Miracle-dz/UniFAR-FTUs huggingface dataset:
Dual gradient‐echo MRI of post‐contraction changes in skeletal muscle blood volume and oxygenation

Analysis of post‐contraction MRI signal intensity (SI) transients may allow noninvasive studies of microvascular reactivity and blood oxygenation recovery. The purpose of this study was to determine the physiological basis for post‐contraction changes in short‐echo (6 ms) and long‐echo (46 ms) gradient‐echo (GRE) MRI signals (S6 and S46, respectively). Six healthy subjects were studied with the use of dual GRE MRI and near‐infrared spectroscopy (NIRS). S6, S46, total hemoglobin concentration ([THb]), and oxyhemoglobin saturation (%HbO2) were measured before, during, and after 2 and 8 s dorsiflexion maximal voluntary contractions, and 5 min of proximal arterial occlusion. The changes in S6 and [THb] after the 2‐s contractions were similar to those following 8‐s contractions, but changes in %HbO2 and S46 were greater following 8‐s contractions than after the 2‐s contractions. [THb] and S6 did not change during and following 5 min of arterial occlusion, but %HbO2 and S46 were both significantly depressed at similar occlusion durations. Also, distance measures indicated similarity between S6 and [THb] and between S46 and %HbO2. We conclude that following brief human skeletal muscle contractions, changes in S6 primarily reflect changes in blood volume and changes in S46 primarily reflect changes in blood oxygenation. Magn Reson Med 57:670–679, 2007. © 2007 Wiley‐Liss, Inc.
Solution structure of the Trp operator of Escherichia coli determined by NMR.

We have assigned the majority of the nonexchangeable protons in the NMR spectrum of the 20 base-pair fragment of DNA corresponding to the Trp operator of Escherichia coli. The sequence (CGTACTAGTTAACTAGTACG) also contains a Pribnow box (underlined). Variation of the intrinsic spin-lattice relaxation rate constants of the H8's along the sequence indicates that the structure of the oligonucleotide is not regular. Splitting patterns of the H1' resonances in the deoxyriboses, obtained from a two-dimensional J-resolved experiment, allowed the dominant pucker mode of each nucleotide to be determined. Intranucleotide NOEs from the sugar protons H1', H2', and H3' to the base protons were used to determine the conformation of each nucleotide (puckers and glycosidic torsion angles). The relative orientations of nucleotide units (roll, propeller twist, helical twist angle, and pitch) were calculated by using internucleotide NOEs between protons of neighboring nucleotides in the sequence. All these parameters were determined for each step along the 20-mer. The structure belongs to the B family of conformations, but variations of the local geometry are observed from step to step. Some of the variations, such as the roll and the twist angles, can be predicted by the rules of Calladine and Dickerson [Calladine, C. R. , & Dickerson, R. E. (1983) J. Mol. Biol. 166, 419-441]. The puckers of the deoxyriboses of purines are found mainly in conformations near C2' endo, while those of the pyrimidines prefer C3' endo and related conformations. Glycosidic torsion angles obtained for purines are larger than those of pyrimidines. Except for this last observation, the general properties of the operator DNA structure are comparable with those of crystal structures of B DNA of other sequences.
Long-term survival following radiofrequency ablation of colorectal liver metastases: A retrospective study.

AIM To retrospectively evaluate the long-term survival of patients that received radiofrequency ablation (RFA) therapies of colorectal liver metastases. METHODS In 2005 to 2008, RFA of 105 colorectal liver metastases (CRLM) were performed on 49 patients in our institution. The liver metastases were evaluated, both before and after ablation therapies, with contrast enhanced computerised tomography and contrast enhanced ultrasonography. Histological evidence of malignant liver metastases was obtained in the few instances where contrast enhanced ultrasonography gave equivocal results. Accesses to the CRLM were guided ultrasonically in all patients. The data obtained from records of these ablations were retrospectively analysed and survival data were compared with existing studies in the literature. RESULTS 1-, 2-, 3-, 4- and 5-year survival rates, when no stringent selection criteria were applied, were 92%, 65%, 51%, 41% and 29% respectively. To explore the impact of the number and size of CRLM on patients' survival, an exclusion of 13 patients (26.5%) with number of CRLM ≥ 5 and tumour size ≥ 40 mm resulted in 1-, 2-, 3-, 4- and 5-year survival rates improving to 94%, 69%, 53%, 42% and 31% respectively. It is of note that 9 of 49 patients developed extra-hepatic metastases, not visible or seen on pre-treatment scans, just after RFA treatment. These patients had poorer survival. The development of extra-hepatic metastases in nearly 20% of the patients included in our study can partly account for modestly lower survival rates as compared with earlier studies in the literature. CONCLUSION Our study underscores the fact that optimum patients' selection before embarking on RFA treatment is vitally important to achieving a superior outcome.
The thiazolidinedione ciglitazone reduces bacterial outgrowth and early inflammation during Streptococcus pneumoniae pneumonia in mice*

