Miracle-dz/UniFAR-FTUs huggingface dataset:
The levels of clarithromycin and its 14-hydroxy metabolite in the lung.

Clarithromycin is a new macrolide that has a longer half-life than erythromycin and is claimed to reach higher tissue concentrations. We aimed to investigate whether, following oral administration, the drug and its 14-hydroxy metabolite reach levels in lung tissue that are likely to be clinically effective against common respiratory pathogens. Ten patients undergoing diagnostic bronchoscopy received seven doses of clarithromycin, 500 mg b.i. d. orally. Bronchoscopy was performed at a mean time of 4.25 h after the last dose. At bronchoscopy, bronchial biopsies and bronchoalveolar lavage were performed. Clarithromycin and its 14-OH metabolite were measured in serum, bronchial biopsies, epithelial lining fluid (ELF) and alveolar cells. Mean levels of clarithromycin were 4.0 mg.l-1 in serum, 16.8 mg.kg in bronchial biopsies, 20.5 mg.l-1 in ELF and 372.7 mg.l-1 in alveolar cells. The equivalent levels of 14-OH metabolite were 0.7, 2.7, 1.9 and 38.6 mg.l-1, respectively. We conclude that there is considerable concentration of clarithromycin and its 14-OH metabolite in alveolar cells, and to a lesser extent in bronchial tissue and ELF; this implies efficacy against susceptible organisms at these sites.
The ghosts of mammals past: biological and geographical patterns of global mammalian extinction across the Holocene

Although the recent historical period is usually treated as a temporal base-line for understanding patterns of mammal extinction, mammalian biodiversity loss has also taken place throughout the Late Quaternary. We explore the spatial, taxonomic and phylogenetic patterns of 241 mammal species extinctions known to have occurred during the Holocene up to the present day. To assess whether our understanding of mammalian threat processes has been affected by excluding these taxa, we incorporate extinct species data into analyses of the impact of body mass on extinction risk. We find that Holocene extinctions have been phylogenetically and spatially concentrated in specific taxa and geographical regions, which are often not congruent with those disproportionately at risk today. Large-bodied mammals have also been more extinction-prone in most geographical regions across the Holocene. Our data support the extinction filter hypothesis, whereby regional faunas from which susceptible species have already become extinct now appear less threatened; they may also suggest that different processes are responsible for driving past and present extinctions. We also find overall incompleteness and inter-regional biases in extinction data from the recent fossil record. Although direct use of fossil data in future projections of extinction risk is therefore not straightforward, insights into extinction processes from the Holocene record are still useful in understanding mammalian threat.
Influence of the reactive processing of recycled poly(ethylene terephthalate)/poly(ethylene‐co‐glycidyl methacrylate) blends

The effect of the amount of reactive additive and screw speed during extrusion on the morphological characteristics and mechanical performance of recycled poly(ethylene terephthalate)(RPET) was investigated. With an increase in the ethylene–glycidyl methacrylate copolymer (E–GMA) additive content, a gradual increase in the Izod impact strength of the RPET/E–GMA blends was initially recorded. Subsequent increases in the E–GMA content to above 13.5 wt % led to a drastic enhancement in the toughness of the blends. Meanwhile, the density of the blends decreased with increasing amount of the additive E–GMA. The toughness and density of the blends were found to be dependent on the screw rotation speed during the extrusion. In addition, ductile and microporous structures were observed on the Izod impact fracture surfaces. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
A Pilot Study on Gender Differences in Conversational Speech on Lexical Richness Measures

