gebhart/patrepeval huggingface dataset:
Temporomandibular joint growth adaptation in Herbst treatment: a prospective magnetic resonance imaging and cephalometric roentgenographic study (1998)

The aim of this investigation was to analyze three possible adaptive TMJ growth processes contributing to the increase in mandibular prognathism accomplished by Herbst appliance therapy: (1) condylar remodeling; (2) glenoid fossa remodeling; and (3) condyle-fossa relationship changes. The subjects were 15 consecutive Class II malocclusions (11 males and four females, aged 11.5-17.5 years) treated with the Herbst appliance for an average period of 7 months. Condylar remodelling, glenoid fossa remodelling, and condyle-fossa relationship changes were analyzed by means of magnetic resonance imaging (MRI). From each subject, four MR images were evaluated: before treatment, start of treatment (when the Herbst appliance was placed), during treatment (6-12 weeks after appliance placement), and after treatment (when the appliance was removed). 'Effective condylar growth' (= the sum of condylar remodelling, fossa remodelling, and condyle-fossa relationship changes) was analyzed with the aid of pre- and post-treatment lateral cephalometric roentgenograms. In all 15 subjects, Herbst therapy resulted in an increase in mandibular prognathism. After 6-12 weeks of treatment MRI-signs of condylar remodelling were seen at the posterior-superior border in 29 of the 30 condyles. MRI-signs of glenoid fossa remodelling at the anterior surface of the postglenoid spine were noted in 22 of the joints. Condylar remodelling seemed to precede fossa remodelling. The condyle-fossa relationship was, on average unaffected by Herbst therapy. 'Effective condylar growth' during treatment was, on average, approximately five times larger in the Herbst group than in an untreated group with ideal occlusion (Bolton Standards) and the direction of the growth changes was relatively more horizontal in the treated cases. The results indicate that condylar as well as glenoid fossa remodelling seem to contribute significantly to the increase in mandibular prognathism resulting from Herbst treatment, while condyle-fossa relationship changes are of less importance. MRI renders an excellent opportunity to visualize temporomandibular remodelling growth processes.
Design, fabrication, and performance of infrared and visible vertical-cavity surface-emitting lasers (1997)

This paper discusses the issues involving the design and fabrication of vertical-cavity surface-emitting lasers (VCSELs). A review of the basic experimental structures is given, with emphasis on recent developments in distributed Bragg reflectors, gain media, as well as current and optical confinement techniques. The paper describes present VCSEL performance, in particular, those involving selective oxidation and visible wavelength operation.
Utility of Nocturnal Home Oximetry for Case Finding in Patients with Suspected Sleep Apnea Hypopnea Syndrome (1993)

A negative home oximetry test result is helpful in ruling out the diagnosis of SAHS in patients clinically suspected of having this syndrome, because a negative test result reduced the probability from 54.1% to 3.1% in our patients. However, a positive oximetry test increased the probability from 46% to 61.4% in our group of patients.
The Kunitz 1 and Kunitz 3 domains of tissue factor pathway inhibitor are required for efficient inhibition of factor Xa (2012)

Tissue factor pathway inhibitor (TFPI) is a slow tight-binding inhibitor that inhibits factor (F)Xa in a biphasic fashion: a rapid formation of loose FXa·TFPI encounter complex is followed by slow rearrangement into a tight FXa·TFPI* complex in which the Kunitz-2 (K2) domain of TFPI binds and inhibits FXa. In the current study, full-length TFPI (TFPIfl) and various truncated TFPI constructs were used to assess the importance of TFPI domains other than K2 in the inhibition of FXa. In the absence of Ca2+ ions, FXa was more effectively inhibited by TFPIfl than Gla-domain less FXa. In turn, Ca2+ ions impaired FXa inhibition by TFPIfl but not by TFPI constructs that lack the C-terminus. This suggests that, in absence of Ca2+ ions, interactions between the C-terminus of TFPI and the Gla-domain of FXa promote FXa-inhibition. TFPIfl and K2K3 had similar efficiencies for encounter complex formation. However, K2K3 showed monophasic inhibition instead of biphasic inhibition, indicating absence of rearrangement into a tight complex. K1K2 and TFPI1-161 showed biphasic inhibition, but had less efficient encounter complex formation than TFPIfl. Finally, K2K3 was a 10-fold more efficient FXa- inhibitor than K2. These results indicate that K3-C-terminus enhances the formation of encounter complex and that K1 is required for isomerisation of the encounter- into tight complex. Since TFPIfl has a 10-fold higher Ki than K2K3-C-terminus, we propose that K1 is not only required for the transition of the loose to the tight FXa·TFPI* complex, but also inhibits FXa·TFPI encounter complex formation. This inhibitory activity is counteracted by K3 and C-terminus.
Synthesis of Crown Ethers Related to Ubiquinones (1993)

