gebhart/patrepeval huggingface dataset:
Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting diverse and conserved epitopes (2021)

Interventions against variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgently needed. Stable and potent nanobodies (Nbs) that target the receptor binding domain (RBD) of SARS-CoV-2 spike are promising therapeutics. However, it is unknown if Nbs broadly neutralize circulating variants. We found that RBD Nbs are highly resistant to variants of concern (VOCs). High-resolution cryoelectron microscopy determination of eight Nb-bound structures reveals multiple potent neutralizing epitopes clustered into three classes: Class I targets ACE2-binding sites and disrupts host receptor binding. Class II binds highly conserved epitopes and retains activity against VOCs and RBD<sub>SARS-CoV</sub>. Cass III recognizes unique epitopes that are likely inaccessible to antibodies. Systematic comparisons of neutralizing antibodies and Nbs provided insights into how Nbs target the spike to achieve high-affinity and broadly neutralizing activity. Structure-function analysis of Nbs indicates a variety of antiviral mechanisms. Our study may guide the rational design of pan-coronavirus vaccines and therapeutics.
Architecture of Ca2+ Channel Pore-lining Segments Revealed by Covalent Modification of Substituted Cysteines (2000)

The cysteine accessibility method was used to explore calcium channel pore topology. Cysteine mutations were introduced into the SS1-SS2 segments of Motifs I-IV of the human cardiac L-type calcium channel, expressed in Xenopus oocytes and the current block by methanethiosulfonate compounds was measured. Our studies revealed that several consecutive mutants of motifs II and III are accessible to methanethiosulfonates, suggesting that these segments exist as random coils. Motif I cysteine mutants exhibited an intermittent sensitivity to these compounds, providing evidence for a beta-sheet secondary structure. Motif IV showed a periodic sensitivity, suggesting the presence of an alpha-helix. These studies reveal that the SS1-SS2 segment repeat in each motif have non-uniform secondary structures. Thus, the channel architecture evolves as a highly distorted 4-fold pore symmetry.
Major phosphorylation of SF1 on adjacent Ser‐Pro motifs enhances interaction with U2AF<sup>65</sup> (2006)

Protein phosphorylation ensures the accurate and controlled expression of the genome, for instance by regulating the activities of pre-mRNA splicing factors. Here we report that splicing factor 1 (SF1), which is involved in an early step of intronic sequence recognition, is highly phosphorylated in mammalian cells on two serines within an SPSP motif at the junction between its U2AF65 and RNA binding domains. We show that SF1 interacts in vitro with the protein kinase KIS, which possesses a 'U2AF homology motif' (UHM) domain. The UHM domain of KIS is required for KIS and SF1 to interact, and for KIS to efficiently phosphorylate SF1 on the SPSP motif. Importantly, SPSP phosphorylation by KIS increases binding of SF1 to U2AF65, and enhances formation of the ternary SF1-U2AF65-RNA complex. These results further suggest that this phosphorylation event has an important role for the function of SF1, and possibly for the structural rearrangements associated with spliceosome assembly and function.
Personalised video retrieval (2011)

A challenging problem in the user profiling domain is to create profiles of users of retrieval systems. This problem even exacerbates in the multimedia domain. Due to the Semantic Gap, the difference between low-level data representation of videos and the higher concepts users associate with videos, it is not trivial to understand the content of multimedia documents and to find other documents that the users might be interested in. A promising approach to ease this problem is to set multimedia documents into their semantic contexts. The semantic context can lead to a better understanding of the personal interests. Knowing the context of a video is useful for recommending users videos that match their information need. By exploiting these contexts, videos can also be linked to other, contextually related videos. From a user profiling point of view, these links can be of high value to recommend semantically related videos, hence creating a semantic-based user profile. This thesis introduces a semantic user profiling approach for news video retrieval, which exploits a generic ontology to put news stories into its context. Major challenges which inhibit the creation of such semantic user profiles are the identification of user's long-term interests and the adaptation of retrieval results based on these personal interests. Most personalisation services rely on users explicitly specifying preferences, a common approach in the text retrieval domain. By giving explicit feedback, users are forced to update their need, which can be problematic when their information need is vague. Furthermore, users tend not to provide enough feedback on which to base an adaptive retrieval algorithm. Deviating from the method of explicitly asking the user to rate the relevance of retrieval results, the use of implicit feedback techniques helps by learning user interests unobtrusively. The main advantage is that users are relieved from providing feedback. A disadvantage is that information gathered using implicit techniques is less accurate than information based on explicit feedback.
The segmented two-phase flow monolithic catalyst reactor. An alternative for liquid-phase hydrogenations (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe segmented two-phase flow monolithic catalyst reactor. An alternative for liquid-phase hydrogenationsVasilios Hatziantoniou and Bengt AnderssonCite this: Ind. Eng. Chem. Fundamen. 1984, 23, 1, 82–88Publication Date (Print):February 1, 1984Publication History Published online1 May 2002Published inissue 1 February 1984https://pubs.acs.org/doi/10.1021/i100013a015https://doi.org/10.1021/i100013a015research-articleACS PublicationsRequest reuse permissionsArticle Views227Altmetric-Citations42LEARN 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 options Get e-Alerts
Stack inspection (2002)

