gebhart/patrepeval huggingface dataset:
Adding the missing sugars to coronavirus protein structures (2020)

Protein structures solved by cryo-electron microscopy (cryo-EM) or X-ray crystallography often miss the sugar molecules known as glycans that cover large swaths of the proteins’ surfaces. The recently reported structures of the spike protein on SARS-CoV-2, the novel coronavirus that causes COVID-19, are no different. Researchers are now working to fill in some of those sugary blanks to better understand the virus’s biology and to help drugmakers develop vaccines and treatments. “People usually go for what they can analyze” and focus mostly on the protein components of a structure, says Andrea Thorn, a structural biologist at the Julius Maximilian University of Würzburg. She is a member of the Coronavirus Structural Task Force, a group of scientists who specialize in modeling and processing crystallographic and cryo-EM data. Because structural biology measurements don’t reveal much about glycans on proteins, “we often fail to recognize what an important part of the structure they
A high-stability clock generator for 13.56MHz passive RFID tags (2012)

This paper presents a clock generator immune with variation of power supply and temperature. This scheme is implemented in a standard 0.18um CMOS technology. Simulation results show that the deviation of the frequency is less than 0.45% with supply variation of 1V; and the temperature drift is 10ppm/°C in the range of -40C - 120°C. The core area of this design is 0.4 × 0.25 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Potential Savings of a Program to Prevent Ankle Sprain Recurrence (2010)

The use of a proprioceptive training program after usual care of an ankle sprain is cost-effective for the prevention of ankle sprain recurrences in comparison with usual care alone. In the Netherlands, an estimated annual €35.9 million in medical and lost productivity costs can be saved solely by advocating a proprioceptive training program as in the present study.
Mono and diterpene production in <i>Escherichia coli</i> (2004)

Mono- and diterpenoids are of great industrial and medical value as specialty chemicals and pharmaceuticals. Production of these compounds in microbial hosts, such as Escherichia coli, can be limited by intracellular levels of the polyprenyl diphosphate precursors, geranyl diphosphate (GPP), and geranylgeranyl diphosphate (GGPP). To alleviate this limitation, we constructed synthetic operons that express three key enzymes for biosynthesis of these precursors: (1). DXS,1-deoxy-d-xylulose-5-phosphate synthase; (2). IPPHp, IPP isomerase from Haematococcus pluvialis; and (3). one of two variants of IspA, FPP synthase that produces either GPP or GGPP. The reporter plasmids pAC-LYC and pACYC-IB, which encode enzymes that convert either FPP or GGPP, respectively, to the pigment lycopene, were used to demonstrate that at full induction, the operon encoding the wild-type FPP synthase and mutant GGPP synthase produced similar levels of lycopene. To synthesize di- or monoterpenes in E. coli using the GGPP and GPP encoding operons either a diterpene cyclase [casbene cyclase (Ricinus communis L) and ent-kaurene cyclase (Phaeosphaeria sp. L487)] or a monoterpene cyclase [3-carene cyclase (Picea abies)] was coexpressed with their respective precursor production operon. Analysis of culture extracts or headspace by gas chromatography-mass spectrometry confirmed the in vivo production of the diterpenes casbene, kaur-15-ene, and kaur-16-ene and the monoterpenes alpha-pinene, myrcene, sabinene, 3-carene, alpha-terpinene, limonene, beta-phellandrene, alpha-terpinene, and terpinolene. Construction and functional expression of GGPP and GPP operons provides an in vivo precursor platform host for the future engineering of di- and monoterpene cyclases and the overproduction of terpenes in bacteria.
Mechanical deformation of neutrophils into narrow channels induces pseudopod projection and changes in biomechanical properties (2005)

