Miracle-dz/UniFAR-FTUs huggingface dataset:
Congenital cytomegalovirus infection in infants infected with human immunodeficiency virus type 1.

OBJECTIVES To determine the rate of in utero transmission of cytomegalovirus (CMV) in perinatally HIV-exposed infants and to determine whether coinfection with CMV in early life affects outcome. METHODS Infants born to HIV-infected women between March, 1988, and March, 1995, were evaluated (n = 206). Congenital or in utero CMV infection was defined as a positive CMV culture or shell vial assay on urine obtained in the first 3 weeks of life. HIV-infected infants either had positive serology beyond 18 months of age or, for an infant younger than 18 months, had a positive HIV PCR or HIV culture on at least two separate occasions. RESULTS There were 30 HIV-infected and 171 uninfected infants (144 who seroreverted and 27 infants with at least 2 negative HIV PCR or culture results and normal immunologic studies during the first 6 months of age). Urine culture for CMV was obtained during the first 3 weeks of life on 154 infants: 24 of 30 (80%) HIV-infected infants; and 130 of 171 (76%) HIV-uninfected infants. Overall 10 of 154 (6.5%) infants were infected with CMV: 5 of 24 (21%) HIV-infected and 5 of 130 (3.8%) HIV-uninfected infants. The rate of in utero CMV infection was significantly higher in HIV-infected infants (P = 0.008). Dually infected infants were more immunosuppressed than their CMV-negative counterparts. At 3 months of age the percentage of CD4+ T lymphocytes (P = 0.0021) and CD4:CD8 ratios (P = 0.0018) were significantly lower in the CMV-infected infants than in the CMV-uninfected infants. At 6 months of age the absolute CD4+ T lymphocyte counts (P = 0.0038), percentage of CD4+ T lymphocytes (P = 0.044) and CD4:CD8 ratios (P = 0.037) were significantly lower in the CMV-infected infants. The mean survival of HIV-infected infants who were coinfected with CMV in early life (5 in utero and 1 perinatally infected infant identified at 7 weeks) was 24.77 months. Kaplan-Meier survival analysis indicated a trend toward decreased survival in the infants who were coinfected with CMV in early life (P = 0.088). CONCLUSIONS Congenital CMV infection is more common in HIV-infected infants than in HIV-uninfected infants. Infection with CMV in early life is associated with greater immunosuppression and may be associated with a more rapid progression of HIV infection in infants.
A comparison of 3D methods for volume quantitation in SPECT

Three methods for detecting the edges of objects for segmentation of SPECT (single photon emission computed tomography) imagery are compared. The methods investigated are 3-D edge detection with nonmaximum suppression, 3-D Lacroix edge linking, and 3-D zero-crossings of the second directional derivative. Studies with simulated SPECT images show that the 3-D second directional derivative operator produces significantly more accurate volume quantitation than the other methods, especially when image contrast is low. <<ETX>>
Inhibition of Allogeneic T Cell Proliferation by Indoleamine 2,3-Dioxygenase–expressing Dendritic Cells

Indoleamine 2,3-dioxygenase (IDO), an enzyme involved in the catabolism of tryptophan, is expressed in certain cells and tissues, particularly in antigen-presenting cells of lymphoid organs and in the placenta. It was shown that IDO prevents rejection of the fetus during pregnancy, probably by inhibiting alloreactive T cells, and it was suggested that IDO-expression in antigen-presenting cells may control autoreactive immune responses. Degradation of tryptophan, an essential amino acid required for cell proliferation, was reported to be the mechanism of IDO-induced T cell suppression. Because we wanted to study the action of IDO-expressing dendritic cells (DCs) on allogeneic T cells, the human IDO gene was inserted into an adenoviral vector and expressed in DCs. Transgenic DCs decreased the concentration of tryptophan, increased the concentration of kynurenine, the main tryptophan metabolite, and suppressed allogeneic T cell proliferation in vitro. Kynurenine, 3-hydroxykynurenine, and 3-hydroxyanthranilic acid, but no other IDO-induced tryptophan metabolites, suppressed the T cell response, the suppressive effects being additive. T cells, once stopped in their proliferation, could not be restimulated. Inhibition of proliferation was likely due to T cell death because suppressive tryptophan catabolites exerted a cytotoxic action on CD3+ cells. This action preferentially affected activated T cells and increased gradually with exposure time. In addition to T cells, B and natural killer (NK) cells were also killed, whereas DCs were not affected. Our findings shed light on suppressive mechanisms mediated by DCs and provide an explanation for important biological processes in which IDO activity apparently is increased, such as protection of the fetus from rejection during pregnancy and possibly T cell death in HIV-infected patients.
A pilot study concerning the infection risk of sputum positive tuberculosis patients on chemotherapy.