Crown ethers in which the two methoxy groups of ubiquinone-0 (2,3-dimethoxy-5-methyl-1, 4-benzoquinone) are replaced by oligoethylene glycol bridges have been obtained in five straightforward steps in 35-40% overall yield from 5-methylpyrogallol. A Fremy salt oxidation of a phenolic precursor is used in the final step. The further elaboration of crown ether analogues of ubiquinone-2 was achieved by enol geranylation of cyclopentadiene adducts of the former quinones and subsequent retro-Diels-Alder reaction. The Claisen rearrangement of 2, 2-dimethoxy-5-methylphenyl allyl ethers and related crown ethers affords ortho- and para-allyl-substituted phenols (3: 1) that are oxidized to give bisnorubiquinone derivatives and their ortho- quinone isomers. All new compounds are characterized by high resolution NMR and mass spectrometry.
Role of heparan sulfate proteoglycans in the binding and uptake of apolipoprotein E-enriched remnant lipoproteins by cultured cells (1993)

Addition of apolipoprotein (apo) E to rabbit beta-very low density lipoproteins (beta-VLDL) has been shown to result in a marked enhancement of their binding and uptake by various cell types. Apolipoprotein E binds to lipoprotein receptors and proteoglycans. To distinguish between apoE binding to these sites, cells were treated with heparinase. Heparinase treatment of receptor-negative familial hypercholesterolemic (FH) fibroblasts and human hepatoma cells (HepG2) released 30-40% of newly synthesized cell surface 35S-labeled proteoglycans and decreased the binding of beta-VLDL+apoE to FH and normal fibroblasts and HepG2 cells by more than 80%. Furthermore, heparinase treatment significantly decreased the uptake of fluorescently labeled beta-VLDL+apoE by HepG2 cells and decreased cholesteryl ester synthesis in FH fibroblasts by 75%. Likewise, canine chylomicron remnants enriched in apoE demonstrated enhanced binding that was 80% inhibited by heparinase treatment of HepG2 cells. Heparinase treatment did not affect beta-VLDL (without added apoE) or low density lipoprotein (LDL) binding to these cells or the binding activity of beta-VLDL+apoE to the LDL receptor-related protein (LRP) or to the LDL receptor on ligand blots. Chinese hamster ovary (CHO) mutant cells lacking the synthesis of either heparan sulfate (pgsD-677) or all proteoglycans (pgsA-745) did not display any enhanced binding of the beta-VLDL+apoE. By comparison, wild-type CHO cells demonstrated enhanced binding of beta-VLDL+apoE that could be abolished by treatment with heparinase. These mutant cells and wild-type CHO cells possessed a similar amount of LRP, as determined by ligand blot analyses and by alpha 2-macroglobulin binding, and possessed a similar amount of LDL receptor activity, as determined by LDL binding. Therefore, we would interpret these data as showing that heparan sulfate proteoglycan may be involved in the initial binding of the apoE-enriched remnants with the subsequent involvement of the LRP in the uptake of these lipoproteins. It remains to be determined whether the heparan sulfate proteoglycan can function by itself in both the binding and internalization of the apoE-enriched remnants or whether the proteoglycan is part of a complex with LRP that mediates a two-step process, i.e. binding and subsequent internalization by the receptor.
Temperature-dependent expression of virulence genes in Shigella species (1984)

