Miracle-dz/UniFAR-FTUs huggingface dataset:
Overlap between pdxA and ksgA in the complex pdxA-ksgA-apaG-apaH operon of Escherichia coli K-12

We report that pdxA, which is required for de novo biosynthesis of pyridoxine (vitamin B6) and pyridoxal phosphate, belongs to an unusual, multifunctional operon. The pdxA gene was cloned in the same 3.5-kilobase BamHI-EcoRI restriction fragment that contains ksgA, which encodes the 16S rRNA modification enzyme m6(2)A methyltransferase, and apaH, which encodes diadenosine tetraphosphatase (ApppA hydrolase). Previously, Blanchin-Roland et al. showed that ksgA and apaH form a complex operon (Mol. Gen. Genet. 205:515-522, 1986). The pdxA gene was located on recombinant plasmids by subcloning, complementation, and insertion mutagenesis, and chromosomal insertions at five positions upstream from ksgA inactivated pdxA function. DNA sequence analysis and minicell translation experiments demonstrated that pdxA encoded a 35.1-kilodalton polypeptide and that the stop codon of pdxA overlapped the start codon of ksgA by 2 nucleotides. The translational start codon of pdxA was tentatively assigned based on polypeptide size and on the presence of a unique sequence that was also found near the translational start of PdxB. This conserved sequence may play a role in translational control of certain pyridoxine biosynthetic genes. RNase T2 mapping of chromosomal transcripts confirmed that pdxA and ksgA were members of the same complex operon, yet about half of ksgA transcripts arose in vivo under some culture conditions from an internal promoter mapped near the end of pdxA. Transcript analysis further suggested that pdxA is not the first gene in the operon. These structural features support the idea that pyridoxine-biosynthetic genes are members of complex operons, perhaps to interweave coenzyme biosynthesis genetically with other metabolic processes. The results are also considered in terms of ksgA expression.
Gating-induced Conformational Rearrangement of the γ-Aminobutyric Acid Type A Receptor β-α Subunit Interface in the Membrane-spanning Domain*

Background: GABAA receptor transmembrane domain undergoes conformational changes during channel gating. Results: Solvent accessibility increases in a cluster of α1 subunit M1 segment residues facing the β2 subunit M3 segment during channel gating. Conclusion: Channel gating induces a conformational change in the subunit interface between α1M1 and β2M3 and within the α1 subunit. Significance: This work increases understanding of pentameric ligand-gated ion channel gating. GABAA receptors mediate fast inhibitory synaptic transmission. The transmembrane ion channel is lined by a ring of five α helices, M2 segments, one from each subunit. An outer ring of helices comprising the alternating M1, M3, and M4 segments from each subunit surrounds the inner ring and forms the interface with the lipid bilayer. The structural rearrangements that follow agonist binding and culminate in opening of the ion pore remain incompletely characterized. Propofol and other intravenous general anesthetics bind at the βM3-αM1 subunit interface. We sought to determine whether this region undergoes conformational changes during GABA activation. We measured the reaction rate of p-chloromercuribenzenesulfonate (pCMBS) with cysteines substituted in the GABAA receptor α1M1 and β2M3 segments. In the presence of GABA, the pCMBS reaction rate increased significantly in a cluster of residues in the extracellular third of the α1M1 segment facing the β2M3 segment. Mutation of the β2M2 segment 19′ position, R269Q, altered the pCMBS reaction rate with several α1M1 Cys, some only in the resting state and others only in the GABA-activated state. Thus, β2R269 is charged in both states. GABA activation induced disulfide bond formation between β2R269C and α1I228C. The experiments demonstrate that α1M1 moves in relationship to β2M2R269 during gating. Thus, channel gating does not involve rigid body movements of the entire transmembrane domain. Channel gating causes changes in the relative position of transmembrane segments both within a single subunit and relative to the neighboring subunits.
Focal Cortical Dysfunction and Blood–Brain Barrier Disruption in Patients With Postconcussion Syndrome

Postconcussion syndrome (PCS) refers to symptoms and signs commonly occurring after mild head injury. The pathogenesis of PCS is unknown. The authors quantitatively analyzed EEG recordings, localized brain sources for abnormal activity, and correlated it with imaging studies. Data from 17 patients with neurologic symptomatology consistent with ICD-10 criteria for PCS was analyzed. Normalized quantitative EEG (QEEG) revealed significantly higher power in the delta band and lower power in the alpha band compared with matched controls. The generators for the abnormal rhythms were focally localized in neocortical regions. Brain computerized tomography and/or MRI did not reveal focal abnormality at the time of diagnosis. Single photon emission computed tomography (SPECT) after 99mTc-ethylcysteinate dimer administration showed a focal reduction in perfusion in 85% (n = 11) of the patients, and abnormal blood–brain barrier (BBB) after 99mTc-diethylenetriaminepentaacetic acid administration in 73% (n = 8). In 75% of these patients, low-resolution brain electromagnetic tomography analysis showed that the generators for abnormal rhythms were closely related to the anatomic location of the BBB lesion. These data point to focal cortical dysfunction in conjunction with BBB disruption and hypoperfusion as a possible mechanism of pathogenesis in at least some PCS patients, and offer QEEG and SPECT as important tools in evaluating these patients.
Extrinsic Rashba spin–orbit coupling effect on silicene spin polarized field effect transistors

