Miracle-dz/UniFAR-FTUs huggingface dataset:
CLONAL PROPAGATION AND EVALUATION OF PEROXIDASE ACTIVITY DURING IN VITRO RHIZOGENESIS IN MENTHA ARVENSIS

A rapid and efficient plant propagation system through nodal explants was developed for in vitro propagation of Mentha arvensis. Nodal explants exhibited high frequency shoot proliferation on Murashige and Skoog’s (MS) basal medium supplemented with 0.5 mg l BAP (6benzylaminopurine). Microshoots were best rooted on 1⁄2 strength MS medium with 0.5 mg l IBA (indole-3-butyric acid) and 2% (w/v) sucrose. Plantlets with high (≥ 0.8) Fv/Fm (φP0 – maximum quantum yield of primary photochemistry) were successfully shifted to natural conditions. The overall survival rate from in vitro growth to field transfer was 74%. The developed micropropagation protocol can be successfully used for large-scale multiplication and genetic modification of this high value medicinal plant species. In addition, the results of this study also indicate the key role of Gpx (guaiacolperoxidase) as a marker of in vitro rhizogenesis in M. arvensis.
The Herpesvirus Saimiri Open Reading Frame 73 Gene Product Interacts with the Cellular Protein p32

ABSTRACT The role of the gamma-2 herpesvirus open reading frame (ORF) 73 gene product has become the focus of considerable interest. It has recently been shown that the Kaposi's sarcoma-associated herpesvirus (KSHV) latency-associated nuclear antigen (LANA) is expressed during a latent infection and can modulate both viral and cellular gene expression. The herpesvirus saimiri (HVS) ORF 73 gene product has some sequence homology to LANA; however, the role of HVS ORF 73 is unknown. We have previously demonstrated that HVS ORF73 is expressed in a stably transduced human carcinoma cell line, where HVS genomes persist as nonintegrated circular episomes. This implies that there may be some functional homology between these proteins. To further investigate the role of the HVS ORF 73 protein, the yeast two-hybrid system was employed to identify interacting cellular proteins. We demonstrate that ORF 73 interacts with the cellular protein p32 and triggers the accumulation of p32 in the nucleus. Using reporter gene-based transient-transfection assays, we demonstrate that ORF 73 can transactivate a number of heterologous promoter constructs and also upregulate its own promoter. Moreover, ORF 73 and p32 act synergistically to transactivate these promoters. The binding of ORF 73 to p32 is mediated by an amino-terminal arginine-rich domain, which contains two functionally distinct nuclear localization signals. The p32 binding domains are required for ORF 73 transactivating abilities and for ORF 73 to induce nuclear accumulation of p32. These results suggest that ORF 73 can function as a regulator of gene expression and that p32 is involved in ORF 73-dependent transcriptional activation.
Some research questions and results of UC3M in the eMadrid excellence network

Universidad Carlos III de Madrid is one of the six main participating institutions in the eMadrid excellence network, as well as its coordinating partner. In this paper, the network is presented together with some of the main research lines carried out by UC3M. The remaining papers in this session present the work carried out by the other five universities in the consortium.
Carrier‐mediated uptake and release of taurine from Bergmann glia in rat cerebellar slices

Taurine uptake is essential for the maintenance of millimolar intracellular concentrations of taurine, which is released during ischaemia and is thought to be neuroprotective. To determine whether Bergmann glia express functional transporters that can mediate both taurine uptake and efflux, whole‐cell patch‐clamp recordings were obtained from these cells in rat cerebellar slices. Taurine‐induced inward currents can be pharmacologically separated into GABAA receptor and taurine transporter currents. In the presence of GABA receptor blockers, residual taurine currents averaged −28 pA at −70 mV and were strictly inwardly rectifying between −70 and +50 mV. These residual currents were also abolished by external Na+ removal and diminished by reduction of external Cl−, consistent with transport currents. Taurine transport currents were reduced by a taurine transporter inhibitor, guanidinoethyl sulphonate (GES). Other classical inhibitors reduced taurine transport currents with an order of potency (hypotaurine > β‐alanine > GES > GABA) similar to that reported for cloned rat taurine transporters. Following intracellular taurine perfusion during the recording, a progressively developing outward current could be observed at −50 mV but not at −70 mV. Intracellular perfusion of taurine also decreased taurine‐induced inward currents at both holding potentials. Outward currents induced by intracellular taurine increased in amplitude with depolarization, activated near −50 mV, and were affected by GES. For the first time, these results demonstrate that taurine activates both GABAA receptors and Na+/Cl−‐dependent taurine transporters in Bergmann glia in slices. In addition, our data show that taurine transporters can work in reverse and can probably mediate taurine efflux under ischaemic conditions.
SU-G-TeP2-13: Patient-Specific Reduction of Range Uncertainties in Proton Therapy by Proton Radiography with a Multi-Layer Ionization Chamber.

