and the Majorization-Minimization (MM) algorithm, resulting in closed-form parameter updates. The algorithm was successfully evaluated in terms of various segmentation indices using the Berkeley image data base.
Expert Opinion on Three Phage Therapy Related Topics: Bacterial Phage Resistance, Phage Training and Prophages in Bacterial Production Strains

Phage therapy is increasingly put forward as a “new” potential tool in the fight against antibiotic resistant infections. During the “Centennial Celebration of Bacteriophage Research” conference in Tbilisi, Georgia on 26–29 June 2017, an international group of phage researchers committed to elaborate an expert opinion on three contentious phage therapy related issues that are hampering clinical progress in the field of phage therapy. This paper explores and discusses bacterial phage resistance, phage training and the presence of prophages in bacterial production strains while reviewing relevant research findings and experiences. Our purpose is to inform phage therapy stakeholders such as policy makers, officials of the competent authorities for medicines, phage researchers and phage producers, and members of the pharmaceutical industry. This brief also points out potential avenues for future phage therapy research and development as it specifically addresses those overarching questions that currently call for attention whenever phages go into purification processes for application.
Argos: an emulator for fingerprinting zero-day attacks for advertised honeypots with automatic signature generation

As modern operating systems and software become larger and more complex, they are more likely to contain bugs, which may allow attackers to gain illegitimate access. A fast and reliable mechanism to discern and generate vaccines for such attacks is vital for the successful protection of networks and systems. In this paper we present Argos, a containment environment for worms as well as human orchestrated attacks. Argos is built upon a fast x86 emulator which tracks network data throughout execution to identify their invalid use as jump targets, function addresses, instructions, etc. Furthermore, system call policies disallow the use of network data as arguments to certain calls. When an attack is detected, we perform 'intelligent' process- or kernel-aware logging of the corresponding emulator state for further offline processing. In addition, our own forensics shellcode is injected, replacing the malevolent shellcode, to gather information about the attacked process. By correlating the data logged by the emulator with the data collected from the network, we are able to generate accurate network intrusion detection signatures for the exploits that are immune to payload mutations. The entire process can be automated and has few if any false positives, thus rapid global scale deployment of the signatures is possible.
Efficacy of Transthoracic Echocardiography for Diagnosing Heart Failure in Septic Shock

Background:Cardiac dysfunction occurs in up to 80% of patients with septic shock. Transthoracic echocardiography (TTE) is an ideal tool for the detailed characterization of cardiac function. Its feasibility is perceived to be poor in critically ill patients, but this has never been studied. To address this question, the authors evaluated the efficacy of TTE to diagnose heart failure in septic shock. Methods:This was a retrospective study. Patients admitted to the intensive care unit with septic shock and who had a TTE within 72 hours of intensive care unit admission were identified by a computer algorithm and validated by chart review. Echocardiography images were reviewed by a single cardiologist blinded to clinical outcomes. Clinical information was collected from patients’ medical record. Results:Seventy-six patients met the studies’ inclusion criteria. The feasibility of TTE to calculate left ventricular ejection fraction was 90% and to assess diastolic function was 74%. Significant mitral regurgitation or aortic stenosis was the most frequent impediments for the assessment of diastolic function. Seventy-four percent of all patients showed some type of cardiac dysfunction (left or right ventricular systolic dysfunction and/or left ventricular diastolic dysfunction). In regression analyses, TTE feasibility was not impacted by factors previously associated with poor image acquisition: high body mass index, mechanical ventilation, tachycardia, advanced age or high severity of illness. Conclusions:This study demonstrated that TTE is a useful tool to assess myocardial function in critically ill patients and suggested its potential to assist in the management of patients with septic shock.
Log-domain wavelet bases

A novel procedure to approximate wavelet bases using analog circuitry is presented. First, an approximation is used to calculate the transfer function of the filter, whose impulse response is the required wavelet. Next, for low-power low-voltage applications, we optimize the state-space description of the filter for dynamic range, sensitivity and sparsity requirements. The filter design that follows is based on an orthonormal ladder structure with log-domain integrators as the main building blocks. Simulations demonstrate that it approximates the required wavelet base (i.e., Morlet) in an excellent way. The circuit operates from a 1.2-V supply voltage and a bias current of 1.2 /spl mu/A.
A catalog of edge-on disk galaxies - From galaxies with a bulge to superthin galaxies

