Miracle-dz/UniFAR-FTUs huggingface dataset:
Biocontrol Strain Pseudomonas sp. W34: Specific Detection and Quantification in the Rhizosphere of Cucumis sativus with a DNA Probe and Genotypic Characterization by DNA Fingerprinting

Abstract A DNA probe specific for biocontrol strains of Pseudomonas was produced by screening randomly amplified polymorphic DNA (RAPD) PCR fragments. Specificity of the probe was assessed by dot blot and colony hybridization. It was used to specifically determine the population of these strains on roots of Cucumis sativus cv. Delikatess. Two polymorphic RAPD fragments of 750 bp, and 550 bp showed identical specificity. The biocontrol strain Pseudomonas sp. W34 was shown to be competitive in the rhizosphere of cucumber and to maintain a stable population for at least 10 days when inoculated on the seed. The phylogenetic relationships between the biocontrol and reference strains were analyzed at the strain level by means of RAPD and repetitive sequence-based PCR genomic finger printing (rep-PCR), and at higher taxonomic levels by means of amplified 16S ribosomal DNA restriction analysis A RDRA . It was shown that the antagonistic strains are closely related, forming a separate cluster from other non-antagonistic and reference Pseudomonas strains, their taxonomic placement remaining uncertain.
MicroRNA-451 Exacerbates Lipotoxicity in Cardiac Myocytes and High-Fat Diet-Induced Cardiac Hypertrophy in Mice Through Suppression of the LKB1/AMPK Pathway

Rationale: In some patients with type 2 diabetes mellitus (DM) without hypertension, cardiac hypertrophy and attenuated cardiac function are observed, and this insult is termed diabetic cardiomyopathy. To date, microRNA (miRNAs or miR) functions in diabetic cardiomyopathy remain to be elucidated. Objective: To clarify the functions of miRNAs involved in diabetic cardiomyopathy caused by type 2 DM. Methods and Results: C57BL/6 mice were fed a high-fat diet (HFD) for 20 weeks, which induced obesity and type 2 DM. miRNA microarray analyses and real-time polymerase chain reaction revealed that miR-451 levels were significantly increased in the type 2 DM mouse hearts. Because excess supply of saturated fatty acids is a cause of diabetic cardiomyopathy, we stimulated neonatal rat cardiac myocytes with palmitic acid and confirmed that miR-451 expression was increased in a dose- and time-dependent manner. Loss of miR-451 function ameliorated palmitate-induced lipotoxicity in neonatal rat cardiac myocytes. Calcium-binding protein 39 (Cab39) is a scaffold protein of liver kinase B1 (LKB1), an upstream kinase of AMP-activated protein kinase (AMPK). Cab39 was a direct target of miR-451 in neonatal rat cardiac myocytes and Cab39 overexpression rescued the lipotoxicity. To clarify miR-451 functions in vivo, we generated cardiomyocyte-specific miR-451 knockout mice. HFD-induced cardiac hypertrophy and contractile reserves were ameliorated in cardiomyocyte-specific miR-451 knockout mice compared with control mice. Protein levels of Cab39 and phosphorylated AMPK were increased and phosphorylated mammalian target of rapamycin (mTOR) was reduced in cardiomyocyte-specific miR-451 knockout mouse hearts compared with control mouse hearts. Conclusions: Our results demonstrate that miR-451 is involved in diabetic cardiomyopathy through suppression of the LKB1/AMPK pathway.
AnonyCast: privacy-preserving location distribution for anonymous crowd tracking systems

Fusion of infrastructure-based pedestrian tracking systems and embedded sensors on mobile devices holds promise for providing accurate positioning in large public buildings. However, privacy concerns regarding handling of sensitive user location data potentially disrupt the adoption of such systems. This paper presents AnonyCast, a novel privacy-aware mechanism for delivering precise location information measured by crowd-tracking systems to individual pedestrians' smartphones. AnonyCast uses sparsely placed Bluetooth Low Energy transmitters to advertise location-dependent, time-varying keys. Using location measurements, AnonyCast estimates a subset of keys that each pedestrian's phone receives along its path. By combining a cryptography scheme called CP-ABE with a novel greedy algorithm for key selection, it encrypts each path before publishing, allowing users to decrypt only their own trajectories. The results from field experiments show that AnonyCast delivers accurate locations over 84% of time, bounding probability of unauthorized access to one's location below 1%.
Interpretable Predictions of Tree-based Ensembles via Actionable Feature Tweaking