In order to measure the risk of new infection among contacts, 21 patients with pulmonary tuberculosis were discharged as outpatients after being treated in hospital for approximately 2 weeks. Sputum smears and cultures were positive for tubercle bacilli in most patients when they were discharged. Tuberculin testing of 107 contacts before the patients were discharged revealed 74 (69 per cent) who were tuberculin negative. Great variability was noted in the number of reactors per patient. No conversions occurred among 72 previously tested tuberculin negative contacts. Tuberculin conversions in 2 contacts were related to another source case and not to early discharge of the patients. The investigation suggested that after a few weeks, many tuberculous patients on chemotherapy can be discharged safely without additional risk to contacts. Sputum smear or culture should not be used as the only criterion for discharge.
Light and electron microscopic examination of fine‐needle aspirates in the preoperative diagnosis of osteogenic tumors: A study of 21 osteosarcomas and two osteoblastomas

Twenty‐three patients with primary osteogenic tumors, two osteoblastomas and 21 osteosarcomas, underwent fine‐needle aspiration biopsy in the preoperative investigation. The cytologic features in smears were compared with the light and electron microscopic findings of resin‐embedded fine‐needle aspirates (16 cases) and the histopathologic findings of the surgical specimens. Cytologic smears clearly indicated a primary bone malignancy in all 20 high‐malignancy osteosarcomas. In the osteoblastic osteosarcomas, the diagnosis of osteosarcoma was strongly suggested by the osteoblastic appearance of the tumor cells and the presence of an osteoid‐like fibrillar matrix in 6 of 11 cases in the May‐Grünwald‐Giemsa‐stained smears. The distinction of chondroblastic osteosarcomas from high‐grade chondrosarcomas and of polymorphic osteosarcomas from malignant fibrous histiocytomas is difficult in smears. Electron microscopic examination and immunocytochemistry indicating a positivity for vimentin but not for cytokeratin helped to exclude the possibility of a carcinoma in osteoblastic osteosarcomas where the tumor cells had epithelium‐like features in the smears. The resin‐embedding technique of fine‐needle aspirates was useful for the typing since it gave additional light microscopic information about growth pattern, structure, and matrix production, as well as ultrastructural information about cell and tissue differentiation. The osteoid‐like material seen in May‐Grünwald‐Giemsa‐stained smears could be proven to represent osteoid with varying degrees of calcification at the ultrastructural examination. The fine‐needle aspiration technique, especially when used for both smears and embedding, may play an important role in the preoperative investigation of bone tumors, provided that it is used with full knowledge of the clinical and radiographic findings.
Consistent treatment of inter‐ and intramolecular polarization in molecular mechanics calculations