Objective:Thiazolidinediones (TZDs) are synthetic agonists for the peroxisome proliferator-activating receptor-gamma receptor and are currently in use as oral glucose-lowering drugs. TZDs have immune-modulating effects in vitro and in vivo. Because patients with type 2 diabetes have an increased risk for pneumonia, we evaluated the influence of ciglitazone, a TZD, on markers of inflammation and outcome during pneumonia caused by Streptococcus pneumoniae. Design:In vivo animal study and in vitro study. Setting:University research laboratory. Subjects:Female C57Bl/6 mice and murine alveolar macrophage-like MH-S cells. Interventions:C57Bl/6 mice were inoculated with 105 colony-forming units of S. pneumoniae intranasally. The following interventions were studied: 1) vehicle at t = 0; 2) ciglitazone 5 mg/kg intraperitoneally at t = 0; and 3) ciglitazone 5 mg/kg intraperitoneally at t = 0 and 24 hours. Mice were killed at either 24 or 48 hours after infection. Additionally, phagocytosis and killing of S. pneumoniae by MH-S cells were assessed in vitro. Measurements and Main Results:Single treatment with ciglitazone reduced bacterial loads at 24 hours but not at 48 hours, whereas repeated ciglitazone treatment did diminish bacterial loads at 48 hours. After 24 hours, cytokine levels in lung homogenate were lower in single-dose ciglitazone-treated mice; however, after 48 hours, there was no difference in lung cytokines between any of the experimental groups. Repeated ciglitazone treatment was associated with less pulmonary inflammation, as judged by histologic examination. On both time points, there was no difference in plasma cytokine levels or lung myeloperoxidase levels between experimental groups. In an additional experiment, ciglitazone treatment (given once daily) tended to reduce mortality. Ciglitazone did not influence phagocytosis or killing of S. pneumoniae by murine alveolar macrophages. Conclusions:Ciglitazone reduces bacterial outgrowth and local inflammation at least during the early stage of S. pneumoniae pneumonia in mice.
Payments discourage coordination in ecosystem services provision: evidence from behavioral experiments in Southeast Asia

The contribution of synthetic pesticides to closing yield gaps around the world is undeniable; however, their use is also a classic double-edged sword. Beyond the well-recognized social costs (e.g., pollution to soil and water, and health effects both on consumers and other species) there are also private costs on farmers beyond the direct costs of inputs, associated with elevated risks of both acute and chronic damage to farmers’ health, and with the destruction of populations of beneficial organisms. Managing agricultural land use to enhance natural pest control services (also called mobile agent-based ecosystem services or MABES) holds promise to reduce this growing reliance on pesticides, though it too carries costs. In particular, uncertainty in crop yield due to pest damages, as well as the need to coordinate pesticide use with neighboring farms, can be important obstacles to establishing the longer-term public good of natural pest regulation. Current thinking on promoting ecosystem services suggests that payments or other economic incentives are a good fit for the promotion of public good ecosystem services such as MABES. We undertook a framed field experiment to examine the role of subsidies for non-crop habitat in improving insect-based ecosystem services in two separate samples in Southeast Asia—Cambodia and Vietnam. Our central finding is that these two contexts are not poised equally to benefit from incentives promoting MABES, and in fact may be left worse off by payments schemes. As the study and practice of payments for ecosystem services programs grows, this finding provides an important qualifier on recent theory supporting the use of payments to promote public good ecosystem services—where the nature of the coordination problem is complex and nonlinear, farm systems can be made worse off by being encouraged to attempt it.
Characterisation by proteomics of peribacteroid space and peribacteroid membrane preparations from pea (Pisum sativum) symbiosomes

