Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative analysis of the naringenin‐inducible proteome in Rhizobium leguminosarum by isobaric tagging and mass spectrometry

The rhizobium–legume interaction is a critical cornerstone of crop productivity and environmental sustainability. Its potential improvement relies on elucidation of the complex molecular dialogue between its two partners. In the present study, the proteomic patterns of gnotobiotic cultures of Rhizobium leguminosarum bv. viciae 3841 grown for 6 h in presence or absence of the nod gene‐inducing plant flavonoid naringenin (10 μM) were analyzed using the iTRAQ approach. A total of 1334 proteins were identified corresponding to 18.67% of the protein‐coding genes annotated in the sequenced genome of bv. viciae 3841. The abundance levels of 47 proteins were increased upon naringenin treatment showing fold change ratios ranging from 1.5 to 25 in two biological replicates. Besides the nod units, naringenin enhanced the expression of a number of other genes, many of which organized in operons, including β(1–2) glucan production and secretion, succinoglycan export, the RopA outer membrane protein with homology to an oligogalacturonide‐specific porin motif, other enzymes for carbohydrate and amino acid metabolism, and proteins involved in the translation machinery. Data were validated at the transcriptional and phenotypic levels by RT‐PCR and an assay of secreted sugars in culture supernatants, respectively. The current approach provides not only a high‐resolution analysis of the prokaryotic proteome but also unravels the rhizobium molecular dialogue with legumes by detecting the enhanced expression of several symbiosis‐associated proteins, whose flavonoid‐dependency had not yet been reported.
Posttranscriptional Control of Type I Interferon Genes by KSRP in the Innate Immune Response against Viral Infection

ABSTRACT Inherently unstable mRNAs contain AU-rich elements (AREs) in the 3′ untranslated regions. Expression of ARE-containing type I interferon transcripts is robustly induced upon viral infection and rapidly shut off thereafter. Their transient accumulation is partly mediated through posttranscriptional regulation. Here we show that mouse embryonic fibroblasts derived from knockout mice deficient in KH-type splicing regulatory protein (KSRP), an RNA-binding protein required for ARE-mediated mRNA decay, produce higher levels of Ifna and Ifnb mRNAs in response to viral infection as a result of decreased mRNA decay. Functional analysis showed that KSRP is required for the decay of Ifna4 and Ifnb mRNAs by interaction with AREs. The increased IFN expression renders Ksrp−/− cells refractory to herpes simplex virus type 1 and vesicular stomatitis virus infection. These findings support a role of a posttranscriptional mechanism in the control of type I IFN expression and highlight the function of KSRP in innate immunity by negatively regulating IFN production.
Molecular Cloning, Expression, and Sequence Analysis of the Endoglycoceramidase II Gene from Rhodococcus Species Strain M-777*

Endoglycoceramidase (EGCase (EC 3.2.1.123)) is a hydrolase that hydrolyzes the linkage between the oligosaccharide and ceramide of various glycosphingolipids. This paper describes the molecular cloning and expression of EGCase II, one of the isoforms of EGCases. The gene encoding EGCase II was obtained by screening of a genomic DNA library from Rhodococcus sp. strain M-777 constructed in pUC19 with oligonucleotide probes deduced from a partial amino acid sequence of the enzyme protein. RecombinantEscherichia coli cells in which the EGCase II gene was expressed produced 14 units of the enzyme per liter of culture medium but did not produce sphingomyelinase. Recombinant EGCase II was a functioning enzyme with substrate specificity identical to that of the wild-type enzyme. Sequence analysis showed the presence of an open reading frame of 1470 base pairs encoding 490 amino acids. The N-terminal region of the deduced amino acid sequence had the general pattern of signal peptides of secreted prokaryotic proteins. Interestingly, the consensus sequence in the active site region of the endo-1,4-β-glucanase family A was found in the amino acid sequence of EGCase II.
Three-dimensional reconstruction from cone-beam data in O(N3logN) time