PURPOSE The conversion from Hounsfield units (HU) to stopping powers is a major source of range uncertainty in proton therapy (PT). Our contribution shows how proton radiographs (PR) acquired with a multi-layer ionization chamber in a PT center can be used for accurate patient positioning and subsequently for patient-specific optimization of the conversion from HU to stopping powers. METHODS A multi-layer ionization chamber was used to measure the integral depth-dose (IDD) of 220 MeV pencil beam spots passing through several anthropomorphic phantoms. The whole area of interest was imaged by repositioning the couch and by acquiring a 45×45 mm2 frame for each position. A rigid registration algorithm was implemented to correct the positioning error between the proton radiographs and the planning CT. After registration, the stopping power map obtained from the planning CT with the calibration curve of the treatment planning system was used together with the water equivalent thickness gained from two proton radiographs to generate a phantom-specific stopping power map. RESULTS Our results show that it is possible to make a registration with submillimeter accuracy from proton radiography obtained by sending beamlets separated by more than 1 mm. This was made possible by the complex shape of the IDD due to the presence of lateral heterogeneities along the path of the beam. Submillimeter positioning was still possible with a 5 mm spot spacing. Phantom specific stopping power maps obtained by minimizing the range error were cross-verified by the acquisition of an additional proton radiography where the phantom was positioned in a random but known manner. CONCLUSION Our results indicate that a CT-PR registration algorithm together with range-error based optimization can be used to produce a patient-specific stopping power map. Sylvain Deffet reports financial funding of its PhD thesis by Ion Beam Applications (IBA) during the confines of the study and outside the submitted work. Francois Vander Stappen reports being employed by Ion Beam Applications (IBA) during the confines of the study and outside the submitted work.
The BtuB Group Col Plasmids and Homology Between the Colicins They Encode

Colicins A, E1, E2, E3, E4, E5, E6, and E7 exhibited reduced activity against BtuB mutants of Escherichia coli K-12 and also against wild-type cells in the presence of vitamin B12. Plasmids encoding representatives of these colicins were specifically immune to high levels of the homologous colicin. Col+ cells grown in media containing mitomycin C accumulated large amounts of colicin polypeptide. ColE2+, ColE3+, ColE4+, ColE5+, and ColE6+ cultures also synthesized large amounts of second, lower-molecular-weight protein under these conditions. Colicins E2 through E7, but not A or E1, reacted with antiserum raised against purified colicin E3. Colicins E2 and E7 induced synthesis of β-galactosidase encoded by lacZ under the control of the colicin Ib gene promotor on a derivative of Col plasmid ColIb.P9. This promotor is usually active only when the cells are treated with agents which damage DNA or block replication. Plasmids encoding various mutant forms of colicin E3 (M. Mock and M. Schwartz, J. Bacteriol. 142:384-390, 1980) recombined with ColE2, ColE4, ColE5, or ColE6 plasmids at a frequency of 10−4 per cell to produce a colicin active against ColE2+, E4+, E5+, or E6+ cells. ColE5 and ColE6 plasmids recombined with ColE3 plasmids bearing mutations affecting colicin E3 receptor recognition, envelope penetration, and catalytic activities. ColE2 and ColE4 plasmids recombined only with ColE3 plasmids bearing mutations affecting receptor recognition and envelope penetration. Recombinants between mutant ColE3 plasmids and ColA, ColE1, or ColE7 plasmids were not detected. We propose the designation BtuB group for the colicins described here, and we divide the group into two classes comprising colicins A and E1, which act on the cytoplasmic membrane, and the related colicins E2 through E7, which have known or putative nuclease activities.
Evaluation of Tricyclic Antidepressant Plasma Levels by an Automated Enzyme Immunoassay (EMIT) in Comparison to a High‐Performance Liquid Chromatographic Method