The legume Rhizobium symbiosis leads to the formation of a new compartment in the plant cell, the symbiosome. This compartment harbours the bacteroids surrounded by a peribacteroid membrane (PBM) originating from the plant plasma membrane. The PBM and the space between the PBM and the bacteroid membrane, called peribacteroid space (PS), mediate the exchange of metabolites between the symbionts. Proteome analysis was used as an approach to characterise the proteins in the PBM and the PS. A standard differential centrifugation procedure including a Percoll gradient was used for symbiosome isolation from pea root nodules. Proteins in the PBM and PS fractions obtained from the symbiosomes were separated by two‐dimensional gel electrophoresis, and 89 spots were analysed by tandem mass spectrometry. The proteins of 46 spots could be identified by database search. The results showed that PS and even PBM preparations from pea symbiosomes always contain abundant amounts of bacteroid proteins as a contaminate. Interestingly, in addition to a few PS/PBM proteins a number of endomembrane proteins (less likely representing a contaminate), including V‐ATPase, BIP, and an integral membrane protein known from COPI‐coated vesicles, were found in the PBM fraction, supporting the role of the endomembrane system in PBM biogenesis.
Detection and quantification of native microbial populations on soil-grown rice roots by catalyzed reporter deposition-fluorescence in situ hybridization.

Catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) was applied to detect microbial cells on the rhizoplane of wetland rice (Oryza sativa L.). Fluorescent signals of high intensity and specificity allowed for a reliable quantification of selected microbial phyla. Absolute cell numbers of archaea and bacteria were observed to be highest at flowering stage of rice plant development (P < 0.05) showing values of 1.32 and 6.26 × 10(4) cells mm(-2) rhizoplane, respectively. Highest colonization densities shifted from the root tip toward more mature regions with increasing plant age. Significant differences between cell numbers observed within a short distance (0-15 mm) indicated irregular distribution patterns of microbiota. Root tips, elongation zones, and openings at the base of lateral roots represented preferential areas for microbial colonization, which were often covered with iron coatings and densely colonized with potential iron-oxidizing Betaproteobacteria (59% of bacteria). Methanogenic archaea were abundant on the rhizoplane (up to 0.96 × 10(3) cells mm(-2) rhizoplane), and the decline of their relative abundance with plant age was also found in the associated rhizosphere soil. Cell numbers of methanotrophic bacteria significantly increased at flowering (6.38 × 10(3) cells mm(-2) rhizoplane; P < 0.05), indicating their stimulation by root-derived substrates which was less pronounced in the rhizosphere soil.
A paraconsistent system of autonomous agents for Brazilian bank check treatment

This work is part of the Multicheck Project that defines the architecture of autonomous agents for the automatic treatment of handwritten Brazilian bank checks. The competence of these agents is implemented in two layers. The first corresponds to pattern recognition algorithms directly applied to image segments. The second one corresponds to reasoning mechanisms applied to the information from the first layer, either to validate or to interpret it. The interpretation process also involves information obtained from other agents. This information can present inconsistencies. This problem is treated properly and naturally through the concepts and operators of paraconsistent logic. This paper focuses on the second layer, on task distribution problems and on communication between agents. The first layer information was obtained through a simulated database.
Limbs synergies based human motion intention estimation algorithm for using cane-type walking-aid robot

Diverse walking-aid robots and the control systems of them have been investigated a lot. These human motion intention estimation methods vary from detecting the bioelectric signal such as EMG, EEG to the measurements of interaction forces. However, most of them just estimate the movements of single kind of limbs, which can not reflect the walk intention in real very well. In this paper we concluded the intuitive and feasible model of normal walking based on limbs synergies by principal components analysis (PCA) method, and proposed the fusion estimation of the human synergies movements of upper limbs and lower limbs based on using the cane-type walking-aid robot we designed. The effectivenesses are valid through the experiments conducted in reality.
Complete Genome Sequence of Uropathogenic Proteus mirabilis, a Master of both Adherence and Motility