A protocol is described for the treatment of molecular polarization in force field calculations. The resulting model is consistent in that both inter‐ and intramolecular polarization are handled within a single scheme. An analytical formula for removing intramolecular polarization from a set of atomic multipoles for an arbitrary static structure or conformation is given. With the help of the intramolecular polarization, these permanent atomic multipoles can then be applied in modeling alternative conformations of a molecule. Equipped with this simple technique, one can derive transferable electrostatic parameters for peptides and proteins using flexible model compounds such as dipeptides. The proposed procedure is tested for its ability to describe the electrostatic potential around various configurations of the N‐methylacetamide dimer. The effect of different intramolecular polarization schemes on the accuracy of a force field model of the electrostatic potential of alanine dipeptide is investigated. A group‐based scheme for including direct intramolecular polarization is shown to be most successful in accounting for the conformational dependence of electrostatic potentials. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1497–1506, 2002
Power system stabiliser for single machine in infinite bus based on optimal control methods

An alternative method for designing a power system stabilizer (PSS) to be used with a single machine and infinite bus system (SMIB) developed on the basis of optimal control (OP) techniques is represented in this paper. The SMIB system is chosen due to simple configuration and useful for understanding the concepts of PSS and its basic effects. The effectiveness of the proposed scheme is tested through simulation to analyse the stability characteristics of the system's small signal about the operating condition at the steady state when a transmission line is lost. The focus of the primary method was on how the control would be performed. This was later proven to possess the responses with shorter settling time and a lower overshoot.
Geometric Unmixing of Large Hyperspectral Images: A Barycentric Coordinate Approach

In hyperspectral imaging, spectral unmixing is one of the most challenging and fundamental problems. It consists of breaking down the spectrum of a mixed pixel into a set of pure spectra, called endmembers, and their contributions, called abundances. Many endmember extraction techniques have been proposed in literature, based on either a statistical or a geometrical formulation. However, most, if not all, of these techniques for estimating abundances use a least-squares solution. In this paper, we show that abundances can be estimated using a geometric formulation. To this end, we express abundances with the barycentric coordinates in the simplex defined by endmembers. We propose to write them in terms of a ratio of volumes or a ratio of distances, which are quantities that are often computed to identify endmembers. This property allows us to easily incorporate abundance estimation within conventional endmember extraction techniques, without incurring additional computational complexity. We use this key property with various endmember extraction techniques, such as N-Findr, vertex component analysis, simplex growing algorithm, and iterated constrained endmembers. The relevance of the method is illustrated with experimental results on real hyperspectral images.
MUCUS IN INTESTINAL CONTENTS OF GERMFREE RATS

The fecal excretion of total nitrogen and of total hexosamines has been determined in germfree and conventional rats. Germfree rats excreted more hexosamines than the conventional rats, while no difference in the nitrogen excretion was found. Infection of the germfree rats with a normal flora resulted in a temporarily increased excretion of hexosamines and nitrogen over a period of 2 to 3 days after which they reached the level of the conventional animals. The contents of the germfree cecum contained 65 to 137 mg of hexosamines and 57 to 127 mg of nitrogen as compared to 1.2 to 5.3 and 7.4 to 23 mg in conventional animals. The high figures for hexosamines were due to an increase in the total amount of contents in the cecum and to a fivefold increase in the concentration of hexosamine-containing material. Studies on the distribution of hexosamine-containing cecal contents between sediment and supernatant after centrifugation at 20,000 g for 2 hours demonstrated that 5 to 10 per cent of the hexosamines occurred in the sediment in the germfree rats, while 75 to 85 per cent was found in this fraction in the conventional rats. The soluble part of the cecal contents in germfree as well as in the conventional rats contained 70 per cent of hexosamines in molecules with a molecular weight above approximatively 100,000 as found by gel filtration experiments on sephadex gels. The higher weight of the germfree cecal wall was reflected in a high total amount of nitrogen and hexosamines. Isolated strains of bacteria capable of reducing the cecal size in vivo did not show any capacity to degrade the mucus in vitro in a test system, where a full intestinal flora was highly active.
Long-lasting perceptual priming and semantic learning in amnesia: a case experiment.