Recent research on gender differences in language has mostly addressed cognitive differences. These differences have been observed on different cognitive verbal and non-verbal tasks and conclusions on the variability in language production and comprehension have been drawn from their results. In this paper, a different approach is presented. This pilot study examines lexical richness measures in conversational speech across a total of thirty subjects. All subjects were recorded and transcribed in a conversational setting. Their transcribed speech was analysed using a set of lexical richness measures based on word-frequencies. On the basis of these measurements, statistical discriminant analysis is able to classify the two groups with 90 per cent (74 per cent with leave-one-out cross-validation) correct prediction rate at a statistically significant level (P = 0.03). The results are discussed in detail, including correlation and principal components analysis. The paper concludes that there are interesting differences across the two groups on the measures studied and further research in this area is needed.
Unusual architecture of the exceedingly tough Macadamia “nut”-shell as revealed by atomic force microscopy and nanomechanics

Abstract Unlike previous assumptions, the 3D microscopic construction of the macadamia wooden shell (a model for bionics' design) is far from being “isotropic”. The consequences for the exceedingly high toughness towards cracking are investigated by atomic force microscopy to evaluate the vertical stiffeners in a fullerene-type surface architecture of the only 160 μm thick hardshell that is known to withstand up to 2000 N compressive load. Nanoindentations provide hardness and elasticity modulus at stiffeners and more compliant polygon material, as well as differences of indentation coefficients and work of indentation. Nanoscratching provides scratch coefficients and specific full scratch work values that can be compared with varied other materials using interpolations with linear relations between nanomechanical parameters. A particular lotus-type effect is found for the macadamia hardshell surface.
Simultaneous Localization and Mapping with Iterative Sparse Extended Information Filter for Autonomous Vehicles

In this paper, a novel iterative sparse extended information filter (ISEIF) was proposed to solve the simultaneous localization and mapping problem (SLAM), which is very crucial for autonomous vehicles. The proposed algorithm solves the measurement update equations with iterative methods adaptively to reduce linearization errors. With the scalability advantage being kept, the consistency and accuracy of SEIF is improved. Simulations and practical experiments were carried out with both a land car benchmark and an autonomous underwater vehicle. Comparisons between iterative SEIF (ISEIF), standard EKF and SEIF are presented. All of the results convincingly show that ISEIF yields more consistent and accurate estimates compared to SEIF and preserves the scalability advantage over EKF, as well.
The Myxococcus xanthus lipopolysaccharide O‐antigen is required for social motility and multicellular development

The gliding bacterium Myxococcus xanthus aggregates to form spore‐filled fruiting bodies when nutrients are limiting. Defective fruiting‐body formation and sporulation result from mutations in the sasA locus, which encodes the wzm wzt wbgA (formerly rfbABC) lipopolysaccharide (LPS) O‐antigen biosynthesis genes. Mutants carrying these same sasA mutations are defective in social motility and form small glossy colonies. We report here that the developmental and motility phenotypes of four mutants each containing different Tn5 insertions in LPS O‐antigen biosynthesis genes are similar to those of the original sasA locus mutants. All of the LPS O‐antigen mutants tested exhibited defective developmental aggregation and sporulated at only 0.02–15% of the wild‐type level. In addition, all of the LPS O‐antigen mutants were determined by genetic analyses to be wild type for adventurous motility and defective in social motility, indicating that the LPS O‐antigen is necessary for normal development and social motility. The two previously identified cell‐surface components required for social motility, type IV pili and the protein‐associated polysaccharide material termed fibrils, were detected on the surfaces of all of the LPS O‐antigen mutants. This indicates that LPS O‐antigen is a third cell‐surface component required for social motility.
Evidential-Link-based Approach for Re-ranking XML Retrieval Results

We propose in this paper a new evidential link-based approach for re-ranking XML retrieval results by using the Dempster-Shafer theory of evidence to combine content relevance evidence for each retrieved XML element with its computed link evidence (score and rank). The use of the DempsterâShafer theory is motivated by the need to improve retrieval accuracy by incorporating the uncertain nature of both bodies of evidence (content and link relevance). The link score is computed according to a new link analysis algorithm based on weighted links, where relevance is propagated through the two types of links, i.e., hierarchical and navigational. The propagation, i.e. the amount of relevance score received by each retrieved XML element, depends on link weight which is defined according to two parameters: link type and link length. To evaluate our proposal we carried out a set of experiments based on INEX data collection.
MicroRNAs as Important Players in Host–Adenovirus Interactions