Machine-learned models are often described as "black boxes". In many real-world applications however, models may have to sacrifice predictive power in favour of human-interpretability. When this is the case, feature engineering becomes a crucial task, which requires significant and time-consuming human effort. Whilst some features are inherently static, representing properties that cannot be influenced (e.g., the age of an individual), others capture characteristics that could be adjusted (e.g., the daily amount of carbohydrates taken). Nonetheless, once a model is learned from the data, each prediction it makes on new instances is irreversible - assuming every instance to be a static point located in the chosen feature space. There are many circumstances however where it is important to understand (i) why a model outputs a certain prediction on a given instance, (ii) which adjustable features of that instance should be modified, and finally (iii) how to alter such a prediction when the mutated instance is input back to the model. In this paper, we present a technique that exploits the internals of a tree-based ensemble classifier to offer recommendations for transforming true negative instances into positively predicted ones. We demonstrate the validity of our approach using an online advertising application. First, we design a Random Forest classifier that effectively separates between two types of ads: low (negative) and high (positive) quality ads (instances). Then, we introduce an algorithm that provides recommendations that aim to transform a low quality ad (negative instance) into a high quality one (positive instance). Finally, we evaluate our approach on a subset of the active inventory of a large ad network, Yahoo Gemini.
wiseMAC, an ultra low power MAC protocol for the wiseNET wireless sensor network

WiseMAC is a medium access control protocol designed for the WiseNETwireless sensor network. It is based on CSMA and uses the preamble sampling technique to minimize the power consumed when listening to an idle medium. A unique feature of this protocol is to exploit the knowledge of the sampling schedule of its direct neighbors in order to use a wake-up preamble of minimized size. This scheme allows not only to reduce the transmit and the receive power consumption, but also brings a drastic reduction of the energy wasted due to overhearing. Backoff and medium reservation schemes have been selected to provide fairness and collision avoidance. WiseMAC requires no set-up signaling, no network-wide time synchronization and is adaptive to the traffic load. It provides an ultra-low average power consumption in low traffic conditions and a high energy efficiency in high traffic conditions.
Improving CoGrOO: the Brazilian Portuguese Grammar Checker

This paper highlights the main results obtained in an effort to im- prove the grammar checker CoGrOO, a hybrid system which initially annotates the text using statistical Natural Language Processing (NLP) techniques, and then apply a rule-based analysis to identify possible grammar errors. The goal was to reduce omissions and false alarms while improving true positives with- out adding new error rules. The work contributed with a detailed evaluation of low-level NLP modules and the results were compared to state-of-the-art re- sults. The low-level NLP modules are available as open source software, thus improvements on their effectiveness will make them robust, free and ready-to-use alternatives for other systems.
A magnetic pulse does not affect homing pigeon navigation: a GPS tracking experiment

SUMMARY The cues by which homing pigeons are able to return to a home loft after displacement to unfamiliar release sites remain debated. A number of experiments in which migratory birds have been treated with a magnetic pulse have produced a disruption in their orientation, which argues that a ferrimagnetic sense is used for navigation in birds. One previous experiment has also indicated an effect of magnetic pulses on homing pigeon navigation, although with inconsistent results. Previous studies have shown that some magnetic-related information is transmitted by the trigeminal nerve to the brain in some bird species, including the homing pigeon. The function of this information is still unclear. It has been suggested that this information is important for navigation. Previous studies with trigeminal nerve lesioned homing pigeons have clearly shown that the lack of trigeminally mediated information, even if magnetic, is not crucial for homing performance. However, this result does not completely exclude the possibility that other ferrimagnetic receptors in the homing pigeon play a role in navigation. Additionally, recent studies on homing pigeons suggested the existence of a ferrimagnetic sense in a novel location presumably located in the inner ear (lagena). In the present study, we tested whether any ferrimagnetic magnetoreceptors, irrespective of their location in the bird's head, are involved in pigeons' homing. To do this, we treated homing pigeons with a strong magnetic pulse before release, tracked birds with GPS loggers and analyzed whether this treatment affected homing performance. In the single previous magnetic pulse experiment on homing pigeons, only initial orientation at a release site was considered and the results were inconsistent. We observed no effect of the magnetic pulse at any of the sites used on initial orientation, homing performance, tortuosity or track efficiency, which does not support a role for the ferrimagnetic sense in homing pigeon navigation, at least not in this geographic area, where magnetic field variations are in the region of 200 nT intensity and 0.8 deg inclination.
Nearest feature line embedding for face hallucination