Spiral galaxies range from bulge-dominated early-type galaxies to late types with little or no bulge. Cosmological models do not predict the formation of disk-dominated, essentially bulgeless galaxies, yet these objects exist. A particularly striking and poorly understood example of bulgeless galaxies are flat or superthin galaxies with large axis ratios. We therefore embarked on a study aimed at a better understanding of these enigmatic objects, starting by compiling a statistically meaningful sample with well-defined properties. The disk axis ratios can be most easily measured when galaxies are seen edge-on. We used data from the Sloan Digital Sky Survey (SDSS) in order to identify edge-on galaxies with disks in a uniform, reproducible, automated fashion. In the five-color photometric database of the SDSS Data Release 1 (2099 deg 2 ) we identified 3169 edge-on disk galaxies, which we subdivided into disk galaxies with bulge, intermediate types, and simple disk galaxies without any obvious bulge component. We subdivided these types further into subclasses: Sa(f), Sb(f), Sc(f), Scd(f), Sd(f), Irr(f), where the (f) indicates that these galaxies are seen edge-on. Here we present our selection algorithm and the resulting catalogs of the 3169 edge-on disk galaxies including the photometric, morphological, and structural parameters of our targets. A number of incompleteness effects affect our catalog, but it contains almost a factor of four more bulgeless galaxies with prominent simple disks (flat galaxies) within the area covered here than previous optical catalogs, which were based on the visual selection from photographic plates (cf. Karachentsev et al. 1999, Bull. Special Astrophys. Obs., 47, 5). We find that approximately 15% of the edge-on disk galaxies in our catalog are flat galaxies, demonstrating that these galaxies are fairly common, especially among intermediate-mass star-forming galaxies. Bulgeless disks account for roughly one third of our galaxies when also puffy disks and edge-on irregulars are included. Our catalog provides a uniform database for a multitude of follow-up studies of bulgeless galaxies in order to constrain their intrinsic and environmental properties and their evolutionary status.
Feeding by the marine planktonic ciliate Strombidinopsis jeokjo on common heterotrophic dinoflagellates

To investigate the interactions between the ciliate Strombidinopsis jeokjo and the heterotrophic dinoflagellates Gyrodinium dominans and Oxyrrhis marina, we measured the growth and ingestion rates of S. jeokjo (mean length and width of fixed specimens = 149 × 70 µm, n = 30) when feeding on each of the heterotrophic dinoflagellates, and calculated grazing coefficients by combining field data on abundances of large Strombidinopsis spp. (>100 µm in length) and co- occurring heterotrophic dinoflagellates with laboratory data on ingestion rates obtained in the pre- sent study. The specific growth rates of S. jeokjo when feeding on G. dominans and O. marina increased rapidly with increasing prey concentration (ca. <300 ng C ml -1 ), but were saturated or slightly increasing at higher concentrations. The maximum specific growth rate of S. jeokjo feeding on G. dominans (0.54 d -1 ) was similar to that when fed on O. marina (0.59 d -1 ). Threshold prey con- centrations (where net growth = 0) were 79 ng C ml -1 for G. dominans and 36 ng C ml -1 for O. marina. The maximum ingestion and clearance rates of S. jeokjo feeding on G. dominans (108 ng C grazer -1 d -1 and 14.5 µl grazer -1 h -1 , respectively) were comparable to those when fed on O. marina (87 ng C grazer -1 d -1 and 13.4 µl grazer -1 h -1 , respectively). Calculated grazing coefficients for large Strom- bidinopsis spp. feeding on G. dominans and O. marina were 0.01 to 0.39 h -1 (i.e. 1 to 33% of G. dom- inans populations were removed by Strombidinopsis spp. populations in 1 h) and 0.002 to 0.004 h -1 (i.e. 0.2 to 0.4% of O. marina populations were removed), respectively. The results of the present study suggest that Strombidinopsis spp. can sometimes have a considerable grazing impact on populations of G. dominans and O. marina.
Environmental microbiology: Too much food for thought? - An argument for reductionism.