MicroRNAs (miRNAs) are powerful regulators of gene expression and fine-tuning genes in all tissues. Cellular miRNAs can control 100s of biologic processes (e.g., morphogenesis of embryonic structures, differentiation of tissue-specific cells, and metabolic control in specific cell types) and have been involved in the regulation of nearly all cellular pathways. Inherently to their involvement in different physiologic processes, miRNAs deregulation has been associated with several diseases. Moreover, several viruses have been described as either, avoid and block cellular miRNAs or synthesize their own miRNA to facilitate infection and pathogenesis. Adenoviruses genome encodes two non-coding RNAs, known as viral-associated (VA) RNAI and VA RNAII, which seem to play an important role either by blocking important proteins from miRNA pathway, such as Exportin-5 and Dicer, or by targeting relevant cellular factors. Drastic changes in cellular miRNA expression profile are also noticeable and several cellular functions are affected by these changes. This review focuses on the mechanisms underlying the biogenesis and molecular interactions of miRNAs providing basic concepts of their functions as well as in the interplay between miRNAs and human adenoviruses.
Repair of Marginal Eyelid Defects With 7–0 Chromic Sutures

Purpose: To report our experience using interrupted 7–0 chromic sutures to close marginal eyelid defects. Methods: A retrospective case series of patients undergoing upper or lower eyelid repair with two 7–0 chromic marginal sutures. Results: Nine upper and 22 lower eyelid defects were closed with the described technique. Elective removal was performed 9 to 27 days after surgery in 5 patients in whom the sutures either were no longer needed or had not spontaneously absorbed. There were no cases of suture-related corneal abrasion. Minimal notching was observed in 2 eyelids after surgery. Conclusions: Closure of marginal eyelid defects with 7–0 chromic sutures simplified postoperative care. There are few complications associated with this procedure, which overall provided excellent wound healing and cosmesis.
Association of a single nucleotide polymorphism at 6q25.1, rs2046210, with endometrial cancer risk among Chinese women

A recent genome-wide association study identified a new susceptibility locus for breast cancer, rs2046210, which is a single nucleotide polymorphism (SNP) located upstream of the estrogen receptor α (ESR1) gene on chromosome 6q25.1. Given that endometrial cancer shares many risk factors with breast cancer and both are related to estrogen exposure and that rs2046210 is in close proximity to the ESR1 gene, we evaluated the association of SNP rs2046210 with endometrial cancer risk among 953 cases and 947 controls in a population-based, case-control study conducted in Shanghai, China. Logistic regression models were used to derive odds ratios (ORs) and 95% confidence intervals (95% CIs) after adjusting for potential confounders. We found that the A allele of rs2046210, linked to an increased risk of breast cancer, was associated with increased but not statistically significant risk of endometrial cancer (OR = 1.16, 95% CI = 0.96-1.41 for the GA and AA genotypes compared with the GG genotype); the association was stronger among post-menopausal women (OR = 1.28, 95% CI = 1.00-1.65). The association tended to be stronger among women with higher or longer estrogen exposure than among women with relatively lower or shorter exposure to estrogen. Our study suggests that rs2046210 may play a role in the etiology of endometrial cancer. Additional studies are needed to confirm our findings.
Genetic analysis of the signalling pathway activated by external amino acids in Saccharomyces cerevisiae

