Miracle-dz/UniFAR-FTUs huggingface dataset:
Simultaneous Identification of 29 Prevalent Invasive Pneumococcal Serotypes or Pairs of Serotypes by Hybridization-Ligation PCR

ABSTRACT A hybridization-ligation PCR assay was developed for the simultaneous detection and identification of 21 pneumococcal serotypes and 8 pairs of serotypes in the same serogroup: 1, 2, 3, 4, 5, 6A, 6B, 6C-6D, 7F-7A, 8, 9A-9V, 9N-9L, 11A, 14, 15B-15C, 16F, 17F, 18B-18C, 19A, 19F, 20, 21, 22A-22F, 23A, 23B, 23F, 28A-28F, 35B and 38. This novel assay was validated with 185 serotyped pneumococcal invasive clinical isolates and 57 culture-negative pleural fluids previously typed by real-time PCR.
A Dynamic Multivariable State-Space Model for Bidirectional Inductive Power Transfer Systems

Bidirectional inductive power transfer (IPT) systems facilitate contactless power transfer between two sides, which are separated by an air gap, through weak magnetic coupling. Typical bidirectional IPT systems are essentially high-order resonant circuits and, therefore, difficult to both design and control without an accurate mathematical model, which is yet to be reported. This paper presents a dynamic model, which provides an accurate insight into the behavior of bidirectional IPT systems. The proposed state-space-based model is developed in a multivariable framework and mapped into frequency domain to compute the transfer function matrix of eight-order bidirectional IPT systems. The interaction between various control variables and degree of controllability of the system are analyzed from the relative gain array and singular values of the system. The validity of the proposed dynamic model is demonstrated by comparing the predicted behavior with that measured from a 1 kW prototype bidirectional IPT system under various operating conditions. Experimental results convincingly indicate that the proposed model accurately predicts the dynamical behavior of bidirectional IPT systems and can, therefore, be used as a valuable tool for transient analysis and optimum controller design.
Intracranial angioplasty without stenting for symptomatic atherosclerotic stenosis: long-term follow-up.

BACKGROUND AND PURPOSE Angioplasty and stent placement have been reported for the treatment of intracranial stenosis. This study was undertaken to assess the efficacy and long-term clinical outcome of angioplasty without stent placement for patients with symptomatic intracranial stenosis. METHODS A retrospective study was done to evaluate 36 patients with 37 symptomatic atherosclerotic intracranial stenosis who underwent primary balloon angioplasty. All patients had symptoms despite medical therapy. Thirty-four patients were available for follow-up ranging from 6 to 128 months. Mean follow-up was 52.9 months. RESULTS Mean pretreatment stenosis was 84.2% before angioplasty and 43.3% after angioplasty. The periprocedural death and stroke rate was 8.3% (two deaths and one minor stroke). Two patients had strokes in the territory of angioplasty at 2 and 37 months after angioplasty. The annual stroke rate in the territory appropriate to the site of angioplasty was 3.36%, and for those patients with a residual stenosis of > or =50% it was 4.5%. Patients with iatrogenic dissection (n=11) did not have transient ischemic attacks or strokes after treatment. CONCLUSION Results of long-term follow-up suggest that intracranial angioplasty without stent placement reduces the risk of further stroke in symptomatic patients.
Energy efficient pseudo-cache architecture through fine-grained reconfigurability

Fueled by the exponential growth in transistors available to processor designers, cache memories became a very significant percentage of the overall area, power dissipation and energy consumption of modern systems. Instruction cache memories, however, typically hold highly redundant information in each of their columns, due to the repeated use of instructions and registers by compilers. Current memory architectures do not exploit this fact to reduce energy, consuming constant amounts of power regardless of switching activity. This work proposes the use of a fine-grained reconfigurable architecture to exploit this redundancy, providing an energy efficient on-chip storage element for embedded processors. The proposed architecture reached consumes up to 86% less energy, with an average reduction of 39%.
Fetal biparietal diameter: a critical re‐evaluation of the relation to menstrual age by means of real‐time ultrasound.