The pathogenicity of Shigella spp. involves the ability of the bacteria to penetrate and replicate within the epithelial cells of the large intestine. Model systems for examining the virulence of shigellae employ Henle intestinal epithelial cells in tissue culture and an in vivo assay for virulence in guinea pig eyes (Sereny test). Using these systems, we studied the genetic and physiological bases for the ability of shigellae to invade epithelial cells. We found that expression of virulence in Shigella spp. is dependent on the temperature at which the bacteria are grown. When grown at 37 degrees C, strains of Shigella flexneri 2a, Shigella sonnei, and Shigella dysenteriae 1 were fully virulent and invaded Henle cells. They also produced keratoconjunctivitis in guinea pigs. When grown at 30 degrees C, the bacteria neither penetrated Henle cells nor produced conjunctivitis in the Sereny test and were phenotypically avirulent. Strains grown at 33 degrees C were only partially invasive in the Henle assay, whereas strains grown at 35 degrees C were as invasive as strains grown at 37 degrees C. Using the Henle cell assay, we determined that the loss of ability to penetrate epithelial cells was completely reversed by shifting the growth temperature from 30 to 37 degrees C. The percentage of Henle cells invaded by bacteria increased with increasing time of growth at 37 degrees C. Restoration of invasiveness after growth at 30 degrees C required protein synthesis. When shigellae were grown at 30 degrees C and shifted to 37 degrees C for 2 h in the presence of chloramphenicol, the bacteria remained noninvasive. Similarly treated bacteria grown at 37 degrees C were still invasive. These results suggested that expression of one or more genes required for virulence of Shigella spp. are subject to regulation by growth temperature.
Generation of inducible Cre systems for conditional gene inactivation in mice (2004)

Inducible gene targeting based on the Cre/loxP system is a novel technique allowing conditional gene modification in mice. Precondition of this method is the regulation of Cre activity by inducible genetic switches. This study aimed at improving inducible systems for the regulation of Cre activity at both the transcriptional and the posttranslational level, which should be tested first in vitro and subsequently in newly generated transgenic mice. In order to detect Cre activity, a special double indicator consisting of DsRed and eGFP was constructed and targeted into the ROSA26 locus of HM-1 ES cells. This indicator should constitutively express the DsRed gene flanked by loxP sites. Cre-mediated recombination excises the DsRed gene and turns on the eGFP gene, as evidenced by a change in fluorescence from red to green. Though the double indicator worked properly in transiently transfected fibroblasts, the targeting strategy used for the integration of the indicator into the ROSA26 locus presumably disrupted a putative stem loop motif of the 5'UTR resulting in a silencing of the indicator at the protein level. However, the ES cell line with the integrated double indicator is suited for targetings of inducible Cre constructs into the HPRT locus, since inducibilities are detectable by Southern Blot analysis. The Cre*PR system was one inducible system I have established. In contrast to the classical CrePR1 system, the background activity of Cre*PR was almost abolished by introducing a point mutation into the 3'end of the Cre part, thus preventing aberrant splicing of the Cre*PR encoding mRNA. Also, the PR-LBD of the Cre*PR system was improved, compared to the CrePR1, to obtain a higher affinity towards the inducer RU486. The Cre*PR system, driven by either the EF1£\\ promoter or the CAGGS promoter, was then targeted into the HPRT locus. The CAGGS Cre*PR worked in ES cells as expected. These targeted ES cells were subsequently used to generate transgenic mice. In these mice, high protein levels of Cre*PR have to be obtained in order to achieve inducible Cre-mediated excision of loxP-flanked gene segments. In addition, I generated a novel B cell specific Cre*PR mouse strain by targeting Cre*PR into the mCD19 locus. In another approach to inducibly regulate Cre, a tet-on system was established consisting of the rtTA-M2 transactivator and the tetresponsive Cre cassette, which was targeted into the HPRT locus of the double indicator ES cell line. This system revealed a tight regulation of Cre expression in a doxycycline dependent manner.
Segmenting Characters from License Plate Images with Little Prior Knowledge (2010)

In this paper, to enable a fast and robust system for automatically recognizing license plates with various appearances, new and simple but efficient algorithms are developed to segment characters from extracted license plate images. Our goal is to segment characters properly from a license plate image region. Different from existing methods for segmenting degraded machine-printed characters, our algorithms are based on very weak assumptions and use no prior knowledge about the format of the plates, in order for them to be applicable to wider applications. Experimental results demonstrate promising efficiency and flexibility of the proposed scheme.
Culturing the Unculturable: Human Coronavirus HKU1 Infects, Replicates, and Produces Progeny Virions in Human Ciliated Airway Epithelial Cell Cultures (2010)