An investigation of perceptual priming and semantic learning in the severely amnesic subject K.C. is reported. He was taught 64 three-word sentences and tested for his ability to produce the final word of each sentence. Despite a total lack of episodic memory, he exhibited (a) strong perceptual priming effects in word-fragment completion, which were retained essentially in full strength for 12 months, and (b) independent of perceptual priming, learning of new semantic facts, many of which were also retained for 12 months. K.C. 's semantic learning may be at least partly attributable to repeated study trials and minimal interference during learning. The findings suggest that perceptual priming and semantic learning are subserved by two memory systems different from episodic memory and that both systems (perceptual representation and semantic memory) are at least partially preserved in some amnesic subjects.
Instrumentation and data management for geoacoustic characterization of shallow water sediments

In order to study the geoacoustic relations for shallow water sediments, a project has started in 2014, bringing together French academic and industrial partners. One of this project objectives is to build a large database of acoustical and sedimentological parameters collected in-situ with specific devices. Therefore, an important task is to manage the data acquisition, storage, and exploitation. A two-step process has been designed to achieve this: first, a mobile application which helps the users during the measurements, and second a relational database system which gathers all the data and favors their exploitation. The first dataset come from extensive measurements on the French coastlines. The data acquisition, visualization, and exploitation have been considerably facilitated with this data management system.
Simulation of Vehicular Ad Hoc Networks with real city scenes

Simulation of Vehicular Ad Hoc Networks (VANET) plays an crucial role on design and development of VANET including routing algorithms, mobility management and so on. In the paper, the SVNRCS system is presented to simulate VANET in realistic scenes. Its vehicle distribution and movement model are based on realistic GPS data. Thus it can simulate more real VANET environment. The architecture and implementation of SVNRCS is presented.
N-Cadherin Sustains Motility and Polarity of Future Cortical Interneurons during Tangential Migration

In the developing brain, cortical GABAergic interneurons migrate long distances from the medial ganglionic eminence (MGE) in which they are generated, to the cortex in which they settle. MGE cells express the cell adhesion molecule N-cadherin, a homophilic cell–cell adhesion molecule that regulates numerous steps of brain development, from neuroepithelium morphogenesis to synapse formation. N-cadherin is also expressed in embryonic territories crossed by MGE cells during their migration. In this study, we demonstrate that N-cadherin is a key player in the long-distance migration of future cortical interneurons. Using N-cadherin-coated substrate, we show that N-cadherin-dependent adhesion promotes the migration of mouse MGE cells in vitro. Conversely, mouse MGE cells electroporated with a construct interfering with cadherin function show reduced cell motility, leading process instability, and impaired polarization associated with abnormal myosin IIB dynamics. In vivo, the capability of electroporated MGE cells to invade the developing cortical plate is altered. Using genetic ablation of N-cadherin in mouse embryos, we show that N-cadherin-depleted MGEs are severely disorganized. MGE cells hardly exit the disorganized proliferative area. N-cadherin ablation at the postmitotic stage, which does not affect MGE morphogenesis, alters MGE cell motility and directionality. The tangential migration to the cortex of N-cadherin ablated MGE cells is delayed, and their radial migration within the cortical plate is perturbed. Altogether, these results identify N-cadherin as a pivotal adhesion substrate that activates cell motility in future cortical interneurons and maintains cell polarity over their long-distance migration to the developing cortex.
Safety and Immunogenicity of a Recombinant Adenovirus Serotype 35-Vectored HIV-1 Vaccine in Adenovirus Serotype 5 Seronegative and Seropositive Individuals.