The relationship between fetal biparietal diameter (BPD) and menstrual age was determined by cross‐sectional analysis of 533 fetuses (12 to 40 weeks) examined with a linear array real‐time (dynamic image) scanner using specifically defined methodology. Mathematical modeling of the data demonstrated that the optimal fit was the linear cubic function (r2 = 99 per cent); predicted BPD values calculated from the function were most comparable with composite data from cross‐sectional studies performed with static scanners after 1974 (average difference, 0.22 mm) and least comparable with composite data from cross‐sectional studies performed with static scanners before 1974 (average difference, 2.0 mm). The variability associated with predicting menstrual age from the BPD increased progressively throughout gestation; the maximal variability was noted between 36 and 42 weeks (+/‐ 3.6 weeks). Comparison with our longitudinal study of BPD growth indicates that the cross‐sectional data represent a valid estimate of the true longitudinal BPD growth curve of the population.
The impact of polyol-containing chewing gums on dental caries: a systematic review of original randomized controlled trials and observational studies.

BACKGROUND The authors conducted a systematic review of original studies that was designed to assess the impact of polyol-containing chewing gum on dental caries compared with the effect with no chewing gum. REVIEW METHODS The authors searched MEDLINE, The Cochrane Library and Google Scholar up to May 2008 to identify peer-reviewed articles that compared polyol-containing chewing gum with no chewing gum. The authors extracted study characteristics, data on incremental dental caries and quality by consensus. Data on prevented fraction (PF) were pooled across studies. RESULTS The results of 19 articles with data from 14 study populations showed that the use of xylitol, xylitol-sorbitol blend and sorbitol were associated with mean PF (95 percent confidence interval) of 58.66 percent (35.42-81.90), 52.82 percent (39.64-66.00) and 20.01 percent (12.74-27.27), respectively. For the sorbitol-mannitol blend, it was 10.71 percent (-20.50-41.93), which was not statistically significant. Sensitivity analyses confirmed the robustness of the findings. CLINICAL IMPLICATIONS Although research gaps exist, particularly on optimal dosing and relative polyol efficacy, research evidence supports using polyol-containing chewing gum as part of normal oral hygiene to prevent dental caries.
Active and specific recruitment of a soluble cargo protein for endoplasmic reticulum exit in the absence of functional COPII component Sec24p

Exit of proteins from the yeast endoplasmic reticulum (ER) is thought to occur in vesicles coated by four proteins, Sec13p, Sec31p, Sec23p and Sec24p, which assemble at ER exit sites to form the COPII coat. Sec13p may serve a structural function, whereas Sec24p has been suggested to operate in selection of cargo proteins into COPII vesicles. We showed recently that the soluble glycoprotein Hsp150 exited the ER in the absence of Sec13p function. Here we show that its ER exit did not require functional Sec24p. Hsp150 was secreted to the medium in a sec24-1 mutant at restrictive temperature 37°C, while cell wall invertase and vacuolar carboxypeptidase Y remained in the ER. The determinant guiding Hsp150 to this transport route was mapped to the C-terminal domain of 114 amino acids by deletion analysis, and by an HRP fusion protein-based EM technology adapted here for yeast. This domain actively mediated ER exit of Sec24p-dependent invertase in the absence of Sec24p function. However, the domain was entirely dispensable for ER exit when Sec24p was functional. The Sec24p homolog Sfb2p was shown not to compensate for nonfunctional Sec24p in ER exit of Hsp150. Our data show that a soluble cargo protein, Hsp150, is selected actively and specifically to budding sites lacking normal Sec24p by a signature residing in its C-terminal domain.
New noise-tolerant dynamic circuit design

Dynamic circuit is suitable for high-speed application, but often suffers from noise related reliability problems which become increasingly prominent as the technology are entering into the scores of nano meter era. This paper presented a new dynamic circuit scheme, which could achieve higher noise margin without sacrificing much power consumption and delay time. This design achieves a higher noise margin (1.2V) by finely tuning the transistor size. The effectiveness of new scheme is demonstrated in both NMOS series and parallel circuits. The simulation result shows that, compared with other published work, the proposed structure has the highest noise margin for the same power-delay product (PDP)1.
Genetic Retargeting of Adenovirus: Novel Strategy Employing “Deknobbing” of the Fiber