Culturing newly identified human lung pathogens from clinical sample isolates can represent a daunting task, with problems ranging from low levels of pathogens to the presence of growth suppressive factors in the specimens, compounded by the lack of a suitable tissue culture system. However, it is critical to develop suitable in vitro platforms to isolate and characterize the replication kinetics and pathogenesis of recently identified human pathogens. HCoV-HKU1, a human coronavirus identified in a clinical sample from a patient with severe pneumonia, has been a major challenge for successful propagation on all immortalized cells tested to date. To determine if HCoV-HKU1 could replicate in in vitro models of human ciliated airway epithelial cell cultures (HAE) that recapitulate the morphology, biochemistry, and physiology of the human airway epithelium, the apical surfaces of HAE were inoculated with a clinical sample of HCoV-HKU1 (Cean1 strain). High virus yields were found for several days postinoculation and electron micrograph, Northern blot, and immunofluorescence data confirmed that HCoV-HKU1 replicated efficiently within ciliated cells, demonstrating that this cell type is infected by all human coronaviruses identified to date. Antiserum directed against human leukocyte antigen C (HLA-C) failed to attenuate HCoV-HKU1 infection and replication in HAE, suggesting that HLA-C is not required for HCoV-HKU1 infection of the human ciliated airway epithelium. We propose that the HAE model provides a ready platform for molecular studies and characterization of HCoV-HKU1 and in general serves as a robust technology for the recovery, amplification, adaptation, and characterization of novel coronaviruses and other respiratory viruses from clinical material.
The DeLey-Doudoroff Pathway of Galactose Metabolism in Azotobacter vinelandii (1994)

Azotobacter vinelandii cell extracts reduced NAD and oxidized d-galactose to galactonate that subsequently was converted to 2-keto-3-deoxy-galactonate. Further metabolism of 2-keto-3-deoxy-galactonate required the presence of ATP and resulted in the formation of pyruvate and glyceraldehyde 3-P. Radiorespirometry indicated a preferential release of CO(2) at the first carbon position of the d-galactose molecule. This suggested that Azotobacter vinelandii metabolizes d-galactose via the DeLey-Doudoroff pathway. The first enzyme of this pathway, d-galactose dehydrogenase, was partially characterized. It has a molecular weight of about 74,000 Da and an isoelectric point of 6.15. The pH optimum of the galactose dehydrogenase was about 9. The apparent K(m)s for NAD and d-galactose were 0.125 and 0.56 mM, respectively. Besides d-galactose, the active fraction of this galactose dehydrogenase also oxidized l-arabinose effectively. The electron acceptor for d-galactose or l-arabinose oxidation, NAD, could not be replaced by NADP. These substrate specificities were different from those reported in Pseudomonas saccharophila, Pseudomonas fluorescens, and Rhizobium meliloti.
Extraintestinal PathogenicEscherichia coli, a Common Human Pathogen: Challenges for Vaccine Development and Progress in the Field (2015)

Extraintestinal pathogenic Escherichia coli (ExPEC) is the most common gram-negative bacterial pathogen in humans. ExPEC causes the vast majority of urinary tract infections (UTIs), is a leading cause of adult bacteremia, and is the second most common cause of neonatal meningitis. Increasing multidrug resistance among ExPEC strains constitutes a major obstacle to treatment and is implicated in increasing numbers of hospitalizations and deaths and increasing healthcare costs associated with ExPEC infections. An effective vaccine against ExPEC infection is urgently needed. The O antigen, a component of the surface lipopolysaccharide, has been identified as a promising vaccine target. With the availability of a novel bioconjugation technology it is expected that multivalent O antigen conjugate vaccines can be produced at industrial scale. Clinical proof of concept of a 4-valent O antigen conjugate vaccine is ongoing. An ExPEC vaccine effective against strains that are associated with major diseases and resistant to multiple drugs could be routinely delivered to individuals at risk of developing severe E. coli infection, such as elderly people, individuals undergoing abdominal surgery and prostatic biopsy procedures, and persons at risk of recurrent and/or complicated UTI.
A Subjective Review of Compaction (1985)

Compaction is the CAD tool used to pack rough sketches or symbolic diagrams to produce IC layouts. Manual compaction is tedious, time-consuming, and error-prone; automated compaction tools can greatly shorten the layout design cycle. This paper reviews the historical background and the major developments in the field of compaction, emphasizing subjective evaluations rather than objective descriptions. The major approaches covered are constraint-graph, shear-line, and virtual-grid. Various ideas for further reducing chip area (such as inserting jog points, shortening wires, dense packing, 2-D compaction, and interactive tools) are also discussed. Because of the critical role of efficient algorithms in VLSI CAD systems, analyses of computational complexities are also included.
Symmetry of projection in the quantitative analysis of mammographic images (1996)