A new homogeneous enzyme immunoassay technique (EMIT) for the measurement of plasma levels of amitriptyline, nortriptyline, imipramine, and desipramine was used with an automated procedure and the results were compared to those of a high-performance liquid chromatographic (HPLC) method. Precision of the EMIT test was similar to that of the HPLC method with within-day coefficients of variation in the range of 3.9–10.9% (EMIT) and 3.9–9.6% (HPLC). The day-to-day coefficients of variation ranged from 4.4 to 11.7% for EMIT and from 6.1 to 8.4% for HPLC. Samples from 124 patients were analyzed by both methods and a good correlation was observed for all the four drugs. A paired t test indicated no significant difference for the EMIT and HPLC values. No significant interferences were observed between the tricyclics tested and other commonly associated drugs, such as benzodiazepines and neuroleptics. The new EMIT assay proved to be rapid and easy to perform and showed sufficient reliability and reproducibility to be used for either emergency or routine analysis.
Manejo de poblaciones de Conyza bonariensis resistentes a glifosato

Las malas hierbas del genero Conyza constituyen un problema agronomico de creciente interes en la peninsula Iberica. Su importancia ha estado asociada al establecimiento del no-laboreo en cultivos lenosos, donde el glifosato es ampliamente utilizado. Recientemente se han encontrado en Andalucia biotipos de C. bonariensis que pueden considerarse resistentes al glifosato constituyendo el primer caso de una mala hierba resistente al glifosato en Europa. Para preservar la eficacia de este excelente herbicida se propone utilizar medidas alternativas en el manejo de las infestaciones de conyzas. Entre las medidas no quimicas, las que presentan mejores resultados son el laboreo y las cubiertas vegetales con gramineas. Entre los herbicidas que mostraron buenas eficacias frente a poblaciones resistentes cabe destacar: paracuat + amitrol, glifosato + amitrol, glifosato + fluroxipir, glifosato + MCPA y glufosinato.
Effects of excitation capacitance and speed on the terminal voltage of self-excited induction generator-based flywheel energy storage system

The objective of this experimental research is to examine the effects of variable operating speeds and capacitance on the terminal voltage and frequency of a stand-alone self-excited induction generator (SEIG)-based flywheel energy storage system (FESS). The experiments were carried out under the no-load and on-load conditions using the SEIG-based FESS prototype, given the variable operating speeds and capacitance. The experimental results are graphically presented and compared. More importantly, the experimental findings are to be further applied to the design of an optimal control scheme for the flywheel energy storage system in our subsequent research.
An automatic method for flooded area extraction based on level set method using remote sensing data

Flooded area extraction using remote sensing data plays a fundamental role on precisely evaluating flooded area and conducting disaster rescue and relief. The flooded area images may have irregular and fuzzy outline. The traditional methods are easily affected by difference image with low contrast obtained by multi-temporal remote sensing images. In order to overcome the above limitations, a new automatic and un-supervised method for extracting flooded area is presented in this paper. The emphasis of this study lies in creating high contrast difference image via weighted combing different features and applying Level Set Method (LSM) to extract flooded area without predefined information. LSM Chan-Vese (C-V) model is a better choice because it can handle topology changes to extract object with variable shapes from image. Besides, the proposed method modifies the initial curve of C-V model to speed up the iteration and improve extraction precision. This paper selects Landsat 8 OLI data set to validate the methodology this paper study. The proposed method provides more accurate and efficient extraction of flooded area extent when compared with Fuzzy C-Mean (FCM) algorithm.
State of the Art in Bipedal Robots Based on Limit Cycle Walking Paradigm

