Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Expression Profiling in Viable but Nonculturable (VBNC) Cells of Pseudomonas syringae pv. syringae

Pseudomonas syringae infects diverse crop plants and comprises at least 50 different pathovar strains with different host ranges. More information on the physiological and molecular effects of the host inhibitory environment on the pathogen is needed to develop resistant cultivars. Recently, we reported an in vitro model system that mimics the redox pulse associated with the oxidative burst in plant cells inoculated with Pseudomonas syringae pv. syringae. Using this system, we demonstrated that oxidation of acetosyringone, a major extracellular phenolic compound induced in some plants in response to bacteria, rendered Pseudomonas syringae pv. syringae to a “viable but nonculturable” (VBNC) state. Here we performed a large scale transcriptome profiling of P. s. pv. syringae in the VBNC state induced by acetosyringone treatment and identified bacterial genes and pathways presumably associated with this condition. The findings offer insight into what events occur when bacterial pathogens are first encountered and host defense responses are triggered. The acquired knowledge will improve our understanding of the molecular mechanisms of stress tolerance. We believe that this is the first work on global gene expression profiling of VBNC cells in plant pathogenic bacteria.
Second Class Minors

CD4 T cells regulate immune responses that cause chronic graft rejection and graft versus host disease but their target antigens remain virtually unknown. We developed a new method to identify CD4 T cell–stimulating antigens. LacZ-inducible CD4 T cells were used as a probe to detect their cognate peptide/MHC II ligand generated in dendritic cells fed with Escherichia coli expressing a library of target cell genes. The murine H46 locus on chromosome 7 was thus found to encode the interleukin 4–induced IL4i1 gene. The IL4i1 precursor contains the HAFVEAIPELQGHV peptide which is presented by Ab major histocompatibility complex class II molecule via an endogenous pathway in professional antigen presenting cells. Both allelic peptides bind Ab and a single alanine to methionine substitution at p2 defines nonself. These results reveal novel features of H loci that regulate CD4 T cell responses as well as provide a general strategy for identifying elusive antigens that elicit CD4 T cell responses to tumors or self-tissues in autoimmunity.
Subspace estimation and hybrid precoding for wideband millimeter-wave MIMO systems

There has been growing interest in millimeter wave (mmWave) multiple-input multiple-output (MIMO) systems, which would likely employ hybrid analog-digital precoding with large-scale analog arrays deployed at wide bandwidths. Primary challenges here are how to efficiently estimate the large-dimensional frequency-selective channels and customize the wideband hybrid analog-digital precoders and combiners. To address these challenges, we propose a low-overhead channel subspace estimation technique for the wideband hybrid analog-digital MIMO precoding systems. We first show that the Gram matrix of the frequency-selective channel can be decomposed into frequency-flat and frequency-selective components. Based on this, the Arnoldi approach, leveraging channel reciprocity and time-reversed echoing, is employed to estimate a frequency-flat approximation of the frequency-selective mmWave channels, which is used to design the analog parts. After the analog precoder and combiner design, the low-dimensional frequency-selective channels are estimated using conventional pilot-based channel sounding. Numerical results show that considerable improvement in data-rate performance is possible.
Combined 18F-FDG PET-CT and DCE-MRI to Assess Inflammation and Microvascularization in Atherosclerotic Plaques

