gebhart/patrepeval huggingface dataset:
The 2.8 Å Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a Heparinoid Pentasaccharide (2017)

Atomic structures of adeno-associated virus (AAV)-DJ, alone and in complex with fondaparinux, have been determined by cryoelectron microscopy at 3 Å resolution. The gene therapy vector, AAV-DJ, is a hybrid of natural serotypes that was previously derived by directed evolution, selecting for hepatocyte entry and resistance to neutralization by human serum. The structure of AAV-DJ differs from that of parental serotypes in two regions where neutralizing antibodies bind, so immune escape appears to have been the primary driver of AAV-DJ's directed evolution. Fondaparinux is an analog of cell surface heparan sulfate to which several AAVs bind during entry. Fondaparinux interacts with viral arginines at a known heparin binding site, without the large conformational changes whose presence was controversial in low-resolution imaging of AAV2-heparin complexes. The glycan density suggests multi-modal binding that could accommodate sequence variation and multivalent binding along a glycan polymer, consistent with a role in attachment, prior to more specific interactions with a receptor protein mediating entry.
The Relative Contribution of Ehrlich and Biosynthetic Pathways to the Formation of Fusel Alcohols (1978)

Ale yeast fermentations were carried out at 20° C with defined media containing a mixture of amino acids totaling 225 mg/L. Radioactive substrates were added individually to the media prior to the fermentation: The resultant beer alcohols were fractionated and their radioactivities were measured. When [14C(U)] glucose was used, 97.7% of the radioactivity acquired by beer alcohols was recovered in the ethanol fraction while the remaining 2.3% was distributed in the four fusel alcohols. When [14C(U)] threonine was added to fermentation media, 30% (on molar basis) of the resultant n-propanol became radioactive. This means that, under the experimental conditions used, the contribution of Ehrlich pathway to the formation of n-propanol is 30%. Similarly, when [14C(U)]-labeled valine, isoleucine, or leucine was used as tracer, the contribution of Ehrlich pathway to the formation of isobutanol, 2-methyl-1-butanol and 3-methyl-1-butanol was found to be 34%, 75%, and 80%, respectively. The results clearly indicate that the relative contributions of the Ehrlich and biosynthetic pathways vary with each fusel alcohol. In another experiment, [14C(U)] glucose was paired with tritiated threonine, valine, isoleucine, and leucine in dual-labeled fermentations. Results obtained also indicate that glucose utilization for the formation of fusel alcohols is relatively small and that the contribution of biosynthetic pathway decreases as the number of carbon atoms in fusel alcohol molecules increases. The application of dual label tracer technique in the present study was discussed. Methods for improving the recovery efficiency of the radioactive materials were suggested.
The SH Integral Membrane Protein of the Paramyxovirus Simian Virus 5 Is Required To Block Apoptosis in MDBK Cells (2001)

In some cell types the paramyxovirus simian virus 5 (SV5) causes little cytopathic effect (CPE) and infection continues productively for long periods of time; e.g., SV5 can be produced from MDBK cells for up to 40 days with little CPE. SV5 differs from most paramyxoviruses in that it encodes a small (44-amino-acid) hydrophobic integral membrane protein (SH). When MDBK cells were infected with a recombinant SV5 containing a deletion of the SH gene (rSV5DeltaSH), the MDBK cells exhibited an increase in CPE compared to cells infected with wild-type SV5 (recovered from cDNA; rSV5). The increased CPE correlated with an increase in apoptosis in rSV5DeltaSH-infected cells over mock-infected and rSV5-infected cells when assayed for annexin V binding, DNA content (propidium iodide staining), and DNA fragmentation (terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling assay). In rSV5DeltaSH-infected MDBK cells an increase in caspase-2 and caspase-3 activities was observed. By using peptide inhibitors of individual caspases it was found that caspase-2 and caspase-3 were activated separately in rSV5DeltaSH-infected cells. Expression of caspase-2 and -3 in rSV5DeltaSH-infected MDBK cells appeared not to require STAT1 protein, as STAT1 protein could not be detected in SV5-infected MDBK cells. When mutant mice homologous for a targeted disruption of STAT1 were used as a model animal system and infected with the viruses it was found that rSV5DeltaSH caused less mortality than wild-type rSV5, consistent with the notion of clearance of apoptotic cells in a host species.
PML in a Patient with Lymphocytopenia Treated with Dimethyl Fumarate (2015)