Regarding the spin field effect transistor (spin FET) challenges such as mismatch effect in spin injection and insufficient spin life time, we propose a silicene based device which can be a promising candidate to overcome some of those problems. Using non-equilibrium Green’s function method, we investigate the spin-dependent conductance in a zigzag silicene nanoribbon connected to two magnetized leads which are supposed to be either in parallel or anti-parallel configurations. For both configurations, a controllable spin current can be obtained when the Rashba effect is present; thus, we can have a spin filter device. In addition, for anti-parallel configuration, in the absence of Rashba effect, there is an intrinsic energy gap in the system (OFF-state); while, in the presence of Rashba effect, electrons with flipped spin can pass through the channel and make the ON-state. The current voltage (I–V) characteristics which can be tuned by changing the gate voltage or Rashba strength, are studied. More importantly, reducing the mismatch conductivity as well as energy consumption make the silicene based spin FET more efficient relative to the spin FET based on two-dimensional electron gas proposed by Datta and Das. Also, we show that, at the same conditions, the current and Ion/Ioff ratio of silicene based spin FET are significantly greater than that of the graphene based one.
Mutational alterations affecting the export competence of a truncated but fully functional maltose-binding protein signal peptide

The wild-type maltose-binding protein (MBP) signal peptide is 26 amino acids in length. A mutationally altered MBP signal peptide has been previously described that is missing one of the basic residues from the hydrophilic segment and seven residues from the hydrophobic core; however, it still facilitates MBP secretion to the periplasm at a rate and efficiency comparable to those of the wild-type structure. Thus, this truncated signal peptide (designated the R2 signal peptide) must retain all of the essential features required for proper export function. In this study, alterations were obtained in the R2 signal peptide that resulted in an export-defective MBP. For the first time, signal sequence mutations were obtained that resulted in the synthesis of a totally export-defective MBP. As was previously the case for the wild-type signal peptide, the introduction of either charged residues or helix-breaking proline residues adversely affected export function. Despite these similarities, the position of these alterations within the R2 signal peptide, their relative effects on MBP secretion and processing, and an analysis of the ability of various extragenic prl mutations to suppress the secretion defects provide additional insight into the minimal requirements for a functional MBP signal peptide.
Musculoskeletal responses of 2-year-old Thoroughbred horses to early training. 7. Bone and articular cartilage response in the carpus

Abstract AIM: To describe features of the morphology of the carpus, quantify the thickness of hyaline and calcified cartilage, and to describe the morphology and density of subchondral bone in the third carpal bone (C3) of young Thoroughbred horses in early training. METHODS: C3 of seven 2-year-old horses in training and seven untrained horses matched for age, sex and breed were assessed by gross appearance, computed tomography, fine-structure radiography, image analysis of high-resolution photographs, and histology. RESULTS: Macroscopic lesions in cartilage were few and mild, and not significantly different between groups. High bone mineral density (BMD), in some cases typical of cortical bone, was confined to the dorsal load path, and was significantly higher in trained than in untrained horses (p<0.01). In the most dorsoproximal aspect of the radial articular facet, apparently outside the dorsal load path, the BMD in both trained and untrained horses was significantly less than in other regions of interest (ROIs). Adaptive increase in density was associated with thickening of the (junctions of) trabeculae oriented proximo-distally. Hyaline cartilage was thicker (p<0.001) in the concavity of the radial articular facet than dorsal or palmar to it, and was thicker in the trained than untrained group (p=0.007). No such differences were detected in the thickness of articular calcified cartilage (ACC). CONCLUSIONS: The rapid response of bone in C3 to relatively small amounts of high-speed exercise was confirmed. A previously unreported increase in thickness of hyaline cartilage was evident, perhaps indicating that this tissue may be more responsive than hitherto thought, at least to particular types of exercise at particular times. These changes occurred with little evidence of abnormality, and thus appeared to be adaptive to the exercise regimen. The model developed should be used for further definition of the exercise stimulus required to produce adaptive, protective changes in sites susceptible to athletic injury. CLINICAL RELEVANCE: The data will serve as reference for use in subsequent imaging studies in which sophisticated aids such as magnetic resonance imaging (MRI) may be used to predict carpal lesions.
Path loss models for urban macro cell scenario at 3.35, 4.9 and 5.4 GHz