A new manifold learning method, called nearest feature line (NFL) embedding, for face hallucination is proposed. While many manifold learning based face hallucination algorithms have been proposed in recent years, most of them apply the conventional nearest neighbour metric to derive the subspace and may not effectively characterise the geometrical information of the samples, especially when the number of training samples is limited. This reported work proposes using the NFL metric to define the neighbourhood relations between face samples to improve the expressing power of the given training samples for reconstruction. The algorithm preserves the linear relationship in a smaller local space than traditional manifold learning based methods, which better reflects the nature of manifold learning theory. Experimental results demonstrate that the method is effective at preserving detailed visual information.
Quantifying Temporomandibular Joint Synovitis in Children With Juvenile Idiopathic Arthritis

Juvenile idiopathic arthritis (JIA) frequently affects the temporomandibular joints (TMJs) and is often undetected by history, examination, and plain imaging. Qualitative assessment of gadolinium‐enhanced magnetic resonance images (MRIs) is currently the standard for diagnosis of TMJ synovitis associated with JIA. The purpose of this study is to apply a quantitative analysis of synovial enhancement to MRIs of patients with and without JIA to establish a disease threshold and sensitivity and specificity for the technique.
Monocular Visual Odometry using a Planar Road Model to Solve Scale Ambiguity

Precise knowledge of a robots’s ego-motion is a crucial requirement for higher level tasks like autonomous navigation. Bundle adjustment based monocular visual odometry has proven to successfully estimate the motion of a robot for short sequences, but it suffers from an ambiguity in scale. Hence, approaches that only optimize locally are prone to drift in scale for sequences that span hundreds of frames. In this paper we present an approach to monocular visual odometry that compensates for drift in scale by applying constraints imposed by the known camera mounting and assumptions about the environment. To this end, we employ a continuously updated point cloud to estimate the camera poses based on 2d-3dcorrespondences. Within this set of camera poses, we identify keyframes which are combined into a sliding window and refined by bundle adjustment. Subsequently, we update the scale based on robustly tracked features on the road surface. Results on real datasets demonstrate a significant increase in accuracy compared to the non-scaled scheme.
Signal reconstruction from the short-time Fourier transform magnitude

This paper presents various conditions that are sufficient for reconstructing a discrete-time signal from samples of its short-time Fourier transform magnitude. For applications such as speech processing, these conditions place very mild restrictions on the signal as well as the analysis window of the transform. Examples of such reconstruction for speech signals are included in the paper.
Interactions of Methylene Blue with Human Disulfide Reductases and Their Orthologues from Plasmodium falciparum