The authors report a fatal case of progressive multifocal leukoencephalopathy in a 54-year-old woman in whom lymphocytopenia developed after treatment with delayed-release dimethyl fumarate for multiple sclerosis.
A retrieval technique for similar shapes (1991)

article Free Access Share on A retrieval technique for similar shapes Author: H. V. Jagadish AT&T Bell Laboratories, Murray Hill, New Jersey AT&T Bell Laboratories, Murray Hill, New JerseyView Profile Authors Info & Claims ACM SIGMOD RecordVolume 20Issue 2June 1991 pp 208–217https://doi.org/10.1145/119995.115821Published:01 April 1991Publication History 176citation1,077DownloadsMetricsTotal Citations176Total Downloads1,077Last 12 Months31Last 6 weeks6 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
The Synthesis and Pharmacologic Evaluation of a Series of 8-Alkylthio-Thiated Theophyllines1 (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Synthesis and Pharmacologic Evaluation of a Series of 8-Alkylthio-Thiated Theophyllines1Albert J. Dietz Jr. and Raymond M. BurgisonCite this: J. Med. Chem. 1966, 9, 4, 500–506Publication Date (Print):July 1, 1966Publication History Published online1 May 2002Published inissue 1 July 1966https://pubs.acs.org/doi/10.1021/jm00322a013https://doi.org/10.1021/jm00322a013research-articleACS PublicationsRequest reuse permissionsArticle Views129Altmetric-Citations9LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Evaluation of the Xpert Methicillin-Resistant Staphylococcus aureus (MRSA) Assay Using the GeneXpert Real-Time PCR Platform for Rapid Detection of MRSA from Screening Specimens (2008)

The need for rapid methods to accurately detect methicillin-resistant Staphylococcus aureus (MRSA) is widely acknowledged, and a number of molecular assays are commercially available. This study evaluated the Xpert MRSA assay, which is run on the GeneXpert real-time PCR platform (Cepheid) for use in a clinical laboratory. The following parameters were investigated: (i) the limits of detection (LoDs) for four MRSA strains; (ii) the ability to detect isolates of MRSA from a collection representative of MRSA in Ireland since 1974 (n = 114) and the ability to detect control strains with staphylococcal cassette chromosome mec types IVa (IV.1.1.1), IVb (IV.2.1.1), IVc (IV.3.1.1), IVd (IV.4.1.1), V (V.1.1.1), V(T), and VI; and (iii) performance in a clinical trial with swabs from nose, throat, and groin/perineum sites from 204 patients, where results were compared with those obtained by direct and enrichment cultures. The average LoD of the four test strains was 610 CFU/ml (equivalent to 58 CFU/swab). All 114 MRSA isolates and 7 control strains tested were detected. Sensitivity, specificity, and positive and negative predictive values for clinical specimens from all sites investigated were 90%, 97%, 86%, and 98%, respectively, but throat specimens yielded poor sensitivity (75%). Sensitivity, specificity, and positive and negative predictive values for nasal specimens were 95%, 98%, 90%, and 99%, respectively. Overall, the assay was rapid and easy to perform, but performance might be enhanced by the inclusion of an equivocal interpretive category based on analysis of all available amplification data.
Regional and Voxel‐Wise Comparisons of Blood Flow Measurements Between Dynamic Susceptibility Contrast Magnetic Resonance Imaging (DSC‐MRI) and Arterial Spin Labeling (ASL) in Brain Tumors (2012)