In this paper, the channel measurements for 5th generation mobile networks (5G) potential spectrum at 3.35 GHz, 4.9 GHz and 5.4 GHz have been performed in the urban macro cell scenarios in China. The measured cases include line-of-sight (LOS) and non-line-of-sight (NLOS) propagation. After acquiring the channel impulse response from the measurement data, the empirical log-distance path loss models are derived. Free-space and ITU-R models are analysed as references. To explore the relation between path loss and carrier frequency, we revise the proposed path loss models by introducing the frequency dependence coefficient (FDC). Furthermore, when FDC is applied, a more accurate description of path loss differences among three frequencies can be obtained in NLOS case. Measurements can be implemented in more scenarios to acquire optimised channel models in the future.
Identification of errors-in-variables models with colored output noise

This paper deals with the problem of identifying linear errors-in-variables (EIV) models corrupted by white noise on the input and colored noise on the output. This allows to take into account the presence of both measurement errors and process disturbances. The proposed approach is based on a nonlinear system of equations whose unknowns are the system parameters and the input noise variance. The obtained set of equations allows mapping the EIV identification problem into a quadratic eigenvalue problem that, in turn, can be mapped into a linear generalized eigenvalue problem. The performance of the proposed approach is illustrated by means of Monte Carlo simulations and compared with those of existing techniques.
Design and Test of Novel Programmable Digital Three Phases SPWM Chip

In order to improve the sinusoidal pulse width modulation (SPWM) control system's real time capability and reduce the system's complexity, a high precision programmable digital three phases SPWM chip based on variable sampling frequency method is designed. The chip can be "programmed" by MCU to set the needed parameters with great flexibility and can be interfaced with multiplexed and non-multiplexed data bus mode. To implement the high precision for any frequency sinusoidal power wave, an improved method is presented by changing the sampling clock frequency for different power frequency while keeping the sampling points constant. In addition, the pipeline structure also has improved the speed of the system. The chip is fabricated with 0.35 mum CMOS technology and the core area is 1755times1746 mum2. The test results show that the chip has reached its specifications. The control resolution for any power frequency is up to 16 bits, the system clock can reach 50 MHz, and the ROM operation period is up to 1.68 mus
Extrapolation of Wideband Electromagnetic Response Using Sparse Representation

Wideband electromagnetic response can be extrapolated using combined low frequency and early time information, which can substantially reduce the computational load. Most existing extrapolation methods are based on orthogonal polynomials, but selecting optimal parameters of orthogonal polynomials is not straightforward. This work proposes to extrapolate wideband electromagnetic response using sparse representation. The electromagnetic response is expressed as linear combination of atoms from an overcomplete dictionary. Optimal linear combination of atoms is then sought through the affine scaling transformation and the support vector regression. By increasing the data length step by step, convergence of the sparse solution is used as a criterion to determine the sufficient data length. Performance analysis shows that our proposed extrapolation method retains lower computational complexity and renders more flexibility in reconstructing a signal. Numerical examples are presented to show the efficacy and advantages of the proposed extrapolation method.
Nocturnal hemodialysis is associated with restoration of early-outgrowth endothelial progenitor-like cell function.

BACKGROUND AND OBJECTIVES Angiogenesis is a key response to tissue ischemia that may be impaired by uremia. Although early-outgrowth endothelial progenitor-like cells promote angiogenesis in the setting of normal renal function, cells from uremic patients are dysfunctional. When compared with conventional hemodialysis, it was hypothesized that nocturnal hemodialysis would improve the in vivo angiogenic activity of these cells in a well described model of ischemic vascular disease. DESIGN, SETTING, PARTICIPANTS, AND MEASUREMENTS Early-outgrowth endothelial progenitor-like cells were cultured from healthy controls (n = 5) and age- and gender-matched conventional hemodialysis (12 h/wk, n = 10) and nocturnal hemodialysis (30 to 50 h/wk, n = 9) patients. Cells (5 × 10(5)) or saline were injected into the ischemic hindlimb of athymic nude rats 1 day after left common iliac artery ligation. RESULTS Although conventional dialysis cell injection had no effect versus saline, nocturnal hemodialysis and healthy control cell injection significantly improved ischemic hindlimb perfusion and capillary density. Nocturnal hemodialysis cell injection was also associated with significant increases in endogenous angiopoietin 1 expression in the ischemic hindlimb compared with saline and conventional dialysis cell injection. CONCLUSIONS In contrast to a conventional dialytic regimen, nocturnal hemodialysis is associated with a significantly improved ability of early-outgrowth endothelial progenitor-like cells to promote angiogenesis and thus restore perfusion in a model of ischemic vascular disease.
Out-of-plane Doppler imaging based on ultrafast plane wave imaging