Background and Purpose— Hallmarks of vulnerable atherosclerotic plaques are inflammation that can be assessed with 18fluorine-fluorodeoxyglucose positron emission tomography/computed tomography, and increased neovascularization that can be evaluated by dynamic contrast–enhanced-MRI. It remains unclear whether these parameters are correlated or represent independent imaging parameters. This study determines whether there is a correlation between inflammation and neovascularization in atherosclerotic carotid plaques. Methods— A total of 58 patients with transient ischemic attack or minor stroke in the carotid territory and ipsilateral carotid artery stenosis of 30% to 69% were included. All patients underwent positron emission tomography/computed tomography and dynamic contrast–enhanced-MRI of the carotid plaque. 18Fluorine-fluorodeoxyglucose standard uptake values with target/background ratio were determined. Neovascularization was quantified by the mean (leakage) volume transfer constant Ktrans. Spearman rank correlation coefficients between target/background ratio and Ktrans were calculated. Results— Images suitable for further analysis were obtained in 49 patients. A weak but significant positive correlation between target/background ratio and mean Ktrans (Spearman &rgr;=0.30 [P=0.035]) and 75th percentile Ktrans (Spearman &rgr;=0.29 [P=0.041]) was found. Conclusions— There is a weak but significant positive correlation between inflammation on positron emission tomography/computed tomography and neovascularization as assessed with dynamic contrast–enhanced-MRI. Future studies should investigate which imaging modality has the highest predictive value for recurrent stroke, as these are not interchangeable. Clinical Trial Registration— URL: http://www.clinicaltrials. gov. Unique identifier: NCT00451529.
Blind Image Deconvolution : An Algorithmic Approach to Practical Image Restoration 1

The goal of image restoration is to reconstruct the original scene from a degraded observation. This recovery process is critical to many image processing applications. Although classical linear image restoration has been thoroughly studied [1], [2], the more di cult problem of blind image restoration has numerous research possibilities. Blind image restoration is the process of estimating both the true image and the blur from the degraded image characteristics using partial information about the imaging system. In classical linear image restoration, the blurring function is given, and the degradation process is inverted using one of the many known restoration algorithms. The various approaches that have appeared in literature depend upon the particular degradation and image models [1], [2]. In many imaging applications an observed image g(x; y), neglecting additive noise, can be estimated to be the two-dimensional convolution of the true image f(x; y) with a linear shiftinvariant blur, also known as the point-spread function (PSF), h(x; y). That is,
Contour blending using warp-guided distance field interpolation

Given (n-1)-dimensional parallel cross-sections of an n-dimensional body, one would like to reconstruct the n-dimensional body. The method based on Distance Field Interpolation (DFI) gives a robust solution to this problem in its ability to deal with any topology in any dimension. Still this method may give undesired solutions to the problem if the changes from one cross-section to the next are significant relative to the size of the details in the cross-sections. We consider the problem of solid reconstruction from contours, which can also be considered as a contour blending or contour morphing problem, where the third dimension is time. The method presented is based on interpolation of the distance field, guided by a warp function which is controlled by a set of corresponding anchor points. Some rules for defining a smooth least-distorting warp function are given. To reduce the distortion of the intermediate shapes, the warp function is decomposed into a rigid rotational part and an elastic part. The distance field interpolation method is modified so that the interpolation is guided by the warp function. The advantage of the new approach is that it is capable of blending between contours having different topological genus, and no correspondence between the geometric primitives should be established. The desired general correspondence is defined by the user in terms of a relatively small number of anchor points.
Ecological determinants of blindness in Nigeria: the Nigeria National Blindness and Visual Impairment Survey.

OBJECTIVE To determine the prevalence and causes of visual loss in different ecological zones across Nigeria. METHODS A population-based survey using multi-stage, stratified, cluster random sampling with probability proportional to size comprising a nationally representative sample of adults aged > or = 40 years from six ecological zones. OUTCOME MEASURES Distance vision was measured using reduced logMAR charts. Clinical examination included basic eye examination for all respondents and a detailed examination including visual fields, gonioscopy and fundus photography for those who were visually impaired or blind (i.e. presenting vision < 20/40 in the better eye). A principal cause of visual loss was assigned to all respondents with presenting vision < 20/40 in the better eye. RESULTS A total of 15 122 persons aged > or = 40 years were enumerated, 13 599 (89.9%) of whom were examined. The prevalence of blindness varied according to ecological zone, being highest in the Sahel region (6.6%; 95% confidence interval (CI) 4.2 - 10.4) and lowest in the rain forest region (3.23%; 95% CI 2.6 - 3.9). Age/ gender-adjusted analyses showed that risk of blindness was highest in Sahel (odds ratio (OR) 3.4; 95% CI 2.1 - 5.8). More than 80% of blindness in all ecological regions was avoidable. Trachoma was a significant cause only in the Sudan savannah belt. The prevalence of all major blinding conditions was highest in the Sahel. CONCLUSIONS The findings of this national survey may be applicable to other countries in West and Central Africa that share similar ecological zones. Onchocerciasis and trachoma are not major causes of blindness in Nigeria, possibly reflecting successful control efforts for both these neglected tropical diseases.
A High-Density Linkage Map for Astyanax mexicanus Using Genotyping-by-Sequencing Technology