The objective of the current study was to evaluate the regional and voxel-wise correlation between dynamic susceptibility contrast (DSC) and arterial spin labeling (ASL) perfusion magnetic resonance imaging (MRI) measurement of cerebral blood flow (CBF) in patients with brain tumors. Thirty patients with histologically verified brain tumors were evaluated in the current study. DSC-MRI was performed by first using a preload dose of gadolinium contrast, then collecting a dynamic image acquisition during a bolus of contrast, followed by posthoc contrast agent leakage correction. Pseudocontinuous ASL was collected using 30 pairs of tag and control acquisition using a 3-dimensional gradient-echo spin-echo (GRASE) acquisition. All images were registered to a high-resolution anatomical atlas. Average CBF measurements within regions of contrast-enhancement and T2 hyperintensity were evaluated between the two modalities. Additionally, voxel-wise correlation between CBF measurements obtained with DSC and ASL were assessed. Results demonstrated a positive linear correlation between DSC and ASL measurements of CBF when regional average values were compared; however, a statistically significant voxel-wise correlation was only observed in around 30-40% of patients. These results suggest DSC and ASL may provide regionally similar, but spatially different measurements of CBF.
Clinicopathological and prognostic significance of programmed cell death ligand1 (PD-L1) expression in patients with non-small cell lung cancer: a meta-analysis. (2015)

Our meta-analysis indicated PD-L1 protein expression in NSCLC was not associated with common clinicopathological characteristics, except tumor differentiation. It was a poor prognostic biomarker for NSCLC. Further research should be performed to investigate the precise clinicopathological and prognostic significance of PD-L1 in NSCLC under uniform testing standard.
Exploiting motion priors in visual odometry for vehicle-mounted cameras with non-holonomic constraints (2011)

This paper presents a new method to estimate the relative motion of a vehicle from images of a single camera. The biggest problem in visual motion estimation is data association; matched points contain many outliers that must be detected and removed so that the motion can be estimated accurately. A very established method for robust motion estimation in the presence of outliers is the five-point RANSAC algorithm. Five-point RANSAC operates by generating motion hypotheses from randomly-sampled minimal sets of five-point correspondences. These hypotheses are then tested against all data points and the motion hypothesis that after a given number of iterations returns the largest number of inliers is taken as the solution to the problem. A typical drawback of RANSAC is that the number of iterations required to find a suitable solution grows exponentially with the number of outliers, often requiring thousands of iterations for typical data from urban environments. Another problem is that - due to its random nature - sometimes the found solution is not the “best” solution to the motion estimation problem. In this paper, we describe an algorithm for relative motion estimation in the presence of outliers, which does not rely on RANSAC. Contrary to RANSAC, motion hypotheses are not generated from randomly-sampled point correspondences, but from a “proposal distribution” that is built by exploiting the vehicle non-holonomic constraints. We show that not only is the proposed algorithm significantly faster than RANSAC, but that the returned solution may also be better in that it favors the underlying motion model of the vehicle, thus overcoming the typical limitations of RANSAC. Additionally, the proposed algorithm provides the likelihood of the motion estimate, which can be very useful in all those applications where a probability distribution of the position of the vehicle is required (e.g., SLAM). Finally, the performance of the proposed method is compared to that of the standard five-point RANSAC on real images collected from a vehicle moving in a cluttered, urban environment.
Concise Review: Scientific and Ethical Roadblocks to Human Embryonic Stem Cell Therapy (2006)

Despite the identified therapeutic potential of embryonic stem cells for treating human disease and injury, a number of roadblocks, scientific and ethical, stand in the way of progress toward this goal. We identify six areas of particular interest: tumorigenicity, animal product contamination, genetic compatibility, funding, cell type for transplantation, "embryo-friendly" derivation methods and discuss avenues for moving beyond the difficulties.
13-cis-Retinoic Acid in the Treatment of Oral Leukoplakia (1986)

13-cis-Retinoic acid has been reported to be effective in treating oral leukoplakia. We randomly assigned 44 patients with this disease to receive 13-cis-retinoic acid (24 patients) or placebo (20), 1 to 2 mg per kilogram of body weight per day for three months, and followed them for six months. There were major decreases in the size of the lesions in 67 percent (16 patients) of those given the drug and in 10 percent (2 patients) of those given placebo (P = 0.0002); dysplasia was reversed in 54 percent (13 patients) of the drug group and in 10 percent (2 patients) of the placebo group (P = 0.01). The clinical response to the drug correlated with the histologic response in 56 percent (9 of 16) of the patients evaluated. Relapse occurred in 9 of 16 patients two to three months after treatment ended. The toxic effects of the drug were acceptable in all but two patients. Cheilitis, facial erythema, and dryness and peeling of the skin were common; conjunctivitis and hypertriglyceridemia also occurred. All adverse reactions could be reversed by reducing the dose or temporarily discontinuing the drug. We conclude that 13-cis-retinoic acid, even in short-term use, appears to be an effective treatment for oral leukoplakia and has an acceptable level of toxicity.
Neurotoxicity of intraventricularly administered alpha-interferon for leptomeningeal disease (1991)