ABSTRACT Methylene blue (MB) has experienced a renaissance mainly as a component of drug combinations against Plasmodium falciparum malaria. Here, we report biochemically relevant pharmacological data on MB such as rate constants for the uncatalyzed reaction of MB at pH 7.4 with cellular reductants like NAD(P)H (k = 4 M−1 s−1), thioredoxins (k = 8.5 to 26 M−1 s−1), dihydrolipoamide (k = 53 M−1 s−1), and slowly reacting glutathione. As the disulfide reductases are prominent targets of MB, optical tests for enzymes reducing MB at the expense of NAD(P)H under aerobic conditions were developed. The product leucomethylene blue (leucoMB) is auto-oxidized back to MB at pH 7 but can be stabilized by enzymes at pH 5.0, which makes this colorless compound an interesting drug candidate. MB was found to be an inhibitor and/or a redox-cycling substrate of mammalian and P. falciparum disulfide reductases, with the kcat values ranging from 0.03 s−1 to 10 s−1 at 25°C. Kinetic spectroscopy of mutagenized glutathione reductase indicates that MB reduction is conducted by enzyme-bound reduced flavin rather than by the active-site dithiol Cys58/Cys63. The enzyme-catalyzed reduction of MB and subsequent auto-oxidation of the product leucoMB mean that MB is a redox-cycling agent which produces H2O2 at the expense of O2 and of NAD(P)H in each cycle, turning the antioxidant disulfide reductases into pro-oxidant enzymes. This explains the terms subversive substrate or turncoat inhibitor for MB. The results are discussed in cell-pathological and clinical contexts.
Extracellular Signals of a Human Epithelial Colorectal Adenocarcinoma (Caco-2) Cell Line Facilitate the Penetration of Pseudomonas aeruginosa PAO1 Strain through the Mucin Layer

Pseudomonas aeruginosa can penetrate the layer of mucus formed by host intestinal epithelial cells, often resulting in sepsis in immunocompromised patients. We have previously demonstrated that P. aeruginosa can penetrate the mucin layer by flagellar motility and the degradation of the mucin layer. However, it remains unclear how P. aeruginosa initially recognizes epithelial cells. Using the human epithelial colorectal adenocarcinoma (Caco-2) cell line, we investigated extracellular signaling that could facilitate the penetration of P. aeruginosa through the mucin layer. The supernatant from Caco-2 cell cultures increased penetration of P. aeruginosa through an artificial mucin layer. The Caco-2 cell supernatant increased bacterial flagella-dependent swarming motility, but it did not influence P. aeruginosa growth or protease activity. Filtering of the Caco-2 cell supernatant indicated that proteins weighing <10 kDa increased mucin penetration, swarming motility, and, based on a tethered cell assay, induced acceleration of the flagellar filament rotational rate. Furthermore, a capillary assay showed that <10 kDa proteins in the Caco-2 cell supernatant attracted P. aeruginosa cells. Finally, we identified that growth-regulated oncogene-α (GRO-α) secreted by Caco-2 cells was a factor facilitating flagellar filament rotation and swarming motility, although it did not attract the bacteria. We conclude that penetration of the mucin layer by P. aeruginosa is facilitated by small proteins (<10 kDa) secreted by Caco-2 cells, both by inducing acceleration of flagellar motility and increasing chemotaxis.
Social support and adolescent cancer survivors: a review of the literature

With survival rates increasing dramatically in pediatric cancer, concern has increasingly focused on the psychosocial aspects of the cancer experience. Clearly, the experience of a cancer diagnosis and treatment of cancer places high demands on the coping of adolescents. Research has shown social support to be effective in decreasing stress and enhancing coping in adolescents facing such demands. A review and critical analysis of studies of social support in adolescent cancer survivors was conducted. The seventeen studies were mainly descriptive and exploratory in nature with social support examined for a number of outcome variables in eight of the studies. Findings from this review indicate that support from parents (especially the mother) and friends were extremely important and that the adolescents were satisfied with family support. Support from friends was described as less satisfactory. Methodological concerns of the reviewed studies include small samples and a lack of consistency in the instruments used to assess social support. Future studies of social support for adolescent cancer survivors should include larger samples to determine gender, age group, and ethnic differences and to allow the examination of social support theoretical models specific to the developmental and chronic illness situation of these adolescents. Copyright © 2006 John Wiley & Sons, Ltd.
Integrated peptide and glycan biomarker discovery using MALDI-TOF mass spectrometry

Quantitative comparison of peptides and glycans in serum is conducted using matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) to identify biomarkers. A peak selection algorithm is developed to identify a panel of integrated peptide and glycan peaks to distinguish hepatocellular carcinoma (HCC) cases from high-risk population of patients with chronic liver disease (CLD). Candidate peptide and glycan markers selected frequently in multiple runs of the algorithm are presented. The performance of these markers is evaluated in terms of their ability to distinguish HCC cases from patients with CLD in a blinded validation set.
Finite reluctance approach: A systematic method for the construction of magnetic network-based dynamic models of electrical machines