The permease‐like amino acid sensor Ssy1p of Saccharomyces cerevisiae is required for transcriptional induction, in response to external amino acids, of several genes encoding peptide and amino acid permeases. Among them is AGP1 encoding a low‐affinity, broad‐specificity amino acid permease important for the utilization of amino acids as a nitrogen source. We report here data from experiments aimed at identifying components of the signalling pathway activated by Ssy1p. Overproduction of the large amino‐terminal tail of Ssy1p interferes negatively with the induction of AGP1 in wild‐type cells. Furthermore, overproduction of this domain can relieve growth defects of a ssy1 null strain, indicating that the N‐terminal tail of Ssy1p is an important functional element of the pathway. Consistent with a role for Ssy1p in the recognition of amino acids, a mutant form of the protein with a Thr to Ile substitution in the eighth predicted transmembrane domain is competent for the induction of AGP1 by leucine but not by other amino acids. In a screen for other mutants defective in the Ssy1p pathway, we confirmed that PTR3 and SSY5 encode additional factors essential for AGP1 expression in response to multiple amino acids. Data obtained by overproducing Ptr3p and Ssy5p in ssy1Δ, ptr3Δ and ssy5Δ mutants suggest that Ptr3p acts downstream from Ssy1p and Ssy5p downstream from Ptr3p in the transduction pathway. Furthermore, two‐hybrid experiments indicated that Ptr3p interacts with Ssy5p and that Ptr3p can self‐associate. Finally, the Cys‐6‐Zn2 transcription factor Uga35p/Dal81p required for the induction of AGP1 is also essential for the expression of two other genes under Ssy1p–Ptr3p–Ssy5p control, namely BAP2 and PTR2, suggesting that the protein is yet another component of the amino acid signalling pathway.
Crystal Structure of the West Nile Virus Envelope Glycoprotein

ABSTRACT The envelope glycoprotein (E) of West Nile virus (WNV) undergoes a conformational rearrangement triggered by low pH that results in a class II fusion event required for viral entry. Herein we present the 3.0-Å crystal structure of the ectodomain of WNV E, which reveals insights into the flavivirus life cycle. We found that WNV E adopts a three-domain architecture that is shared by the E proteins from dengue and tick-borne encephalitis viruses and forms a rod-shaped configuration similar to that observed in immature flavivirus particles. Interestingly, the single N-linked glycosylation site on WNV E is displaced by a novel α-helix, which could potentially alter lectin-mediated attachment. The localization of histidines within the hinge regions of E implicates these residues in pH-induced conformational transitions. Most strikingly, the WNV E ectodomain crystallized as a monomer, in contrast to other flavivirus E proteins, which have crystallized as antiparallel dimers. WNV E assembles in a crystalline lattice of perpendicular molecules, with the fusion loop of one E protein buried in a hydrophobic pocket at the DI-DIII interface of another. Dimeric E proteins pack their fusion loops into analogous pockets at the dimer interface. We speculate that E proteins could pivot around the fusion loop-pocket junction, allowing virion conformational transitions while minimizing fusion loop exposure.
Performance of a rapid phage-based test, FASTPlaqueTB, to diagnose pulmonary tuberculosis from sputum specimens in South Africa.