Nine patients with leptomeningeal disease are reported who were treated with intraventricular alpha-interferon (alpha-IFN). In seven of these patients, a progressive vegetative state developed during treatment. The patients became unresponsive to verbal commands but opened their eyes with auditory or tactile stimulation. It took an average of 3 weeks for these patients to become verbally responsive after treatment was discontinued. Electroencephalographic findings showed evidence of irritative involvement of the deep midline nuclei in 80% of patients. Periventricular white matter changes developed during treatment in three of six patients who underwent computed tomographic scans. All patients with this severe neurotoxicity received whole-brain irradiation before treatment. Possible mechanisms for the development of this neurotoxic syndrome are discussed. The neurotoxicity of alpha-IFN and brain irradiation may be additive, suggesting a cautious approach when using this combination for treatment.
Residue Gln-30 of human erythrocyte anion transporter is a prime site for reaction with intrinsic transglutaminase. (1994)

Elevating the intracellular concentration of Ca2+ ions in human erythrocytes leads to the formation of membrane-associated polymers, composed of skeletal and cytoplasmic proteins. The anion transporter band 3 serves as a membrane anchor for this N epsilon-(gamma-glutamyl)lysine cross-linked polymer. The reaction is catalyzed by an intrinsic transglutaminase, and it can be observed in broken cells merely by the addition of Ca2+. Certain primary amines, such as dansylcadaverine, inhibit the process by virtue of competition against the epsilon-lysyl or donor functionalities of the protein substrates. Dansylcadaverine itself becomes incorporated into the enzyme-specific gamma-glutaminyl or acceptor residues, blocking these from participating in the formation of protein-to-protein cross-links. This labeling procedure, coupled with an anti-dansyl antibody affinity procedure to isolate dansyl-labeled compounds, was employed to identify Gln-30 as the preferred transglutaminase-reactive acceptor site in the band 3 protein.
Association of CYP2C9*2 With Bosentan-Induced Liver Injury (2013)

Bosentan (Tracleer) is an endothelin receptor antagonist prescribed for the treatment of pulmonary arterial hypertension (PAH). Its use is limited by drug-induced liver injury (DILI). To identify genetic markers of DILI, association analyses were performed on 56 Caucasian PAH patients receiving bosentan. Twelve functional polymorphisms in five genes (ABCB11, ABCC2, CYP2C9, SLCO1B1, and SLCO1B3) implicated in bosentan pharmacokinetics were tested for associations with alanine aminotransferase (ALT), aspartate aminotransferase (AST), and DILI. After adjusting for body mass index, CYP2C9*2 was the only polymorphism associated with ALT, AST, and DILI (β = 2.16, P = 0.024; β = 1.92, P = 0.016; odds ratio 95% CI = 2.29-∞, P = 0.003, respectively). Bosentan metabolism by CYP2C9*2 in vitro was significantly reduced compared with CYP2C9*1 and was comparable to that by CYP2C9*3. These results suggest that CYP2C9*2 is a potential genetic marker for prediction of bosentan-induced liver injury and warrants investigation for the optimization of bosentan treatment.
Cranial nerve modulation of human cortical swallowing motor pathways (1997)

Animal data indicate that cortical swallowing pathways can be modulated by cranial nerve afferent stimulation. We therefore studied the effects of human trigeminal and vagal nerve excitation on the corticofugal pathways to the oropharynx and esophagus, using electromagnetic stimulation. Unilateral stimulation of either the trigeminal or vagus nerve evoked two distinct reflex electromyographic responses in the pharynx and esophagus, an early response (latency range 19-30 ms) and a late response (latency range 42-72 ms). In the mylohyoid muscles, however, only a single response was seen (latency range 36-64 ms). Cortical stimulation also evoked electromyographic responses in the mylohyoid muscles, pharynx, and esophagus, with latencies of 8.5 +/- 0.3, 9.3 +/- 0.3, and 10.1 +/- 0.4 ms, respectively. When either trigeminal or vagus nerve stimulation preceded cortical stimulation, the cortically evoked responses were facilitated, with maximal effects at interstimulation intervals of 30-200 ms for pharynx and esophagus (P < 0.02) and at interstimulation intervals of 50-100 ms for mylohyoid muscles (P < 0.05). Our results demonstrate that stimulation of human cranial nerve afferent fibers facilitates cortical swallowing motor pathways.
Development of a Method for the Identification of S-IgA-Coated Bacterial Composition in Mouse and Human Feces (2010)