The authors have used direct Fourier techniques to modify and implement the 3D reconstruction method from cone-beam projections proposed by Grangeat (1987, 1991). In this way the authors manage to decrease the computational complexity from O(N4) to O(N3logN). Just as Grangeat's original method is exact in the mathematical sense, so is the authors' method, provided a complete set of projection data is acquired. Also in accordance with Grangeat, the authors' algorithm consists of two distinct phases: phase 1, from cone-beam data to derivatives of Radon data; phase 2, from derivatives of Radon data to reconstructed 3D object. In phase 1 the authors use the direct Fourier method in reverse to obtain line integrals in the detector plane. In phase 2 the 2D linogram method is employed for reconstruction of vertical and horizontal planes in the Radon space.
Virus-Induced Gene Silencing of Argonaute Genes in Nicotiana benthamiana Demonstrates That Extensive Systemic Silencing Requires Argonaute1-Like and Argonaute4-Like Genes1

Several distinct pathways of RNA silencing operate in plants with roles including the suppression of virus accumulation, control of endogenous gene expression, and direction of DNA and chromatin modifications. Proteins of the Dicer-Like and Argonaute (AGO) families have key roles within these silencing pathways and have distinct biochemical properties. We are interested in the relationships between different silencing pathways and have used Nicotiana benthamiana as a model system. While not being an amenable plant for traditional genetics, N. benthamiana is extensively used for RNA-silencing studies. Using virus-induced gene silencing technology we demonstrate that both NbAGO1- and NbAGO4-like genes are required for full systemic silencing but not for silencing directed by an inverted repeat transgene. Phenotypic differences between the virus-induced gene silencing plants indicate that NbAGO1 and NbAGO4 like act at different stages of the silencing pathways. Suppression of NbAGO1 expression recapitulated the hypomorphic mutant phenotype of certain Arabidopsis (Arabidopsis thaliana) ago1 alleles, however, suppression of NbAgo4 like resulted in phenotypes differing in some respects from those reported for Arabidopsis ago4. We suggest that the small interfering RNA amplification step required for full systemic silencing is dependent upon a nuclear event requiring the activity of NbAGO4 like.
An Empirical Random-Cluster Model for Subway Channels Based on Passive Measurements in UMTS

Recently, a measurement campaign for characterizing the channels in underground subway environments was conducted in Shanghai, China. Downlink signals transmitted by 46 universal mobile telecommunication system cells deployed along a 34-km-long subway were collected. Channel impulse responses are extracted from the data received in the common pilot channels, based on which parameters of multipath components are estimated by using a high-resolution parameter algorithm derived using the space-alternating generalized expectation-maximization principle. Multiple time-evolving clusters are obtained, each representing the channel from a remote-radio-unit of a base station to the receiver. Based on a total of 98 time-evolving clusters, channels observed in the station scenario and the tunnel scenario are modeled separately for their distinctive behaviors in many aspects, particularly in the variations of clusters' trajectories. Intracluster characteristics parameterized by cluster delay and Doppler frequency spreads, K -factor, and dependences among these parameters are investigated. Intercluster parameters, including coexisting cluster number, delay offset, power offset, and cross correlations, are investigated for the station scenario. A path loss model is established for the tunnel scenario.
Robust hand gesture recognition system using motion templates

This paper presents a robust hand gesture analysis system. The approach uses the video analytic technique of motion templates rather than conventional gesture recognition algorithms. Also, it utilizes background modeling and skin pixel detection which further strengthens the approach by making it tolerant to background clutter and noise. In addition it reduces the false detections to a considerable extent. The system does not necessitate the user to wear any coloured caps or gloves for the hands. Encouraging results were obtained and it was found that the methodology is flexible and can be manipulated to suit gesture based interaction as per the requirements of a system. It can also be implemented as a standalone system.
[Effects of chuanxiong-chishao dispensing ratio on the pharmacokinetics of paeoniflorin in the canine].