ABSTRACT For efficient and versatile use of adenovirus (Ad) as an in vivo gene therapy vector, modulation of the viral tropism is highly desirable. In this study, a novel method to genetically alter the Ad fiber tropism is described. The knob and the last 15 shaft repeats of the fiber gene were deleted and replaced with an external trimerization motif and a new cell-binding ligand, in this case the integrin-binding motif RGD. The corresponding recombinant fiber retained the basic biological functions of the natural fiber, i.e., trimerization, nuclear import, penton formation, and ligand binding. The recombinant fiber bound to integrins but failed to react with antiknob antibody. For virus production, the recombinant fiber gene was rescued into the Ad genome at the exact position of the wild-type (WT) fiber to make use of the native regulation of fiber expression. The recombinant virus Ad5/FibR7-RGD yielded plaques on 293 cells, but the spread through the monolayer was two to three times delayed compared to WT, and the ratio of infectious to physical particles was 20 times lower. Studies on virus tropism showed that Ad5/FibR7-RGD was able to infect cells which did not express the coxsackie-adenovirus receptor (CAR), but did express integrins. Ad5/FibR7-RGD virus infectivity was unchanged in the presence of antiknob antibody, which neutralized the WT virus. Ad5/FibR7-RGD virus showed an expanded tropism, which is useful when gene transfer to cells not expressing CAR is needed. The described method should also make possible the construction of Ad genetically retargeted via ligands other than RGD.
Chronic inhibition of endopeptidase 24.11 in essential hypertension: evidence for enhanced atrial natriuretic peptide and angiotensin II

Aim: To determine the renal, endocrine and haemodynamic effects of an orally active inhibitor of the neutral endopeptidase EC 3.4. 24.11 in essential hypertension Methods: Two groups of 12 white male patients with essential hypertension were treated with candoxatril at 25 mg every 12 h (group 1) or at 200 mg every 12 h (group 2) for 5 days in double-blind, placebo-controlled, crossover studies Results: Candoxatril enhanced natriuresis over the initial 48 h of treatment. Twenty-fourhour diurnal hormone profiles (day 4) showed modest elevations in plasma atrial natriuretic factor (ANF) concentrations and more clear-cut increases in plasma and urinary cyclic CMP. Plasma angiotensin II and aldosterone concentrations were also significantly increased. Plasma catecholamine concentrations were significantly increased by the higher dose of candoxatril. Blood pressure (day 4, 24-h intra-arterial recordings) fell significantly with both doses. The infusions of exogenous ANF and angiotensin II on day 5 showed that candoxatril impaired the metabolic clearance of both ANF and angiotensin II with consequent enhancement of the biological effects of both effector peptides Conclusions: Candoxatril augments the effects of ANF and lowers blood pressure in patients with hypertension. However, the antihypertensive effects may be offset by increased angiotensin-aldosterone and sympathetic nervous system activity. The blood pressure response to endopeptidase inhibition in hypertensive patients may depend on the relative effects on humoral vasodilator (including ANF) and vasoconstrictor (including the angiotensin-aldosterone and sympathetic) systems
Computational Modeling of Serum‐Binding Proteins and Clearance in Extrapolations Across Life Stages and Species for Endocrine Active Compounds

One measure of the potency of compounds that lead to the effects through ligand‐dependent gene transcription is the relative affinity for the critical receptor. Endocrine active compounds that are presumed to act principally through binding to the estrogen receptor (e.g., estradiol, genistein, bisphenol A, and octylphenol) comprise one class of such compounds. For making simple comparisons, receptor‐binding affinity has been equated to in vivo potency, which consequently defines the dose‐response characteristics for the compound. Direct extrapolation of in vitro estimated affinities to the corresponding in vivo system and to specific species or life stages (e.g., neonatal, pregnancy) can be misleading. Accurate comparison of the potency of endocrine active compounds requires characterization of biochemical and pharmacokinetic factors that affect their free concentration. Quantitative in vitro and in vivo models were developed for integrating pharmacokinetics factors (e.g., serum protein and receptor‐binding affinities, clearance) that affect potency. Data for parameterizing these models for several estrogenic compounds were evaluated and the models exercised. While simulations of adult human or rat sera were generally successful, difficulties in describing early life stages were identified. Exogenous compounds were predicted to be largely ineffective at competing estradiol off serum‐binding proteins, suggesting this was unlikely to be physiologically significant. Discrepancies were identified between relative potencies based upon modeling in vitro receptor‐binding activity versus in vivo activity in the presence of clearance and serum‐binding proteins. The examples illustrate the utility of this approach for integrating available experimental data from in vitro and in vivo studies to estimate the relative potency of these compounds.
Evolution of Diagnostic Tests for Chronic Wasting Disease, a Naturally Occurring Prion Disease of Cervids