Some commensal intestinal bacteria in humans and mice are coated with secretory immunoglobulin A (S-IgA). It has been suggested that the S-IgA coating of commensal bacteria does not occur at random and thus identification of S-IgA-coated bacterial genera/species should help in elucidating the interaction between S-IgA and commensal intestinal bacteria, but no method of identifying the genera/species of S-IgA-coated bacteria has been established. To identify S-IgA-coated bacterial composition, we developed a method combining immunohistochemical detection of S-IgA and subsequent 16S rRNA targeted fluorescence in situ hybridization (FISH) analysis. Human and mouse fecal S-IgA coated bacterial composition was evaluated by this newly developed method with 10 frequently-used FISH probes. Fecal S-IgA-coated bacterial composition was successfully analyzed by this method, and this suggests that Enterobacteriaceae is preferably coated with S-IgA, whereas Bacteroides/Prevotella and Lactobacillus/Enterococcus groups appear to be poorly coated with S-IgA.
Spatial search by quantum walk (2004)

Grover's quantum search algorithm provides a way to speed up combinatorial search, but is not directly applicable to searching a physical database. Nevertheless, Aaronson and Ambainis showed that a database of $N$ items laid out in $d$ spatial dimensions can be searched in time of order $\sqrt{N}$ for $d&gt;2$, and in time of order $\sqrt{N}\phantom{\rule{0.3em}{0ex}}\text{poly}(\mathrm{log}\phantom{\rule{0.3em}{0ex}}N)$ for $d=2$. We consider an alternative search algorithm based on a continuous-time quantum walk on a graph. The case of the complete graph gives the continuous-time search algorithm of Farhi and Gutmann, and other previously known results can be used to show that $\sqrt{N}$ speedup can also be achieved on the hypercube. We show that full $\sqrt{N}$ speedup can be achieved on a $d$-dimensional periodic lattice for $d&gt;4$. In $d=4$, the quantum walk search algorithm takes time of order $\sqrt{N}\phantom{\rule{0.3em}{0ex}}\text{poly}(\mathrm{log}\phantom{\rule{0.3em}{0ex}}N)$, and in $d&lt;4$, the algorithm does not provide substantial speedup.
Structural and sequence elements required for the self-cleaving activity of the hepatitis delta virus ribozyme (1993)

The hepatitis delta virus (HDV) is a subviral RNA that contains a self-cleaving activity that is similar to the ribozyme activity found in certain plant pathogens. However, the sequences surrounding the cleavage site are unrelated to the hammerhead or hairpin ribozyme motifs, and it is considered to be a distinct ribozyme type. We made site-specific changes within two regions of the smallest contiguous HDV sequence that has optimal activity and kinetically analyzed the data at different temperatures to determine the potential roles of the residues. We distinguish between those changes that affect the rate of catalysis and those that promote the formation of inactive structures. We find that nucleotides +45 to +72 downstream from the cleavage site, which can form a hairpin structure, are dispensable for catalytic activity but that they enhance the cleavage efficiency. Nucleotides +17 to +19 and +28 to +30 form Watson and Crick base pairs that are important for activity, but the actual sequence is not critical. In contrast, the nucleotides between +21 and +26 are important for activity, and they may be involved in significant tertiary interactions.
Prevalence of infantile hypertrophic pyloric stenosis in Texas, 1999–2002 (2008)

This study confirmed previous findings that female infants and Black infants have a lower rate of IHPS. Large decreases in rates of IHPS were observed among foreign-born Hispanics and foreign-born Asians, but not among their US-born counterparts. These findings may be explained by differences in the frequency of behavioral risk factors for IHPS or differences in the frequency of ascertainment of mild cases of IHPS by ethnicity or nativity.