ABSTRACT The gram-negative enteric bacterium Proteus mirabilis is a frequent cause of urinary tract infections in individuals with long-term indwelling catheters or with complicated urinary tracts (e.g., due to spinal cord injury or anatomic abnormality). P. mirabilis bacteriuria may lead to acute pyelonephritis, fever, and bacteremia. Most notoriously, this pathogen uses urease to catalyze the formation of kidney and bladder stones or to encrust or obstruct indwelling urinary catheters. Here we report the complete genome sequence of P. mirabilis HI4320, a representative strain cultured in our laboratory from the urine of a nursing home patient with a long-term (≥30 days) indwelling urinary catheter. The genome is 4.063 Mb long and has a G+C content of 38.88%. There is a single plasmid consisting of 36,289 nucleotides. Annotation of the genome identified 3,685 coding sequences and seven rRNA loci. Analysis of the sequence confirmed the presence of previously identified virulence determinants, as well as a contiguous 54-kb flagellar regulon and 17 types of fimbriae. Genes encoding a potential type III secretion system were identified on a low-G+C-content genomic island containing 24 intact genes that appear to encode all components necessary to assemble a type III secretion system needle complex. In addition, the P. mirabilis HI4320 genome possesses four tandem copies of the zapE metalloprotease gene, genes encoding six putative autotransporters, an extension of the atf fimbrial operon to six genes, including an mrpJ homolog, and genes encoding at least five iron uptake mechanisms, two potential type IV secretion systems, and 16 two-component regulators.
Localization of Cystic Fibrosis Transmembrane Conductance Regulator to Lipid Rafts of Epithelial Cells Is Required for Pseudomonas aeruginosa-Induced Cellular Activation 1

The cystic fibrosis (CF) transmembrane conductance regulator (CFTR) protein is an epithelial cell receptor for the outer core oligosaccharide of the Pseudomonas aeruginosa LPS. Bacterial binding leads to CFTR-dependent bacterial internalization, initiation of NF-κB nuclear translocation, cellular desquamation, and eventual apoptosis of the infected cells, all of which are critical for innate immune resistance to infection with this pathogen. Lack of this reaction in CF patients underlies their hypersusceptibility to chronic P. aeruginosa infection. In this study we tested whether these epithelial cell responses are dependent upon the localization of CFTR to lipid rafts. Confocal microscopy showed that green fluorescent protein-tagged CFTR (GFP-CFTR) and the lipid raft marker ganglioside GM1 colocalized at sites of P. aeruginosa contact and internalization. GFP-CFTR localized to low density Triton X-100-insoluble fractions in lysates of Madin-Darby canine kidney GFP-CFTR cells, and P. aeruginosa infection increased the levels of GFP-CFTR in these fractions as determined by Western blot. Cells expressing GFP-ΔF508-CFTR did not have rafts with detectable CFTR protein. Extraction of cell surface cholesterol via cyclodextrin treatment of the cells inhibited CFTR entry into rafts. In addition, cyclodextrin treatment of both human and canine epithelial cells inhibited cellular ingestion of P. aeruginosa, NF-κB nuclear translocation, and apoptosis. These results indicate that lipid raft localization of CFTR is required for signaling in response to P. aeruginosa infection. Such signaling is needed for the coordination of innate immunity to P. aeruginosa lung infection, a process that is defective in CF.
Myocardial Perfusion Imaging With Gadobutrol: A Comparison Between 3 and 1.5 Tesla With an Identical Sequence Design

Objectives:To implement myocardial first-pass perfusion imaging at 3 Tesla and to evaluate the potential benefit with regard to signal parameters in comparison to 1.5 Tesla using identical sequence settings and an intraindividual comparison. Materials and Methods:In 16 volunteers, myocardial first-pass perfusion imaging was performed at 1.5 Tesla (Magnetom Avanto) and 3 Tesla (Magnetom TIM Trio) after injection of 0.05 mmol/kg body weight Gadobutrol using an accelerated saturation recovery TurboFLASH technique (GRAPPA; R = 2) at 1.5 and 3 Tesla. Detailed sequence parameters (TR 2.3 milliseconds, TE 0.93 milliseconds, flip angle 15°, bandwidth 780 Hz/px) as well as spatial resolution were kept identical for both field strengths. Artifacts were assessed quantitatively and qualitatively, signal-to-noise ratio (SNR) and contrast enhancement ratio (CER) were calculated from raw data signal intensity–time curves. A linear fit on the upslope was performed for semiquantitative perfusion analysis. Results:SNR was significantly higher at 3 Tesla than at 1.5 Tesla (35.7 ± 11.9 vs. 18.0 ± 5.5, P < 0.001). CER was significantly greater at 3 Tesla than at 1.5 Tesla (2.2 ± 0.9 vs. 1.4 ± 0.5, P < 0.001). Maximum upslope was significantly higher at 3 Tesla than at 1.5 Tesla (3.3 ± 2.4 vs. 2.0 ± 1.0, P < 0.001). A qualitative examination of all images for artifacts by 2 board-certified radiologists yielded no significant differences between the field strengths. Conclusions:Three Tesla significantly improves CER and SNR compared with 1.5 Tesla with identical sequence parameters. In addition, the most important semiquantitative perfusion parameter maximum upslope is significantly increased. This may allow for an improvement of spatial resolution and potentially for a better delineation of perfusion defects. However, further studies are necessary to potentially demonstrate a benefit of 3 Tesla perfusion imaging in a clinical setting.
IgVH Mutational Status and Clonality Analysis of Richter's Transformation: Diffuse Large B-cell Lymphoma and Hodgkin Lymphoma in Association With B-cell Chronic Lymphocytic Leukemia (B-CLL) Represent 2 Different Pathways of Disease Evolution