Neutrophils traversing the pulmonary microcirculation are subjected to mechanical stimulation during their deformation into narrow capillaries. To better understand the time-dependant changes caused by this mechanical stimulus, neutrophils were caused to flow into a microchannel, which allowed simultaneous visualization of cell morphology and passive rheological measurement by tracking the Brownian motion of endogenous granules. Above a threshold stimulus, mechanical deformation resulted in neutrophil activation with pseudopod projection. The activation time was inversely correlated to the rate of mechanical deformation experienced by the neutrophils. A reduction in shear moduli was observed within seconds after the onset of the mechanical stimulus, suggesting a sudden disruption of the neutrophil cytoskeleton when subjected to mechanical deformation. However, the magnitude of the reduction in moduli was independent of the degree of deformation. Recovery to nearly the initial values of viscoelastic moduli occurred within 1 min. These observations confirm that mechanical deformation of neutrophils, similar to conditions encountered in the pulmonary capillaries, is not a passive event; rather, it is capable of activating the neutrophils and enhancing their migratory tendencies.
One-dimensional diffusion model for extended solid solution in laser cladding (1987)

A mathematical model is presented for determining the composition of extended solid solution formed due to rapid cooling in laser cladding. This model considers a diffusion mechanism for mass transport in a one-dimensional semi-infinite molten pool of the cladding material from which heat is removed by conduction through a one-dimensional semi-infinite solid substrate. The rate of solidification has been obtained by modeling the cooling process as a composite medium heat transfer problem. The discontinuity of the concentration field has been simulated using a nonequilibrium partition coefficient, and then a nonsimilar exact solution for the mass transport equation has been obtained using a set of similarity variables which has been derived using Lie group theory.
Genetic and Immunologic Analyses of PlpE, a Lipoprotein Important in Complement-Mediated Killing of<i>Pasteurella haemolytica</i>Serotype 1 (1998)

Pasteurella haemolytica serotype 1 is the bacterium most commonly associated with bovine shipping fever. The presence of antibodies against P. haemolytica outer membrane proteins (OMPs) correlates statistically with resistance to experimental P. haemolytica challenge in cattle. Until now, specific P. haemolytica OMPs which elicit antibodies that function in host defense mechanisms have not been identified. In this study, we have cloned and sequenced the gene encoding one such protein, PlpE. Analysis of the deduced amino acid sequence revealed that PlpE is a lipoprotein and that it is similar to an Actinobacillus pleuropneumoniae lipoprotein, OmlA. Affinity-purified, anti-PlpE antibodies recognize a protein in all serotypes of P. haemolytica except serotype 11. We found that intact P. haemolytica and recombinant E. coli expressing PlpE are capable of absorbing anti-PlpE antibodies from bovine immune serum, indicating that PlpE is surface exposed in P. haemolytica and assumes a similar surface-exposed conformation in E. coli. In complement-mediated killing assays, we observed a significant reduction in killing of P. haemolytica when bovine immune serum that was depleted of anti-PlpE antibodies was used as the source of antibody. Our data suggest that PlpE is surface exposed and immunogenic in cattle and that antibodies against PlpE contribute to host defense against P. haemolytica.
Response after One Dose of a Monovalent Influenza A (H1N1) 2009 Vaccine — Preliminary Report (2009)

Abstract Background A novel influenza A (H1N1) 2009 virus is responsible for the first influenza pan-demic in 41 years. A safe and effective vaccine is urgently needed. A randomized, observer-blind, parallel-group trial evaluating two doses of an inactivated, split-virus 2009 H1N1 vaccine in healthy adults between the ages of 18 and 64 years is ongoing at a single site in Australia. Methods This preliminary report evaluates the immunogenicity and safety of the vaccine 21 days after the first of two scheduled doses. A total of 240 subjects, equally divided into two age groups (<50 years and ≥50 years), were enrolled and underwent ran -domization to receive either 15 µg or 30 µg of hemagglutinin antigen by intramus -cular injection. We measured antibody titers using hemagglutination-inhibition and microneutralization assays at baseline and 21 days after vaccination. The co-primary immunogenicity end points were the proportion of subjects with antibody titers of 1:40 or more on hemagglutination-inhibition assay, the proportion of sub -jects with either seroconversion or a significant increase in antibody titer, and the factor increase in the geometric mean titer.
Enhanced secretory group II PLA2 activity in the tears of chronic blepharitis patients. (1999)