The finite reluctance approach is based on a simple synergy between a basic magnetic domain decomposition rule and the voltage balance at the terminals of any winding acting in the domain. The finite reluctance approach is thought as a tool for fast dynamic simulations of any kind of machine, but it is particularly adapt for irregular flux geometries as in fractional-slot surface-mounted permanent magnet machines with large slots and high slot flux leakages, for which only the finite element method has found good usage. This approach is based on the definition of a complementary mesh interlaced with the reluctance mesh, on the concept of material cell, and on unique rules to carry out both reluctances and magneto-motive forces. At this scope, definitions of mesh nodes, co-nodes, and auxiliary nodes are shown. The iron saturation can be easily taken in account, as well as motion effects. The circuit flux linkages are elected as state variables for integration, and they are directly linked to the loop fluxes in the magnetic network. The finite reluctance approach has been applied in this paper for dynamic modeling of an inverter-fed permanent-magnet linear synchronous motor.
Fibroblast-dependent tumorigenicity of cells in nude mice: implication for implantation of metastases.

The inadequate nature of the microenvironment is one of several factors considered in the failure of tumor engraftment in athymic mice; in the present work, we have tried to more adequately reconstitute it by injecting tumor cells together with fibroblasts. We have demonstrated that the s.c. co-inoculation of fibroblasts with different kinds of tumor cells of animal origin [rat rhabdomyosarcoma (RMS) 9-4/0, rat hepato-carcinoma FAO] or human origin (colonic adenocarcinoma HT29, Ewing's sarcoma pleural metastasis EW-S1) is necessary for tumor take and growth when the number of tumor cells alone is below the tumorigenic dose. We have shown that the s.c. coinoculation of 10(6) fibroblasts and 10(2) RMS 9-4/0 tumor cells induced a tumor take in all the recipient mice, while 10(2) tumor cells alone never gave any tumor. With a tumorigenic number of RMS 9-4/0 tumor cells (10(4), addition of 10(6) fibroblasts decreased the delay between cell injection and tumor appearance, thereby increasing tumor take and growth rate. These results were observed not only in nude animals (mice and rats) used as recipient animals but also in normal WAG rats receiving the syngeneic RMS 9-4/0 tumor cells, and they were independent of the nature or origin of the different fibroblasts cells. This helper effect has also been observed in the normal WAG rats. I.v. injection of tumor cells from a poorly metastatic 9-4/8 subline, derived from the RMS 9-4/0 line and mixed with 10(6) fibroblasts, gave a high number of lung colonies. Addition of 10(6) irradiated 9-4/8 tumor cells instead of fibroblasts did not increase the lung colonizing potential. Fibroblast-conditioned medium mixed with tumor cells instead of fibroblasts also enhanced tumor take and size but to a lesser extent than did the fibroblasts themselves. Only endothelial cells cultured from porcine aorta had a similar helper effect among the cells tested. It is argued in the discussion that the proliferating state of cultivated fibroblasts is a determinant factor conferring upon them the ability to promote tumor cell growth, while fibroblasts very numerous at the implantation site but quiescent might not be efficient in cooperation. Changes in fibroblast morphology and physiology may be necessary in order for tumor cells to express their tumorigenicity.
A Novel Genetic Algorithm for Static Task Scheduling in Distributed Systems

The static task scheduling problem in distributed systems is very important because of optimal usage of available machines and accepted computation time for scheduling algorithm. Solving this problem using the dynamic programming and the back tracking needs much more time. Therefore, there are more attempts to solve it using the heuristic methods. In this paper, a new genetic algorithm, named TDGASA, is presented which its running time depends on the number of tasks in the scheduling problem. Then, the computation time of TDGASA to find a sub-optimal schedule is improved by Simulated Annealing (SA). The results show that the computation time of the proposed algorithm decreases compared to an existing GA-based algorithm, although, the completion time of the final scheduled task in the system decreases a little.