Approximately 5% of B-cell chronic lymphocytic leukemia (B-CLL) patients develop a secondary aggressive lymphoma, usually of diffuse large B-cell type (DLBCL), termed Richter's transformation (RT). Rarely, classic Hodgkin lymphoma (HL) is observed. Published small series suggest that tumor cells in DLBCL and HL can be clonally identical to the B-CLL clone or arise as an independent, secondary lymphoma. We describe the morphology, immunophenotype, and clinical features of 34 classic RT patients with DLBCL, 6 cases of B-CLL with HL, and 8 cases with scattered CD30-positive Hodgkin and Reed-Sternberg (HRS)-like cells. The clonal relationship of the 2 components was analyzed using sequencing analysis of immunoglobulin heavy chain variable region (IgVH) genes. In classic RT, 18/23 B-CLL cases (78%) showed clonal progression to DLBCL with identical IgVH sequences in both lymphoma components, whereas in 5 cases (22%) the DLBCL was clonally unrelated. Among clonally related RT samples, 73% carried unmutated IgVH genes, whereas 4/5 unrelated cases were mutated. Immunophenotypically, most cases of DLBCL irrespective of clonal relatedness showed significant differences in phenotype compared with the B-CLL, with common loss of CD5 and CD23. Using immuno-laser capture microdissection, sequencing of the IgVH CDR3 region of isolated HRS cells showed that 2/2 cases with HL were clonally unrelated, whereas they were clonally identical in 1/2 cases of B-CLL with scattered HRS-like cells. HRS or HRS-like cells in all 3 unrelated cases showed evidence of Epstein-Barr virus infection. Of interest, 5/6 cases of B-CLL with HL, and 5/6 cases of B-CLL with HRS cells showed mutated IgVH genes.
Exact Bayesian and particle filtering of stochastic hybrid systems

The standard way of applying particle filtering to stochastic hybrid systems is to make use of hybrid particles, where each particle consists of two components, one assuming Euclidean values, and the other assuming discrete mode values. This paper develops a novel particle filter (PF) for a discrete-time stochastic hybrid system. The novelty lies in the use of the exact Bayesian equations for the conditional mode probabilities given the observations. Therefore particles are needed for the Euclidean valued state component only. The novel particle filter is referred to as the interacting multiple model (IMM) particle filter (IMMPF) because it incorporates a filter step which is of the same form as the interaction step of the IMM algorithm. Through Monte Carlo simulations, it is shown that the IMMPF has significant advantage over the standard PF, in particular for situations where conditional switching rate or conditional mode probabilities have small values
Dual‐frequency, dual‐quadrature, birdcage RF coil design with identical b1 pattern for sodium and proton imaging of the human brain at 1.5 T

Rapid quantification of tissue metabolites in vivo by MRS or MRI can be achieved using dual‐frequency RF coils with identical B1 field distributions at the observation frequencies of the metabolites and tissue water protons. Tissue sodium is used as an example for optimizing the dual‐frequency, dual‐quadrature RF coils for such measurements in humans. In the setting of sodium imaging, the challenge of dual‐quadrature birdcage configurations is to decouple the sodium and proton channels because the fourth harmonic of the sodium frequency is very close to the proton frequency. A generalizable method for effectively decoupling these two RF frequencies is presented in this paper. The method is demonstrated with the design of an EPI compatible, dual‐quadrature, double‐tuned, 23Na/1H birdcage coil. The performance of the RF probe is reported at 1.5 Tesla in terms of signal‐to‐noise ratio, B1 homogeneity and image quality.