This paper presents information focused upon state of the art bipedal robots based on the paradigm of limit cycle walking. This paradigm consists of reducing the constraints that are used in the joints of the robot, and allowing robot inertia forces to provide energy for its movement. In this way, it is possible to obtain higher energy efficiency and better disturbance rejection. A review of robots based upon this paradigm is provided. The main challenge of these robots is on involving increasing versatility and disturbance rejection.
Promotion by Helicobacter hepaticus-Induced Hepatitis of Hepatic Tumors Initiated by N-Nitrosodimethylamine in Male A/JCr Mice

A new murine Helicobacter species, Helicobacter hepaticus, infects the livers of mice, causing a progressive chronic active hepatitis culminating in hepatocellular tumors. To examine the role of chronic H. hepaticus infection in carcinogenesis, H. hepaticus-infected male infant mice of A/JCr strain were given a single ip dose of N-nitrosodimethylamine (NDMA). Noninfected A/J mice similarly treated with NDMA served as controls. The effect of hepatitis induced by H. hepaticus was studied for 64 wk. At 31-36 wk, the incidence of hepatocellular adenomas in infected mice was significantly higher than in noninfected mice (82 vs 52%; p = 0.05). The multiplicity of hepatocellular tumors was also significantly higher in infected mice compared to noninfected mice (3.2 ± 0.09 vs 0.09 ± 0.2; p = 0.03). At 51-64 wk, many (10/18) infected mice developed hepatocellular carcinomas while only 2 of 19 control mice developed such tumors (p = 0.005). Overexpression of cyclin D was observed in hepatocytes as well as adenomas induced by NDMA in H. hepaticus-infected mice, suggesting its role in inflammation, abnormal cell growth, and early neoplasia. High molecular weight keratins were highly expressed in hyperplastic oval cells in hepatitis and in liver tumors in mice with hepatitis, establishing a reliable marker for oval cells in formalin-fixed, paraffin-embedded tissue. Thus, chronic H. hepaticus infection significantly stimulated cyclin D expression, accelerated the development of liver tumors, increased the multiplicity of such lesions, and enhanced the progression of benign to malignant tumors.
Human Insulin Secreted from Insulinogenic Xenograft Restores Normoglycemia in Type 1 Diabetic Mice without Immunosuppression

In the present study, we examined the therapeutic potential of human amnion-derived insulin-secreting cells for type 1 diabetes. Human amniotic mesenchymal stem cells (hAMs) were isolated from amnion and cultivated to differentiate into insulin-secreting cells in vitro. After culture in vitro, the differentiated cells (hAM-ISCs) were intensively stained with dithizone and secreted insulin and c-peptide in a high-glucose-dependent manner. They expressed mRNAs of pancreatic cell-related genes, including INS, PDX1, Nkx6-1, NEUROG3, ISL1, NEUROD1, GLUT1, GLUT2, PC1/3, PC2, GCK, PPY, SST, and GC, and were positive for human insulin and c-peptide. Transplantation of hAM-ISCs into the kidneys of mice with streptozotocin-induced diabetes restored body weight and normalized the blood glucose levels, which lasted for 210 days. Only human insulin and c-peptide were detected in the blood of normalized mice after 2 months of transplantation, but little mouse insulin and c-peptide. Removal of graft-bearing kidneys from these mice resulted in causing hyperglycemia again. Human cell-specific gene, hAlu, and human pancreatic cell-specific genes, insulin, PDX1, GLUT1, GLP1R, Nkx6-1, NEUROD1, and NEUROG3, were detected in the graft-bearing kidneys. Colocalization of human insulin and human nuclei antigen was also observed. These results demonstrate that hAMs could differentiate into functional insulin-secreting cells in vitro, and human insulin secreted from hAM-ISCs following transplantation into type 1 diabetic mice could normalize hyperglycemia, overcoming immune rejection for a long period.
Phylogenetic Analysis of the Chlamydia trachomatis Major Outer Membrane Protein and Examination of Potential Pathogenic Determinants