The Mexican tetra, Astyanax mexicanus, is a unique model system consisting of cave-adapted and surface-dwelling morphotypes that diverged >1 million years (My) ago. This remarkable natural experiment has enabled powerful genetic analyses of cave adaptation. Here, we describe the application of next-generation sequencing technology to the creation of a high-density linkage map. Our map comprises more than 2200 markers populating 25 linkage groups constructed from genotypic data generated from a single genotyping-by-sequencing project. We leveraged emergent genomic and transcriptomic resources to anchor hundreds of anonymous Astyanax markers to the genome of the zebrafish (Danio rerio), the most closely related model organism to our study species. This facilitated the identification of 784 distinct connections between our linkage map and the Danio rerio genome, highlighting several regions of conserved genomic architecture between the two species despite ∼150 My of divergence. Using a Mendelian cave-associated trait as a proof-of-principle, we successfully recovered the genomic position of the albinism locus near the gene Oca2. Further, our map successfully informed the positions of unplaced Astyanax genomic scaffolds within particular linkage groups. This ability to identify the relative location, orientation, and linear order of unaligned genomic scaffolds will facilitate ongoing efforts to improve on the current early draft and assemble future versions of the Astyanax physical genome. Moreover, this improved linkage map will enable higher-resolution genetic analyses and catalyze the discovery of the genetic basis for cave-associated phenotypes.
A Model to Classify Users of Social Networks Based on PageRank

In this paper, we present a model to classify users of Social Networks. In particular, we focus on Social Network Sites. The model is based on the PageRank algorithm. We use the personalization vector to bias the PageRank to some users. We give an explicit expression of the personalization vector that allows the introduction of some typical features of the users of SNSs. We describe the model as a seven-step process. We illustrate the applicability of the model with two examples. One example is based on real links of a Facebook network. We also indicate how to take into account real actions of Facebook users to implement the model.
Electrotonic Coupling Interacts with Intrinsic Properties to Generate Synchronized Activity in Cerebellar Networks of Inhibitory Interneurons

Exploring the organization and function of local inhibitory networks is an essential step on the way to understand the principles of brain operation. We show here that molecular layer inhibitory interneurons of the guinea pig cerebellar cortex are organized as local networks, generating synchronous activity. Simultaneous recording from two adjacent interneurons revealed a direct current flow between synchronized pairs of neurons. Blocking inhibitory or excitatory synaptic transmission did not alter the synchronization. The electrotonic coupling coefficient (average 0.1) depended mainly on the input resistance of the postsynaptic cell, indicating a homogenous coupling resistance between different pairs. A presynaptic action potential generated a short, attenuated spikelet in the postsynaptic cell. The passive current flow was amplified by voltage-dependent intrinsic currents to create a reciprocal interplay between the presynaptic and postsynaptic cells. This interplay results in a time window for synchronization that is wider than expected from the duration of the spikelet. Intracellular staining with biocytin revealed high incidence of dye coupling. Furthermore, the interneurons located superficially in the molecular layer tend to form larger networks compared with the inner interneurons. We propose that weakly coupled inhibitory networks can generate loosely synchronous activity, which results from the interaction of electrical coupling and intrinsic currents.
Extending Dependencies with Conditions