Secretory group II PLA2 activity was significantly enhanced in the tears of the chronic blepharitis patients compared with that of the normal controls. It is suggested that this increased enzymatic activity may decrease the tear film stability through increased hydrolysis of phospholipids.
An effective class-centroid-based dimension reduction method for text classification (2013)

Motivated by the effectiveness of centroid-based text classification techniques, we propose a classification-oriented class-centroid-based dimension reduction (DR) method, called CentroidDR. Basically, CentroidDR projects high-dimensional documents into a low-dimensional space spanned by class centroids. On this class-centroid-based space, the centroid-based classifier essentially becomes CentroidDR plus a simple linear classifier. Other classification techniques, such as K-Nearest Neighbor (KNN) classifiers, can be used to replace the simple linear classifier to form much more effective text classification algorithms. Though CentroidDR is simple, non-parametric and runs in linear time, preliminary experimental results show that it can improve the accuracy of the classifiers and perform better than general DR methods such as Latent Semantic Indexing (LSI).
Native Mass Spectrometry, Ion Mobility, and Collision-Induced Unfolding for Conformational Characterization of IgG4 Monoclonal Antibodies (2018)

Although the majority of FDA and EMA approved therapeutic monoclonal antibodies (mAbs) are IgG1, the number of IgG4-based formats reaching the market is increasing. IgG4 differs from other mAb isotypes by its specificity to form half mAbs that recombine into bispecific (bsAbs) molecules, through a process termed fab-arm exchange (FAE). We report here the complementarity of native mass spectrometry (MS), ion mobility (IM), and collision-induced unfolding (CIU) experiments for the structural characterization of members of the IgG4 subfamily (wild-type (wt), hinge-stabilized (hs, S228P mutation), and the resulting bsAb IgG4s). Native MS allows confirming/invalidating the occurrence of FAE as a function of these different types of IgG4. While IM-MS was unable to distinguish iso-cross-section IgG4 species, CIU experiments provide unique specific structural signatures of each individual IgG4 based on their specific unfolding pathways. Common CIU features of IgG4 formats include the observation of three conformational states and two transitions. In addition, CIU experiments demonstrated that S228P mutation stabilizes gas phase conformations of hsIgG4, in agreement with increased stability related to more rigid hinge regions. CIU patterns also appear to be more informative than IM-MS for bsAb structural characterization, unfolding signature of the bsAb being intermediate to the ones of the former parent wt-IgG4s, highlighting that bsAb CIU profiles keep the memory of their origins. Altogether, our results demonstrate that CIU patterns can serve as mAb specific structural signatures and are mature to be included in MS-based analytical workflows for conformational/structural characterization of mAb formats in early development phases and for multiple attribute monitoring.
Poly[propylene-graft-(4-vinylpyridinium dichromate)]: a novel fibrous polymer-supported oxidizing agent (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPoly[propylene-graft-(4-vinylpyridinium dichromate)]: a novel fibrous polymer-supported oxidizing agentRobert T. Peltonen, Kenneth B. Ekman, and Jan H. NasmanCite this: Ind. Eng. Chem. Res. 1994, 33, 2, 235–238Publication Date (Print):February 1, 1994Publication History Published online1 May 2002Published inissue 1 February 1994https://pubs.acs.org/doi/10.1021/ie00026a009https://doi.org/10.1021/ie00026a009research-articleACS PublicationsRequest reuse permissionsArticle Views152Altmetric-Citations4LEARN 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
Melvin L. Moss (1923-2006) (2018)

N/A
The Use of Computerized Image Guidance in Lumbar Disk Arthroplasty (2006)