Since chronic wasting disease (CWD) was first identified nearly 50 years ago in a captive mule deer herd in the Rocky Mountains of the United States, it has slowly spread across North America through the natural and anthropogenic movement of cervids and their carcasses. As the endemic areas have expanded, so has the need for rapid, sensitive, and cost effective diagnostic tests—especially those which take advantage of samples collected antemortem. Over the past two decades, strategies have evolved from the recognition of microscopic spongiform pathology and associated immunohistochemical staining of the misfolded prion protein to enzyme-linked immunoassays capable of detecting the abnormal prion conformer in postmortem samples. In a history that parallels the diagnosis of more conventional infectious agents, both qualitative and real-time amplification assays have recently been developed to detect minute quantities of misfolded prions in a range of biological and environmental samples. With these more sensitive and semi-quantitative approaches has come a greater understanding of the pathogenesis and epidemiology of this disease in the native host. Because the molecular pathogenesis of prion protein misfolding is broadly analogous to the misfolding of other pathogenic proteins, including Aβ and α-synuclein, efforts are currently underway to apply these in vitro amplification techniques towards the diagnosis of Alzheimer’s disease, Parkinson’s disease, and other proteinopathies. Chronic wasting disease—once a rare disease of Colorado mule deer—now represents one of the most prevalent prion diseases, and should serve as a model for the continued development and implementation of novel diagnostic strategies for protein misfolding disorders in the natural host.
Cutting Edge: Lymphoid Tissue Inducer Cells Maintain Memory CD4 T Cells within Secondary Lymphoid Tissue

Phylogeny shows that CD4 T cell memory and lymph nodes coevolved in placental mammals. In ontogeny, retinoic acid orphan receptor (ROR)γ-dependent lymphoid tissue inducer (LTi) cells program the development of mammalian lymph nodes. In this study, we show that although primary CD4 T cell expansion is normal in RORγ-deficient mice, the persistence of memory CD4 T cells is RORγ-dependent. Furthermore, using bone marrow chimeric mice we demonstrate that LTi cells are the key RORγ-expressing cell type sufficient for memory CD4 T cell survival in the absence of persistent Ag. This effect was specific for CD4 T cells, as memory CD8 T cells survived equally well in the presence or absence of LTi cells. These data demonstrate a novel role for LTi cells, archetypal members of the innate lymphoid cell family, in supporting memory CD4 T cell survival in vivo.
Sensorless control of SPMSM using complex number model based position estimation and EKF

This paper provides an improvement in sensorless control performance of surface permanent magnet synchronous motor(SPMSM). One method of the rotor position estimation by the complex number model based position estimator is proposed for the sensorless control of SPMSM. And, in order to eliminate the position estimation error that may be occurred by the uncertainty of motor parameters, a position type PI controller is applied to the error part of the position estimator. The proposed position estimation method does not need any information about the mechanical system of a motor. A control scheme to identify the permanent magnet flux of SPMSM by Extended Kalman Filter(EKF) is also proposed to increase the rotor position estimation accuracy. A rotor-flux-oriented vector control is employed as the basic control strategy for SPMSM drive system. The simulation results demonstrated the validity and feasibility of the proposed control system.
Exploiting Attribute Correlations: A Novel Trace Lasso-Based Weakly Supervised Dictionary Learning Method