OBJECTIVE To explore the effects of dispensing ratio of Chinese herbs on the pharmacokinetic characteristics of effective components. METHODS Paeoniflorin (PF) in serum was determined by RP-HPLC with UV-detector. The concentration-time data were fitted using 3P87 Pharmacokinetic Program, and the pharmacokinetic parameters were compared by t-test. RESULTS The concentration-time curves of PF in both groups of Chuanxiong: Chishao 1:2 and 2:1 Xiongshao Pharmaceutics administrated intragastrically fitted open one compartment model. Parameters of Chuanxiong: Chishao 1:2 and 2:1 groups: Ka = 0.0082 +/- 0.0010 and 0.0088 +/- 0.0011(min-1), Ke = 0.0060 +/- 0.0015 and 0.0071 +/- 0.0008(min-1), t1/2Ka = 86.10 +/- 12.38 and 79.11 +/- 18.69(min), t1/2Ke = 119.95 +/- 27.23 and 98.14 +/- 10.82(min), tpeak = 169.16 +/- 21.18 and 149.39 +/- 29.51(min), Cmax = 3845.89 +/- 716.70 and 1635.81 +/- 230.95 (micrograms.L-1) respectively. The pharmacokinetic parameters of the two groups had no statistically significant differences (p > 0.05). CONCLUSION Different formulae of Chinese herbs do not always result in changes of pharmacokinetic characteristics of some one component.
NMR‐based metabonomic approaches for evaluating physiological influences on biofluid composition

Strategies such as genomics, proteomics and metabonomics are being applied with increasing frequency in the pharmaceutical industry. For each of these approaches, toxicological response can be measured by terms of deviation from control or baseline status. However, in order to accurately define drug‐induced response, it is necessary to characterize the normal degree of physiological variation in the absence of stimuli. Here, 1H NMR spectroscopic‐based analyses of the metabolic composition of urine in experimental animals under various normal physiological conditions are reviewed. In particular, the effects of inter‐animal and diurnal variation, gender, age, diet, species, strain, hormonal status and stress on the biochemical composition of urine are explored. Pattern recognition methods facilitate the comparison of urine NMR spectra over a given time‐course, enabling the establishment of changes in profile and highlighting the dynamic metabolic status of an organism. Thus metabonomic approaches based on information‐rich spectroscopic data sets can be used to evaluate normal physiological variation and for investigation of drug safety issues. Copyright © 2004 John Wiley & Sons, Ltd.
Distribution of iron oxide nanoparticles in rat lymph nodes studied using electron energy loss spectroscopy (EELS) and electron spectroscopic imaging (ESI)

Superparamagnetic iron nanoparticles have been developed as contrast agents for magnetic resonance lymphography. The kinetics of uptake of these particles has not yet been accurately determined. We have therefore monitored the distribution of individual iron particles (ferumoxtran, AMI‐227, Sinerem) in rat lymph nodes 1.5, 3, 6, 12, and 24 hours after i.v. injection (two rats per time point). The ultrastructural distribution of the iron was determined by energy‐filtered transmission electron microscopy (EFTEM). This method allows the identification of elements using element‐specific energy‐loss electrons. Iron was identified by the Fe‐L2,3 edge (EELS), and iron maps were obtained using iron‐specific electrons for imaging (ESI). The background was calculated by simplex optimization (EELS) and by the two‐window method (ESI). Ferumoxtran particles were regularly observed at the periphery of the lymph nodes but not in their centers. Isolated iron particles were seen extracellularly within lymph vessels and, 3 hours after injection, as small dots in phagocytic cells. Numerous dense clusters appeared within the cells at later times (6 and 12 hours after injection). These results suggest that the contrast agent moves rapidly across the capillary wall to the lymph and is then taken up by phagocytic cells. J. Magn. Reson. Imaging 2000;12:505–509. © 2000 Wiley‐Liss, Inc.
Characterization of a major late herpes simplex virus type 1 mRNA