This paper introduces a class of conditional inclusion dependencies (CINDs), which extends traditional inclusion dependencies (INDs) by enforcing bindings of semantically related data values. We show that CINDs are useful not only in data cleaning, but are also in contextual schema matching [7]. To make effective use of CINDs in practice, it is often necessary to reason about them. The most important static analysis issue concerns consistency, to determine whether or not a given set of CINDs has conflicts. Another issue concerns implication, i.e., deciding whether a set of CINDs entails another CIND. We give a full treatment of the static analyses of CINDs, and show that CINDs retain most nice properties of traditional INDs: (a) CINDs are always consistent; (b) CINDs are finitely axiomatizable, i.e., there exists a sound and complete inference system for implication of CINDs; and (c) the implication problem for CINDs has the same complexity as its traditional counterpart, namely, PSPACE-complete, in the absence of attributes with a finite domain; but it is EXPTIME-complete in the general setting. In addition, we investigate the interaction between CINDs and conditional functional dependencies (CFDs), an extension of functional dependencies proposed in [9]. We show that the consistency problem for the combination of CINDs and CFDs becomes undecidable. In light of the undecidability, we provide heuristic algorithms for the consistency analysis of CFDs and CINDs, and experimentally verify the effectiveness and efficiency of our algorithms.
Silicotic lymph node reactions in mice: genetic differences, correlation with macrophage markers, and independence from T lymphocytes

Quartz was injected into a hind foot of BALB/c and DBA/2 mice and on days 40, 90, and 180 the progressive response ensuing in the draining popliteal lymph node (PLN) was investigated by histopathology and immunohistopathology. The area of silicotic nodules (ASN) was measured by morphometry, and, by this parameter, strain BALB/c proved to be a high responder to quartz, and strain DBA/2 a low responder, albeit both strains showed a similar degree of reactive lymphoid hyperplasia in the draining PLN. Both strains also showed a similar quartz content in the draining PLN but in BALB/c mice quartz particles were concentrated in the ASN, whereas in DBA/2 mice they were evenly dispersed over the PLN. Because the silicotic response of athymic BALB/c nu/nu mice was even stronger than that of euthymic BALB/c mice, T cells are not required for the development of silicotic nodules. This fits the notion that quartz is not an antigen and that high and low responder strains are MHC‐identical. Because quartz‐treated BALB/c, but not DBA/2 mice, showed a persistent expression of the macrophage differentiation markers MRP8 and MRP14, phenotypically the observed strain difference in silicotic responsiveness seems to be expressed at the level of macrophages.
Maximal Ca2+‐Activated Force Elicited by Tetanization Ferret Papillary Muscle and Whole Heart: Mechanism and Characteristics of Steady Contractile Activation in Intact Myocardium

Rapid (8–12 Hz) stimulation of intact heart muscle treated with ryanodine results in steady contractile activation known as tetanus, the amplitude of which can be graded by changing extracellular Ca2+ concentration ([Ca2+]0). The mechanism of the sustained force generation was explored in ferret papillary muscles by measuring membrane potential and by determining the responsiveness of force and intracellular free Ca2+ concentration ([Ca2+]i, estimated with aequorin) to dihydropyridine Ca channel ligands. Membrane potential during tetani ranged from − 25 to − 60 mV, suggesting that fast or slow Ca channels, or Na-Ca exchange, might be mediating Ca2+ entry. Dihydropyridine effects indicated that slow Ca channels play a predominant role: The agonist Bay K 8644 (0.3-1 μM) increased force and aequorin luminescence, whereas the antagonist nitrendipine (1–30 μM) abolished the tetanus. Under conditions analogous to those in the papillary muscle experiments, tetani were produced in whole Langendorff-perfused ferret hearts following exposure to ryanodine. Contraction saturated as a function of [Ca2+]0 in both papillary muscles and whole hearts; i.e., as [Ca2+]0 was increased above 10 mM, no further increase in force or pressure generation occurred. In contrast, aequorin luminescence measured in the papillary muscles showed no such saturation. Thus, maximal Ca2+-activated force (or pressure) was achieved during tetani at [Ca2+]o ± 10 mM. Calculations of wall stress during tetani in whole heart (15 mM [Ca2+]0) agree well with direct measurements of maxima] tension in papillary muscles (5.84 g/mm2 vs. 6.41 g/mm2, respectively). We conclude that maximal Ca2+-activated force (or pressure) can be produced during tetani at high [Ca2+]0 in either whole hearts or isolated papillary muscles following exposure to ryanodine.
Circulating growth differentiation factor‐15 correlates with myocardial fibrosis in patients with non‐ischaemic dilated cardiomyopathy and decreases rapidly after left ventricular assist device support