BACKGROUND Recombinant adenovirus serotype 5 (rAd5)-vectored HIV-1 vaccines have not prevented HIV-1 infection or disease and pre-existing Ad5 neutralizing antibodies may limit the clinical utility of Ad5 vectors globally. Using a rare Ad serotype vector, such as Ad35, may circumvent these issues, but there are few data on the safety and immunogenicity of rAd35 directly compared to rAd5 following human vaccination. METHODS HVTN 077 randomized 192 healthy, HIV-uninfected participants into one of four HIV-1 vaccine/placebo groups: rAd35/rAd5, DNA/rAd5, and DNA/rAd35 in Ad5-seronegative persons; and DNA/rAd35 in Ad5-seropositive persons. All vaccines encoded the HIV-1 EnvA antigen. Antibody and T-cell responses were measured 4 weeks post boost immunization. RESULTS All vaccines were generally well tolerated and similarly immunogenic. As compared to rAd5, rAd35 was equally potent in boosting HIV-1-specific humoral and cellular immunity and responses were not significantly attenuated in those with baseline Ad5 seropositivity. Like DNA, rAd35 efficiently primed rAd5 boosting. All vaccine regimens tested elicited cross-clade antibody responses, including Env V1/V2-specific IgG responses. CONCLUSIONS Vaccine antigen delivery by rAd35 is well-tolerated and immunogenic as a prime to rAd5 immunization and as a boost to prior DNA immunization with the homologous insert. Further development of rAd35-vectored prime-boost vaccine regimens is warranted.
A topological approach for protein classification

Abstract Protein function and dynamics are closely related to its sequence and structure.However, prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein classification, which is typically done through measuring the similarity between proteins based on protein sequence or physical information, serves as a crucial step toward the understanding of protein function and dynamics. Persistent homology is a new branch of algebraic topology that has found its success in the topological data analysis in a variety of disciplines, including molecular biology. The present work explores the potential of using persistent homology as an independent tool for protein classification. To this end, we propose a molecular topological fingerprint based support vector machine (MTF-SVM) classifier. Specifically,we construct machine learning feature vectors solely fromprotein topological fingerprints,which are topological invariants generated during the filtration process. To validate the presentMTF-SVMapproach, we consider four types of problems. First, we study protein-drug binding by using the M2 channel protein of influenza A virus. We achieve 96% accuracy in discriminating drug bound and unbound M2 channels. Secondly, we examine the use of MTF-SVM for the classification of hemoglobin molecules in their relaxed and taut forms and obtain about 80% accuracy. Thirdly, the identification of all alpha, all beta, and alpha-beta protein domains is carried out using 900 proteins.We have found a 85% success in this identification. Finally, we apply the present technique to 55 classification tasks of protein superfamilies over 1357 samples and 246 tasks over 11944 samples. Average accuracies of 82% and 73% are attained. The present study establishes computational topology as an independent and effective alternative for protein classification.
Research of MEMS pressure sensor stability with PDA-NFL circuit

: The stability of pressure sensor chip output characteristics using the piezoresistive 6 method in the form of microelectromechanical system (MEMS) is one of the most important fea-7 tures for sensors, which simultaneously demonstrates the relevance of the principles for design 8 construction and the choice of fabrication technology for all element structures. The research ana-9 lyzes the changes in the useful signal, as well as errors in mechanical and temperature characteris-10 tics of highly sensitive pressure sensor chips, which are more explicitly dependent on external 11 factors. The main feature of this development is the application of a new electrical circuit in the 12 form of piezoresistive differential amplifier with negative feedback loop (PDA-NFL) utilizing bi-13 polar junction transistors (BjT), which allows to achieve a balance between high sensitivity, small 14 chip area and low errors. This research considers the variations of two batch with pressure sensor 15 chip PDA-NFL samples (area 4.00x4.00 mm 2 ) for range of 1 kPa after 4.5 years (8 samples, sensitiv-16 ity S 1 after = (40.6 ± 6.4) mV/V/kPa, nonlinearity 2K NL 1 after = (0,81 ± 0.15) %/FS) and range of 5 kPa after 17 3.0 years (14 samples, sensitivity S 5 after = (11.2 ± 1.8) mV/V/kPa, nonlinearity 2K NL 5 after = (0.10 ± 0.06) 18 %/FS). The study demonstrates the unidirectional influence of residual mechanical stresses (RMS) 19 from the pressure sensor assembly design on sensitivity and nonlinearity when pressure is applied 20 from different sides of chip, initial membrane deflection, and temperature hysteresis