A major, late 6-kilobase (6-kb) mRNa mapping in the large unique region of herpes simplex virus type 1 (HSV-1) was characterized by using two recombinant DNA clones, one containing EcoRI fragment G (0.190 to 0.30 map units) in lambda. WES.B (L. Enquist, M. Madden, P. Schiop-Stansly, and G. Vandl Woude, Science 203:541-544, 1979) and one containing HindIII fragment J (0.181 to 0.259 map units) in pBR322. This 6-kb mRNA had its 3' end to the left of 0.231 on the prototypical arrangement of the HSV-1 genome and was transcribed from right to left. It was bounded on both sides by regions containing a large number of distinct mRNA species, and its 3' end was partially colinear with a 1.5-kb mRNA which encoded a 35,000-dalton polypeptide. The 6-kb mRNA encoded a 155,000-dalton polypeptide which was shown to be the only one of this size detectable by hybrid-arrested translation encoded by late polyadenylated polyribosomal RNA. The S1 nuclease mapping experiments indicated that there were no introns in the coding sequence for this mRNA and that its 3' end mapped approximately 800 nucleotides to the left of the BglII site at 0.231, whereas its 5' end extended very close to the BamHI site at 0.266.
Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structures.

The strength in vivo of 14 promoters was determined in a system which permits the quantitation of RNA synthesis with high accuracy. Up to 75‐fold differences in promoter strength were measured and the most efficient signals are promoters from coliphages T7 and T5. Their activity approaches the strength of fully induced promoters of the rRNA operons which may be close to the functional optimum of a single sequence. By contrast, a synthetic ‘consensus promoter’ belongs to the less efficient signals. Our data show that optimal promoter function can be achieved by alternate structures and strongly suggest that information outside of the ‘classical’ promoter region contributes to promoter activity.
Breast tissue characterization with photon-counting spectral CT imaging: a postmortem breast study.

PURPOSE To investigate the feasibility of breast tissue characterization in terms of water, lipid, and protein contents with a spectral computed tomographic (CT) system based on a cadmium zinc telluride (CZT) photon-counting detector by using postmortem breasts. MATERIALS AND METHODS Nineteen pairs of postmortem breasts were imaged with a CZT-based photon-counting spectral CT system with beam energy of 100 kVp. The mean glandular dose was estimated to be in the range of 1.8-2.2 mGy. The images were corrected for pulse pile-up and other artifacts by using spectral distortion corrections. Dual-energy decomposition was then applied to characterize each breast into water, lipid, and protein contents. The precision of the three-compartment characterization was evaluated by comparing the composition of right and left breasts, where the standard error of the estimations was determined. The results of dual-energy decomposition were compared by using averaged root mean square to chemical analysis, which was used as the reference standard. RESULTS The standard errors of the estimations of the right-left correlations obtained from spectral CT were 7.4%, 6.7%, and 3.2% for water, lipid, and protein contents, respectively. Compared with the reference standard, the average root mean square error in breast tissue composition was 2.8%. CONCLUSION Spectral CT can be used to accurately quantify the water, lipid, and protein contents in breast tissue in a laboratory study by using postmortem specimens.
Buffer control in H.264/AVC applications by implementing dynamic complexity-rate-distortion analysis

In this work we present a novel optimal buffer control approach for H.264/AVC low-delay applications by dynamically allocating computational complexity (such as a number of CPU clocks) and bits for encoding each coding element (basic unit) within a video sequence, according to its predicted MAD (Mean Absolute Difference), while considering buffer size limitations (preventing underflow/overflow of the buffer) and buffer delay. Our buffer control approach is based on a computational complexity-rate-distortion (C-R-D) analysis, which adds a complexity dimension to the conventional rate-distortion (R-D) analysis. Both theoretically and experimentally, we prove that by implementing the proposed buffer control approach better results are achieved. In addition, we present an optimal buffer control method and system for implementing the proposed approach, and for controlling computational complexity and bit allocation in real-time and off-line video coding. We divide each frame into one or more basic units, wherein each basic unit consists of at least one macroblock (MB), whose contents are related to a number of coding modes. We determine how much computational complexity and bits should be allocated for encoding each basic unit, while considering buffer size limitations and buffer delay, and then we allocate a corresponding group of coding modes and a quantization step-size, according to the estimated distortion (calculated by a linear regression model) of each basic unit and according to the remaining computational complexity and bits for encoding remaining basic units. For allocating a corresponding group of coding modes and the quantization step-size, we develop computational complexity - complexity step - rate (C-I-R) and rate - quantization step-size - computational complexity (R-Q-C) models.
Weft-Knitted Strain Sensor for Monitoring Respiratory Rate and Its Electro-Mechanical Modeling