Growth differentiation factor‐15 (GDF‐15) is a stress‐responsive cytokine and is emerging as a biomarker of cardiac remodelling. Left ventricular assist devices (LVADs) provide unloading of the left ventricle, resulting in partial reverse remodelling. Our aim was to study GDF‐15 in patients with a non‐ischaemic dilated cardiomyopathy (DCM) during LVAD support.
Determining the transgene containment level provided by chloroplast transformation

Plastids (chloroplasts) are maternally inherited in most crops. Maternal inheritance excludes plastid genes and transgenes from pollen transmission. Therefore, plastid transformation is considered a superb tool for ensuring transgene containment and improving the biosafety of transgenic plants. Here, we have assessed the strictness of maternal inheritance and the extent to which plastid transformation technology confers an increase in transgene confinement. We describe an experimental system facilitating stringent selection for occasional paternal plastid transmission. In a large screen, we detected low-level paternal inheritance of transgenic plastids in tobacco. Whereas the frequency of transmission into the cotyledons of F1 seedlings was ≈1.58 × 10−5 (on 100% cross-fertilization), transmission into the shoot apical meristem was significantly lower (2.86 × 10−6). Our data demonstrate that plastid transformation provides an effective tool to increase the biosafety of transgenic plants. However, in cases where pollen transmission must be prevented altogether, stacking with other containment methods will be necessary to eliminate the residual outcrossing risk.
Seismoelectric wave propagation numerical modelling in partially saturated materials

To better understand and interpret seismoelectric measurements acquired over vadose environments, both the existing theory and the wave propagation modelling programmes, available for saturated materials, should be extended to partial saturation conditions. We propose here an extension of Pride's equations aiming to take into account partially saturated materials, in the case of a water-air mixture. This new set of equations was incorporated into an existing seismoelectric wave propagation modelling code, originally designed for stratified saturated media. This extension concerns both the mechanical part, using a generalization of the Biot-Gassmann theory, and the electromagnetic part, for which dielectric permittivity and electrical conductivity were expressed against water saturation. The dynamic seismoelectric coupling was written as a function of the streaming potential coefficient, which depends on saturation, using four different relations derived from recent laboratory or theoretical studies. In a second part, this extended programme was used to synthesize the seismoelectric response for a layered medium consisting of a partially saturated sand overburden on top of a saturated sandstone half-space. Subsequent analysis of the modelled amplitudes suggests that the typically very weak interface response (IR) may be best recovered when the shallow layer exhibits low saturation. We also use our programme to compute the seismoelectric response of a capillary fringe between a vadose sand overburden and a saturated sand half-space. Our first modelling results suggest that the study of the seismoelectric IR may help to detect a sharp saturation contrast better than a smooth saturation transition. In our example, a saturation contrast of 50 per cent between a fully saturated sand half-space and a partially saturated shallow sand layer yields a stronger IR than a stepwise decrease in saturation.
Breath and repeat: An attempt at enhancing speech-laugh synthesis quality

In this work, we present a study dedicated to improve the speech-laugh synthesis quality. The impact of two factors is evaluated. The first factor is the addition of breath intake sounds after laughter bursts in speech. The second is the repetition of the word interrupted by laughs in the speech-laugh sentences. Several configurations are evaluated through subjective perceptual tests. We report an improvement of the synthesized speech-laugh naturalness when the breath intake sounds are added. We were unable, though, to make a conclusion concerning a possible positive impact of the repetition of the interrupted words on the speech-laugh synthesis quality.