With the explosion of DNA sequencing and information technology, environmental microbiology goes through a big data driven period. In view of the central role of bacteriophages in the development of microbiology and molecular biology and their emerging role in ecosystem functioning, an argument is formulated to complement this trend of complexity inventorisation by a renewed reductionist approach. It is proposed to investigate the interaction of three biological model systems that are naturally linked, namely phage T4 infecting Escherichia coli colonizing the gut of mice, using molecular cell biology techniques at an organismal level. Like the opposition of a thesis and an antithesis leads to a new synthesis, complexity surveys and reductionist experiments need each other for scientific progress. This article is protected by copyright. All rights reserved.
Solution Structure of a Post-transition State Analog of the Phosphotransfer Reaction between the A and B Cytoplasmic Domains of the Mannitol Transporter IIMannitol of the Escherichia coli Phosphotransferase System*

The solution structure of the post-transition state complex between the isolated cytoplasmic A (IIAMtl) and phosphorylated B (phospho-IIBMtl) domains of the mannitol transporter of the Escherichia coli phosphotransferase system has been solved by NMR. The active site His-554 of IIAMtl was mutated to glutamine to block phosphoryl transfer activity, and the active site Cys-384 of IIBMtl (residues of IIBMtl are denoted in italic type) was substituted by serine to permit the formation of a stable phosphorylated form of IIBMtl. The two complementary interaction surfaces are predominantly hydrophobic, and two methionines on IIBMtl, Met-388 and Met-393, serve as anchors by interacting with two deep pockets on the surface of IIAMtl. With the exception of a salt bridge between the conserved Arg-538 of IIAMtl and the phosphoryl group of phospho-IIBMtl, electrostatic interactions between the two proteins are limited to the outer edges of the interface, are few in number, and appear to be weak. This accounts for the low affinity of the complex (Kd ∼ 3.7 mm), which is optimally tuned to the intact biological system in which the A and B domains are expressed as a single polypeptide connected by a flexible 21-residue linker. The phosphoryl transition state can readily be modeled with no change in protein-protein orientation and minimal perturbations in both the backbone immediately adjacent to His-554 and Cys-384 and the side chains in close proximity to the phosphoryl group. Comparison with the previously solved structure of the IIAMtl-HPr complex reveals how IIAMtl uses the same interaction surface to recognize two structurally unrelated proteins and explains the much higher affinity of IIAMtl for HPr than IIBMtl
PERSONALIZED RANKING OF MOVIES: EVALUATING DIFFERENT METADATA TYPES AND RECOMMENDATION STRATEGIES

This paper proposes a study and comparison among a variety of metadata types in order to identify the most relevant pieces of information in order to identify the most relevant pieces of information in personalized ranking of movie items. We used four algorithms available in the literature to analyze the descriptions, and compared each other using the metadata extracted from two datasets, namely MovieLens and IMDB. As a result of our evaluation, we found out that the movies' genres and actors are the kind of description that generates better predictions for the considered content-based recommenders.
ar X iv : 1 20 6 . 34 60 v 2 [ cs . S Y ] 28 S ep 2 01 2 ConstrainedDistributedAlgebraicConnectivity Maximization inRoboticNetworks ! — Technical Report —

We consider the problem of maximizing the algebraic connectivity of the communication graph in a network of mobile robots by moving them into appropriate positions. We define the Laplacian of the graph as dependent on the pairwise distance between the robots and we approximate the problem as a sequence of Semi-Definite Programs (SDP). We propose a distributed solution consisting of local SDP’s which use information only from nearby neighboring robots. We show that the resulting distributed optimization framework leads to feasible subproblems and through its repeated execution, the algebraic connectivity increases monotonically. Moreover, we describe how to adjust the communication load of the robots based on locally computable measures. Numerical simulations show the performance of the algorithm with respect to the centralized solution.