The StealthStation with FluoroNav appears to be at least equivalent to standard fluoroscopy and may offer improved accuracy with rotational alignment while minimizing radiation exposure to the surgeon. Surgical guidance systems may offer improved accuracy and less interprocedure variation in the placement of intervertebral disk replacements than standard fluoroscopy. Further study regarding surgical navigation systems for intervertebral disk replacement is warranted.
<i>N</i>‐Acyl Isocyanides (1977)

The first acyl isocyanides have now become available. The pronounced carbonyl‐activation of benzoyl isocyanide (1) is manifested, e.g. , in the acylation of ynamines; in contrast, (1) undergoes cycloaddition with acetylenedicarboxylates. equation image
Study on Water Supply System of Efficiency Optimization Control of Induction Motor (2010)

Research on efficiency optimization control of induction motor(IM) driving pump in water supply system was presented,which has great meaning to energy conversion and emission reduction for all society.Based on the loss minimization control of IM and the relation between the flow,pressure and speed of pump,the control system of water supply system was set.The comparative study with constant V/f algorithm was done,and the results show the loss minimization control can keep the acceptable dynamic response and improves the efficiency of IM at low load.Application of this algorithm in water supply system will secure a higher level of energy conversion.
ERGOTHIONEINE IN THE CENTRAL NERVOUS SYSTEM (1972)

Abstract— Further investigations have been made into ergothioneine in the brains of several mammalian species, and the distribution of ergothioneine in the brain of the ox is described. It has not been possible to confirm many of the findings of earlier workers and the results do not appear to support their conclusion that ergothioneine is identical with the cerebellar factor.
Specifying a real-time kernel (1990)

The application of formal methods to a safety-critical system is illustrated. The objective of the study was to improve the existing documentation of a diagnostic X-ray machine to serve later reimplementations. The separation of the kernel from applications helped identify a design flaw in the kernel that could have caused damage by the X-ray application. The case study which shows that mathematical techniques have an important role to play in documenting systems and avoiding design flaws, is a good example of the use of the Z (pronounced 'Zed') notation and its methods for modeling systems. The limitations of this specification are delineated, showing that there is a need for other specification techniques to tackle the remaining properties, like real-time performance, for completeness and comparison.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Results of preliminary clinical trials of the positron emission mammography system PEM-I: a dedicated breast imaging system producing glucose metabolic images using FDG. (2000)

Our preliminary results suggest that PEM can offer a noninvasive method for the diagnosis of breast cancer. Metabolic images from PEM contain unique information not available from conventional morphologic imaging techniques and aid in expeditiously establishing the diagnosis of cancer. In all subjects, the PEM images were of diagnostic quality, with an imaging time of 2-5 min.
Considerations on efficiency increase for power electronic circuits that interconnect renewable energy sources to the grid (2016)

This paper presents some considerations regarding the efficiency increase for a circuit that assures the interconnection of a renewable energy source that produces electricity to the grid. The authors use as a link between the renewable source and the grid a quasi-resonant zero current switching half wave buck converter, in order to decrease the switching losses for the main switch of the circuit and to improve the overall efficiency of the system. The simulation results confirm the operation of the circuit proposed by the authors.
Contribution of Sinerem used as blood-pool contrast agent: detection of cerebral blood volume changes during apnea in the rabbit. (1996)

International audience
Comparison of in vitro models for the study of Mycobacterium tuberculosis invasion and intracellular replication (1996)