SETTING Twelve primary health care clinics in the South Peninsula Administration, Cape Town, Western Cape Province, South Africa. OBJECTIVE To evaluate the performance of FAST-PlaqueTB, a new phage-based test, for the rapid diagnosis of TB in individuals with no previous history of TB treatment presenting at primary health care clinics in Cape Town, South Africa. DESIGN A comparative study of FASTPlaqueTB, auramine smear microscopy and Lowenstein-Jensen culture of 1692 decontaminated sputum specimens from 853 patients suspected of having TB. Resolution of discrepant results was undertaken by review of clinical information, chest X-ray and follow-up of treatment outcomes. RESULTS FASTPlaqueTB detected TB in 75.2% of culture-confirmed cases and 70.3% of all cases with a clinical diagnosis of TB, with a specificity of 98.7% and 99.0%, respectively. The performance parameters of FASTPlaqueTB were significantly superior to those of concentrated auramine smear microscopy (63.4% and 61.3% sensitivity, and 97.4% and 97.3% specificity in culture-confirmed and all cases, respectively). Of those patients with two negative sputum smears, FAST-PlaqueTB detected TB in 54.1% of TB cases confirmed by culture and 48.8% of all cases with a clinical diagnosis of TB. A combination of smear microscopy and FASTPlaqueTB enabled 81.2% of culture-confirmed cases and 78.4% of total TB cases to be detected within 2 days of presentation. CONCLUSION FASTPlaqueTBTM is a rapid, manual test for the diagnosis of TB. The test has significantly higher sensitivity overall compared with auramine sputum smear microscopy in individuals with no previous history of TB treatment, although smear microscopy did detect the most infectious of the TB cases. The FAST-PlaqueTB test is easy to perform, requires no dedicated equipment, and results are read by eye within 48 hours. This test can be useful for the diagnosis of TB in developing countries with a high burden of TB where other rapid diagnostic tests may not be appropriate. The test shows promising performance, particularly in the diagnosis of smear-negative disease, and could be used in conjunction with smear microscopy to aid in the diagnosis of additional cases of TB.
Relation of Urinary Retention and Functional Recovery in Stroke Patients During Rehabilitation Program

Objective To investigate the relationship between urinary retention and short-term functional recovery in subacute stage after stroke. Methods The medical records of 94 patients admitted to the rehabilitation unit of Korea University Guro Hospital were reviewed retrospectively. The postvoid residual urine (PVR) was measured at least once a day using a bladder scan, and urinary retention (UR) was defined when the daily PVR volume consistently checked more than 100 mL. Clinical data and functional outcomes of patients in the rehabilitation ward were collected. Functional outcomes were measured using the Mini-Mental State Examination (MMSE), Berg Balance Scale (BBS), Functional Ambulation Category (FAC) level, Fugl-Meyer Assessment (FMA), and Modified Barthel Index (MBI) at admission (or transfer) and discharge. The data of patients with and without urinary retention were compared and analyzed. Results Of the 94 participants, 25 patients were classified to the UR group and 69 were classified to the non-UR group. At the initial stage of rehabilitation, the scores of MMSE, BBS, FAC, MBI were significantly worse in the UR group (p<0.05). Both groups showed significant improvements of all functional outcomes after rehabilitation (p<0.05). The non-UR group showed more prominent recovery of BBS, FAC, MBI scores (p<0.05). Conclusion Urinary retention in post-stroke patients is significantly related to the poor functional status at initial stage of rehabilitation, and also to poor recovery after rehabilitation.
Electrode dependence of hydrogen-induced degradation in ferroelectric Pb(Zr,Ti)O3 and SrBi2Ta2O9 thin films

Forming gas annealing causes changes in the remanent polarization (Pr), coercive field (Ec), and leakage current (I) in both PZT [Pb(Zr,Ti)O3] and SBT (SrBi2Ta2O9) samples with a variety of top electrode materials (Pt, Au, Ag, Cu, Ni, and In2O3), and the degree of degradation depends strongly on the top electrode material. These results may be explained by a model that is based on the catalytic activities of the top electrode to dissociate hydrogen molecules into hydrogen atoms, with the latter subsequently migrating into PZT or SBT films to cause oxygen deficiency and its associated property degradation. This model can be expanded to explain the recovery phenomenon resulting from oxygen annealing, which also depends on the catalytic activity of the top electrode to produce atomic oxygen from molecular oxygen.
A multihop multi-OPS optical interconnection network

In this paper, we study the design of regular multicast networks implemented with optical passive star (OPS) couplers. We focus on an architecture based on both Kautz graphs and stack-graphs, and show that it is very cost-effective with respect to its resources requirements, namely the number of OPS couplers, power budget, scalability and number of transceivers, and presents a large ratio number-of-nodes/diameter. The important issue of medium access control is also addressed and control protocol for accessing the optical couplers are given and analyzed. Finally, we show through simulation that these control protocols efficiently implement shortest path routing on these networks.