ABSTRACT Phylogenetic analysis was utilized to investigate biological relationships (tissue tropism, disease presentation, and epidemiologic success), as evidenced by coevolution, among human strains ofChlamydia trachomatis. Nucleotide sequences ofomp1, the gene encoding the major outer membrane protein (MOMP) of C. trachomatis, were determined for 40 strains representing 11 serovars. These data were combined with availableomp1 sequences from GenBank for an analysis encompassing a total of 69 strains representing 17 serovars infecting humans. Phylogenetic analysis of the nucleotide and inferred amino acid sequences showed no evolutionary relationships among serovars that corresponded to biological or pathological phenotypes (tissue tropism, disease presentation, and epidemiologic success). In addition, no specific residues that may have evolved to play a role in determining biologically relevant characteristics of chlamydia, such as tissue specificity, disease presentation, and epidemiologic success, were apparent in the MOMP. These results suggest that variation in MOMP may have arisen from a need to be diverse in the presence of immune pressure rather than as a function of pathogenicity. Therefore, the role of MOMP in disease pathogenesis and infection may be passive, and it may not be the major ligand responsible for directing infection of various human cell types.
Dose response signal detection under model uncertainty

We investigate likelihood ratio contrast tests for dose response signal detection under model uncertainty, when several competing regression models are available to describe the dose response relationship. The proposed approach uses the complete structure of the regression models, but does not require knowledge of the parameters of the competing models. Standard likelihood ratio test theory is applicable in linear models as well as in nonlinear regression models with identifiable parameters. However, for many commonly used nonlinear dose response models the regression parameters are not identifiable under the null hypothesis of no dose response and standard arguments cannot be used to obtain critical values. We thus derive the asymptotic distribution of likelihood ratio contrast tests in regression models with a lack of identifiability and use this result to simulate the quantiles based on Gaussian processes. The new method is illustrated with a real data example and compared to existing procedures using theoretical investigations as well as simulations.
A Selective Erasure Channel Model for Packet Collision Channels within Wireless Sensor Networks

Wireless sensor networks typically exhibit a collision channel environment. Error correction over collision channels has been frequently treated by investigating packet erasure codes over binary erasure channels (BEC). Modeling collision channels as BEC overlooks the possibility to salvage valuable information from collided bits. Moreover, in often times, sensor network transmissions are sporadic such that packet erasure codes might not be suitable. In this paper, a selective erasure channel (SEC) model is used to characterize the collision channel. Each bit is classified as an erasure or a bit to be detected in accordance with an erasure threshold applied to the corresponding received signal level. Optimal erasure threshold that maximizes the channel capacity is derived. It is shown that the SEC model supports superior capacities which ultimately approach those of BEC at inferior signal-to-interference ratios. Finally, convolutional and turbo codes are tested as candidates for FEC within wireless sensor networks assuming a star topology. Simulation results suggest that it might be worth to adopt turbo codes for such networks given they significantly outperform convolutional codes even within the scope of short packet lengths that feature wireless sensor networks.
The Potential and Limitation of Probability-Based Combinational Equivalence Checking

This paper presents a probability based approach to logic equivalence checking. First, a general probability assignment procedure is proposed to uniquely characterize output probability of a network. Thus, the equivalence of two networks can be asserted by the equality of output probabilities. To improve the efficiency of probability calculation, a new encoding scheme and operations are proposed. These encoding scheme and operations also solve the signal correlation issue during the output probability evaluation. As a result, an exact output probability of a network is successfully derived in one pass. Finally, the equivalence of internal gates between two networks are exploited to reduce the number of required input assignments and improve the efficiency of our approach. In the experiments, our approach is compared with a BDD based approach in terms of CPU time and memory usage. The results disclose the potential and limitation of the probabilistic approach to logic equivalence checking
Rethinking the concept of failed state

This study summarises the history of failed state concept, the difficulties of a clear definition of failed state and the reasons why the categories of various linking expressions like weak, fragile, failing, collapsed states are mixing. 2015 remained a turbulent year of conflicts in the world, which drew attention on failed states. One of the symptoms of failed states is the form of forced migration when people leave their home due to intrastate armed conflicts, terrorist activities, brutal violation of human rights, poverty, lack of humanitarian aid and poor public services. The study outlines the connection with security and one of the biggest actual global phenomena, the mass refugee movements. That has become in the focus of the European discourse due to the humanitarian catastrophe in the Mediterranean. The current measurement of instable states is problematic which has strong impact on interventions and aid operations.