We recently evaluated several tissue culture model systems for the study of invasion and intracellular multiplication of Mycobacterium tuberculosis. These model systems include a human alveolar pneumocyte epithelial cell line, a murine macrophage cell line (J774), and fresh human peripheral blood-derived macrophages. Our data indicated that the initial level of association of M. tuberculosis with human alveolar pneumocyte cells (2%) was less than that observed with fresh human peripheral blood macrophages (9%) or J774 murine macrophages (13%) within 6 h of the addition of the bacteria. M. tuberculosis replicated in association with the pneumocyte cells by more than 55-fold by day 7 postinfection. In contrast, total bacteria] growth in the J774 cells and human macrophages was considerably less, with increases of only fourfold and threefold, respectively, over the same 7-day period. Amikacin, an aminoglycoside antimicrobial agent, was added to inhibit the growth of extracellular bacteria after the initial 6-h infection period. Decreases in viable counts were observed in all three cell cultures within the first 3 days after infection. However, unlike the case with either macrophage culture, intracellular bacterial CFU obtained from the infected pneumocytes increased by fourfold by day 7 after the addition of amikacin. These data indicate that M. tuberculosis infects and multiplies intracellularly in human lung epithelial cells and that these cells may be an alternative in vitro model for the study of intracellular multiplication of M. tuberculosis in the human lung.
Micromachined conformal electrode array for retinal prosthesis application (2003)

Retinal prosthesis projects around the world have been pursuing a functional replacement system for those with retinal degeneration. In this paper, we will outline the concept for a micromachined conformal electrode array and present preliminary fabrication results. Individual electrodes are designed to float on micromachined springs on a substrate that will enable the adjustment of spring constants and therefore contact force by adjusting the dimensions of the springs at each electrode. This will also allow us to accommodate the varying curvature/topography of the retina. We believe that this approach will provide several advantages by improving the electrode/tissue interface as well as generating some new options for in-situ measurements and overall system design.
Hydrodynamic properties of the chromaffin granule hydrogen ion pumping adenosine triphosphatase (1987)

We have determined the hydrodynamic properties of detergent-solubilized ATPase, which is coupled to H+ pumping in bovine adrenal chromaffin granules, by sedimentation equilibrium centrifugation and gel permeation chromatography. The protein solubilized with detergent containing phosphatidylserine sediments as a particle of 264,000 daltons and partial specific volume 0.829 cm3/g. Assuming a protein v of 0.73 and using the v measured for detergent and lipid mixed micelles of 0.93 cm3/g, we calculated that the protein component has a mass of 134,000 daltons and that the equivalent of approximately 1.5 micelles of detergent are bound per particle. The particle exhibits a Stokes radius of 43 A, which, together with the calculated particle volume, indicates an axial ratio close to 1. We conclude that the ATPase is an intrinsic membrane protein with a structure very different from that of mitochondrial F1F0 ATPase.
The <i>Xenopus</i> homologue of <i>Otx2</i> is a maternal homeobox gene that demarcates and specifies anterior body regions (1995)

In this paper we study Xotx2, a Xenopus homeobox gene related to orthodenticle, a gene expressed in the developing head of Drosophila. The murine cognate, Otx2, is first expressed in the entire epiblast of prestreak embryos and later in very anterior regions of late-gastrulae, including the neuroectoderm of presumptive fore- and mid-brain. In Xenopus, RNase protection experiments reveal that Xotx2 is expressed at low levels throughout early development from unfertilized egg to late blastula, when its expression level significantly increases. Whole-mount in situ hybridization shows a localized expression in the dorsal region of the marginal zone at stage 9.5. At stage 10.25 Xotx2 is expressed in dorsal bottle cells and in cells of the dorsal deep zone fated to give rise to prechordal mesendoderm, suggesting a role in the specification of very anterior structures. In stage 10.5 gastrulae, Xotx2 transcripts start to be detectable also in presumptive anterior neuroectoderm, where they persist in subsequent stages. Various treatments of early embryos cause a general reorganization of Xotx2 expression. In particular, retinoic acid treatment essentially abolishes Xotx2 expression in neuroectoderm. Microinjection of Xotx2 mRNA in 1-, 2- and 4-cell stage embryos causes the appearance of secondary cement glands and partial secondary axes in embryos with reduced trunk and tail structures. The presence of the Xotx2 homeodomain is required to produce these effects. In particular, this homeodomain contains a specific lysine residue at position 9 of the recognition helix. Microinjected transcripts of Xotx2 constructs containing a homeodomain where this lysine is substituted by a glutamine or a glutamic acid residue fail to cause these effects.