Mammographic parenchymal patterns are among the strongest indicators of the risk of developing breast cancer. Risk evaluation through breast patterns may have an important role in studies of the aetiology of breast cancer and for monitoring changes in the breast in evaluating potential risk-modifying interventions. Typically, patterns are assessed by an experienced radiologist according to Wolfe grade, or on a coarse quantitative scale according to percent density. Parenchymal characterization methods, to overcome variability of classification by human observer, are under investigation. These include image segmentation using semi-automatic thresholding and automatic classification through textural and density measures. An important practical question relates to the extent to which information about mammographic pattern is carried by any one of the four views obtained in a typical examination. Specifically, variations of right-left breast symmetry and variations between the two standard views of each breast were tested. The mammograms of 30 premenopausal women, comprising 90 images [30 each of the right cranial-caudal (RCC), left cranial-caudal (LCC) and right medial-lateral oblique (RMLO)] were evaluated. Parameters included both subjective (radiologist classification and interactive image thresholding) and objective (fractal and skewness indices) quantitative measurements of parenchymal pattern. For the parameters tested, a high degree of correlations was observed for measurements on the RCC, LCC and RMLO views. Pearson correlation coefficients between 0.86-0.96 were found for the comparisons of quantitative parameters. The strong correlations suggest that, in the study and application of mammographic density classification, representative information is provided in a single view.
Chronic sinusitis refractory to standard management in patients with humoral immunodeficiencies (1997)

Chronic refractory sinusitis is a common feature in patients with primary immunodeficiencies. The efficacy of standard therapeutic strategies is questionable. In an open trial we evaluated the efficacy of azithromycin, N-acetylcysteine and topical intranasal beclomethasone (100 microg twice daily for 6 weeks) in 16 patients with primary immunodeficiencies (median age 13.5 years, range 5-32 years). All patients suffered from chronic sinusitis despite regular immunoglobulin replacement therapy every 3 weeks. Magnetic resonance imaging (MRI) scans were performed before and after 6 weeks of treatment to evaluate morphological changes in the paranasal sinuses. Nasal swabs and washings were taken for microbial analysis and measurement of inflammatory mediators (IL-8, tumour necrosis factor-alpha (TNF-alpha), eosinophilic cationic protein (ECP)) before and post therapy. Inflammatory mediators in nasal secretions were significantly elevated in patients: IL-8 median 2436 pg/ml (range 441-5435 pg/ml), TNF-alpha 37.3 pg/ml (3.75-524 pg/ml) and ECP 33 ng/ml (1.5-250 ng/ml) versus age-matched healthy controls: IL-8 median 212 pg/ml (99-825 pg/ml), TNF-alpha 3.77 pg/ml (2.8-10.2 pg/ml) and ECP 1.5 ng/ml (1.5-14.8 ng/ml) (P < 0.0001). Inflammation of the maxillary sinuses was confirmed by MRI scans in all patients, additionally infection of the ethmoidal and frontal sinuses was recorded in five patients. Bacterial growth appeared in 11 out of 16 cultures. In spite of therapy, no improvement in sinal inflammation visualized by MRI was achieved. Moreover, no significant decrease in pathogens and levels of inflammatory mediators could be detected (IL-8 1141 pg/ml, 426-4556 pg/ml; TNF-alpha 13.9 pg/ml, 4.1-291.6 pg/ml; ECP 32.3 ng/ml, 3.7-58.4 ng/ml). Our results demonstrate that conventional management of sinusitis is of little benefit in patients with chronic refractory sinusitis with an underlying immunodeficiency. More studies are needed to test antibiotic regimens, probably combined with surgical drainage and anti-inflammatory agents.
Relationship between the Structures of Taxane Derivatives and Their Microtubule Polymerization Activity (2012)

Paclitaxel (Taxol), one of the most potent anticancer drugs, is a microtubule-stabilizing compound that inhibits microtubule depolymerization within the cell. The structure of paclitaxel is composed of two key elements, a taxane ring and an N-benzoylphenylisoserine side chain at C-13. A number of natural and artificial compounds with taxane skeletons have been isolated, but almost none of their bioactivities have been evaluated. In this study, we focused on compounds having a taxane skeleton structure and examined their effects on tubulin dynamics. Although none of these compounds had an N-benzoylphenylisoserine side chain, three were found to promote tubulin assembly. On the other hand, one compound inhibited tubluin assembly in a way similar to nocodazole. These compounds exhibited novel structureactivity relationships of taxane compounds.