It is now well established that sparse representation models are working effectively for many visual recognition tasks, and have pushed forward the success of dictionary learning therein. Recent studies over dictionary learning focus on learning discriminative atoms instead of purely reconstructive ones. However, the existence of intraclass diversities (i.e., data objects within the same category but exhibit large visual dissimilarities), and interclass similarities (i.e., data objects from distinct classes but share much visual similarities), makes it challenging to learn effective recognition models. To this end, a large number of labeled data objects are required to learn models which can effectively characterize these subtle differences. However, labeled data objects are always limited to access, committing it difficult to learn a monolithic dictionary that can be discriminative enough. To address the above limitations, in this paper, we propose a weakly-supervised dictionary learning method to automatically learn a discriminative dictionary by fully exploiting visual attribute correlations rather than label priors. In particular, the intrinsic attribute correlations are deployed as a critical cue to guide the process of object categorization, and then a set of subdictionaries are jointly learned with respect to each category. The resulting dictionary is highly discriminative and leads to intraclass diversity aware sparse representations. Extensive experiments on image classification and object recognition are conducted to show the effectiveness of our approach.
DNA aptamers developed against a soman derivative cross‐react with the methylphosphonic acid core but not with flanking hydrophobic groups

Twelve rounds of systematic evolution of ligands by exponential enrichment (SELEX) were conducted against a magnetic bead conjugate of the para‐aminophenylpinacolylmethylphosphonate (PAPMP) derivative of the organophosphorus (OP) nerve agent soman (GD). The goal was to develop DNA aptamers that could scavenge GD in vivo, thereby reducing or eliminating the toxic effects of this dangerous compound. Aptamers were sequenced and screened in peroxidase‐based colorimetric plate assays after rounds 8 and 12 of SELEX. The aptamer candidate sequences exhibiting the highest affinity for the GD derivative from round 8 also reappeared in several clones from round 12. Each of the highest affinity PAPMP‐binding aptamers also bound methylphosphonic acid (MPA). In addition, the aptamer with the highest overall affinity for PAPMP carried a sequence motif (TTTAGT) thought to bind MPA based on previously published data (J. Fluoresc 18: 867–876, 2008). This sequence motif was found in several other relatively high affinity PAPMP aptamer candidates as well. In studies with the nerve agent GD, pre‐incubation of a large molar excess of aptamer candidates failed to protect human butyrylcholinesterase (BuChE) from inhibition. With the aid of three‐dimensional molecular modeling of the GD derivative it appears that a hydrophilic cleft sandwiched between the pinacolyl group and the p‐aminophenyl ring might channel nucleotide interactions to the phosphonate portion of the immobilized GD derivative. However, bona fide GD free in solution may be repulsed by the negative phosphate backbone of aptamers and rotate its phosphonate and fluorine moieties away from the aptamer to avoid being bound. Future attempts to develop aptamers to GD might benefit from immobilizing the pinacolyl group of bona fide GD to enhance exposure of the phosphonate and fluorine to the random DNA library. Copyright © 2008 John Wiley & Sons, Ltd.
Identification of a locus required for the regulation of bvg-repressed genes in Bordetella pertussis

In Bordetella pertussis, the coordinate regulation of virulence factor expression is controlled by the products of the bvgAS locus. In the presence of modulating signals such as MgSO4, nicotinic acid, or reduced temperature, the expression of bvg-activated genes is reduced while the expression of bvg-repressed genes is induced. One model for the regulation of bvg-repressed genes predicts the existence of a repressor protein encoded by a bvg-activated gene. Once activated, the product of this bvg-activated gene would bind to and repress transcription from the bvg-repressed genes. We isolated five genetically independent transposon insertion mutants of B. pertussis that have a phenotype consistent with the knockout of a putative bvg-regulated repressor. These mutants constitutively expressed a vrg6-phoA transcriptional fusion but demonstrated normal bvgAS function. Genomic mapping and DNA sequence analysis of the sites of transposon insertion demonstrated that these mutants define a locus downstream of bvgAS. Introduction of an in-frame, 12-bp insertion within this locus also conferred the mutant phenotype, confirming that the phenotype seen in the transposon mutants is the result of disruption of a distinct gene, which we have designated bvgR, and is not a consequence of polar effects on bvgAS.
Complete Genome Sequence of Bacillus thuringiensis Serovar Tolworthi Strain Pasteur Institute Standard

ABSTRACT The genome sequence of Bacillus thuringiensis serovar tolworthi strain Pasteur Institute Standard was determined. The genome consists of a 5.9-Mb chromosome and eight plasmids, one of which is linear. The second largest plasmid (293 kb) carries the genes encoding insecticidal proteins.