Retrieving the out-of-plane blood flow velocity vector from two-dimensional transverse acquisitions of large vessels could improve the quantification of flow rate and maximum speed. The in-plane vector flow component can be computed easily using the Doppler frequency shift. The main problem is estimating the angle between the probe imaging plane and the vessel axis to derive the out-of-plane component from in-plane measurements. In this article, we study the case in which the velocity vector can be decomposed on two directions: the out-of-plane direction and the in-plane depth direction. We explore the combination of a technique called intrinsic spectral broadening with ultrafast plane wave imaging to retrieve the out-of-plane component of the flow velocity vector. Using a one-time probe calibration of this intrinsic spectral broadening, out-of-plane angle and flow speed can be recovered easily, thus avoiding approximations of a complex theoretical analysis. For the calibration step, ultrafast plane wave imaging permits a fast calibration procedure for the Doppler intrinsic spectral broadening. In vitro experimental validations are performed on a homogeneous flow phantom and a Poiseuille flow; the absolute speed was retrieved with 6% error. The potential of the technique is demonstrated in vivo on the human carotid artery. Combined with in-plane vector flow approaches, this out-of-plane Doppler imaging method paves the way to threedimensional vector flow imaging using only conventional onedimensional probe technology.
Extraction methods for the removal of phospholipids and other endogenous material from a biological fluid.

BACKGROUND A comparison of three different sample preparation techniques for the analysis of plasma samples has been investigated to highlight the effect that these approaches have on the removal of endogenous material. The three techniques under investigation are: SPE, support assisted liquid-liquid extraction and nonspecific solvent-based protein precipitation. RESULTS Comparisons are made on the practicalities of each approach and to allow a semiquantitative assessment between the effectiveness of these different techniques the relative amounts of phospholipids present within the sample are analyzed. Total ion chromatograms are also obtained to further study the effects of different extraction techniques in the removal of endogenous components from a biological matrix. Both of these approaches provide a very coarse measure of the cleanliness of the extracts and demonstrate that support assisted liquid-liquid extraction and an optimized SPE approach remove a greater amount of endogenous material. CONCLUSION This study highlights the importance of sample preparation in removing endogenous material, which may have a detrimental effect on the performance of a bioanalytical assay.
Interaction Patterns between Potato Virus Y and eIF4E-Mediated Recessive Resistance in the Solanaceae

ABSTRACT The structural pattern of infectivity matrices, which contains infection data resulting from inoculations of a set of hosts by a set of parasites, is a key parameter for our understanding of biological interactions and their evolution. This pattern determines the evolution of parasite pathogenicity and host resistance, the spatiotemporal distribution of host and parasite genotypes, and the efficiency of disease control strategies. Two major patterns have been proposed for plant-virus genotype infectivity matrices. In the gene-for-gene model, infectivity matrices show a nested pattern, where the host ranges of specialist virus genotypes are subsets of the host ranges of less specialized viruses. In contrast, in the matching-allele (MA) model, each virus genotype is specialized to infect one (or a small set of) host genotype(s). The corresponding infectivity matrix shows a modular pattern where infection is frequent for plants and viruses belonging to the same module but rare for those belonging to different modules. We analyzed the structure of infectivity matrices between Potato virus Y (PVY) and plant genotypes in the family Solanaceae carrying different eukaryotic initiation factor 4E (eIF4E)-coding alleles conferring recessive resistance. Whereas this system corresponds mechanistically to an MA model, the expected modular pattern was rejected based on our experimental data. This was mostly because PVY mutations involved in adaptation to a particular plant genotype displayed frequent pleiotropic effects, conferring simultaneously an adaptation to additional plant genotypes with different eIF4E alleles. Such effects should be taken into account for the design of strategies of sustainable control of PVY through plant varietal mixtures or rotations. IMPORTANCE The interaction pattern between host and virus genotypes has important consequences on their respective evolution and on issues regarding the application of disease control strategies. We found that the structure of the interaction between Potato virus Y (PVY) variants and host plants in the family Solanaceae departs significantly from the current model of interaction considered for these organisms because of frequent pleiotropic effects of virus mutations. These mutational effects allow the virus to expand rapidly its range of host plant genotypes, make it very difficult to predict the effects of mutations in PVY infectivity factors, and raise concerns about strategies of sustainable management of plant genetic resistance to viruses.