In this paper, a textile-based strain sensor has been developed to create a respiration belt. The constituent materials and the knitted structure of the textile sensor have been specifically selected and tailored for this application. Electromechanical modeling has been developed by exploiting Peirce's loop model in order to describe the fabric geometry under static and dynamic conditions. Kirchhoff's node and loop equations have been employed to create a generalized solution for the equivalent electrical resistance of the textile sensor for a given knitted loop geometry and for a specified number of loops. A laboratory test setup was built to characterize the prototype sensor and the resulting equivalent resistance under strain levels up to 40%, and consistent resistance response levels have been obtained from the sensor which correlate well with the modelled data. Production of the respiration belt was realized by bringing together knitted sensor and a relatively inelastic textile strap. Both machine simulations and real-time measurements on a human subject have been performed in order to calculate average breathing frequencies under different static and dynamic conditions. Also, different scenarios have been performed, such as slow breathing and rapid breathing. The sensory belt was located in either the chest area or in the abdominal area during the experimental measurements and the sensor yielded a good response under both static and dynamic conditions. However, body motion artefacts affected the signal quality under dynamic conditions and an additional signal-processing step was added to eliminate unwanted interference from the breathing signal.
Different Pathways Act Downstream of the CEP Peptide Receptor CRA2 to Regulate Lateral Root and Nodule Development1[OPEN]

C-terminally encoded peptides together with the CRA2 receptor regulate nodulation and lateral root development through ethylene-dependent and ethylene-independent pathways, respectively, in Medicago truncatula. C-TERMINALLY ENCODED PEPTIDEs (CEPs) control root system architecture in a non-cell-autonomous manner. In Medicago truncatula, MtCEP1 affects root development by increasing nodule formation and inhibiting lateral root emergence by unknown pathways. Here, we show that the MtCEP1 peptide-dependent increase in nodulation requires the symbiotic signaling pathway and ETHYLENE INSENSITIVE2 (EIN2)/SICKLE (SKL), but acts independently of SUPER NUMERIC NODULES. MtCEP1-dependent inhibition of lateral root development acts through an EIN2-independent mechanism. MtCEP1 increases nodulation by promoting rhizobial infections, the developmental competency of roots for nodulation, the formation of fused nodules, and an increase in frequency of nodule development that initiates at proto-phloem poles. These phenotypes are similar to those of the ein2/skl mutant and support that MtCEP1 modulates EIN2-dependent symbiotic responses. Accordingly, MtCEP1 counteracts the reduction in nodulation induced by increasing ethylene precursor concentrations, and an ethylene synthesis inhibitor treatment antagonizes MtCEP1 root phenotypes. MtCEP1 also inhibits the development of EIN2-dependent pseudonodule formation. Finally, mutants affecting the COMPACT ROOT ARCHITECTURE2 (CRA2) receptor, which is closely related to the Arabidopsis CEP Receptor1, are unresponsive to MtCEP1 effects on lateral root and nodule formation, suggesting that CRA2 is a CEP peptide receptor mediating both organogenesis programs. In addition, an ethylene inhibitor treatment counteracts the cra2 nodulation phenotype. These results indicate that MtCEP1 and its likely receptor, CRA2, mediate nodulation and lateral root development through different pathways.
Social Media Networks Unveiled. Mapping the Romanian and German Youth

: In the present study we focus on the use of social network sites by Romanian and German youth in a comparative manner. Our research questions are 1. Are there differences in the use of social network sites by young people in Germany and Romania? 2. Are there differences in the motivation to use social network sites? and 3. How do they see the information shared on social networks? The present study is of exploratory nature and it was only the first step in analyzing the differences between Romanian and German students with respect to the use of SNS such as Facebook, Instagram, Snapchat and WhatsApp. Based on a qualitative methodology, our results cannot be subject for generalization. Neverthe-less, we emphasized some relevant tendency such as: a migration towards Journal Research, Instagram in both Romania and Germany and similar reasons for this behavior. Privacy seemed to be much more relevant for the German students than for the Romanian and this is reflected in news sharing behavior. Differences in the diffusion of information and innovation are not that relevant taking into consideration a global digital perspective.