Stack inspection is a security mechanism implemented in runtimes such as the JVM and the CLR to accommodate components with diverse levels of trust. Although stack inspection enables the fine-grained expression of access control policies, it has rather a complex and subtle semantics. We present a formal semantics and an equational theory to explain how stack inspection affects program behaviour and code optimisations. We discuss the security properties enforced by stack inspection, and also consider variants with stronger, simpler properties.
Molecular classification of head and neck squamous cell carcinoma using cDNA microarrays. (2002)

Squamous cell carcinomas of the head and neck constitute an anatomically heterogeneous group of neoplasms that share in common a causal association with tobacco and alcohol exposure. The clinical course of these neoplasms is difficult to predict based on established prognostic clinicopathological criteria. Given the genetic complexity of head and neck cancers, it is not surprising that correlations with individual genetic abnormalities have also been disappointing. Several authors have suggested that global gene expression patterns can be used to subgroup patients with cancer. Here we report the use of cDNA microarrays containing 9216 clones to measure global patterns of gene expression in these neoplasms. We have used a statistical algorithm to identify 375 genes, which divide patients with head and neck tumors into two clinically distinct subgroups based on gene expression patterns. Our results demonstrate that gene expression profiling can be used as a predictor of outcome.
Two Methods for Increased Specificity and Sensitivity in Loop-Mediated Isothermal Amplification (2015)

The technique of loop-mediated isothermal amplification (LAMP) utilizes four (or six) primers targeting six (or eight) regions within a fairly small segment of a genome for amplification, with concentration higher than that used in traditional PCR methods. The high concentrations of primers used leads to an increased likelihood of non-specific amplification induced by primer dimers. In this study, a set of LAMP primers were designed targeting the prfA gene sequence of Listeria monocytogenes, and dimethyl sulfoxide (DMSO) as well as Touchdown LAMP were employed to increase the sensitivity and specificity of the LAMP reactions. The results indicate that the detection limit of this novel LAMP assay with the newly designed primers and additives was 10 fg per reaction, which is ten-fold more sensitive than a commercial Isothermal Amplification Kit and hundred-fold more sensitive than previously reported LAMP assays. This highly sensitive LAMP assay has been shown to detect 11 strains of Listeria monocytogenes, and does not detect other Listeria species (including Listeria innocua and Listeria invanovii), providing some advantages in specificity over commercial Isothermal Amplification Kits and previously reported LAMP assay.
The role of cell death during morphogenesis of the mammalian eye (1973)

Abstract Serial sections of embryonic rat eyes were stained with hematoxylin and eosin, quantified (by counting pycnotic and viable nuclei), reproduced by camera lucida on wax plates, and moulded into reconstructions in order to study the normal progression of cellular death during morphogenesis. At least nine distinct necrotic loci (A through I) can be distinguished. Immediately following contact between the retina and surface ectoderm (day 11) degenerating cells were observed in (A) the ventral extent of the optic vesicle, beginning in the mid‐retinal primordium and continuing ventrally in the optic stalk, (B) in the rostral optic stalk base, and (C) in the surface ectoderm encircling the early lens placode. No degeneration was observed in the dorsal half of the presumptive retina, in the entire pigment epithelium, or in the lens placode proper. During day 11.5 the lens placode thickens and forms a degenerating locus (D) in its ventral portion opposite the underlying pycnotic zone in the retina (A). During day 12 the ventral pycnotic zone (A) divides into two subunits (A 1 and A 2 ). Invagination of the lens displaces its marginal and ventral components (C and D) so that they come to occupy the lens pore area and presumptive corneal epithelium. Simultaneous invagination of the retinal rudiment juxtaposes the pigment epithelium which concurrently forms a necrotic area (E) adjacent ventrally to that in the retina (A 1 ). Degeneration appears in the caudal optic stalk (I). The density of viable cells decreases adjacent to pycnotic areas in the retina and pigment epithelium and increases within these death centers. During day 13 the optic fissure forms within the subunits of the ventral pycnotic zone (A 1 and A 2 ). Degenerations are seen in the dorsal optic stalk (F) and in the walls of the optic fissure (G and H). Throughout these stages necrosis appears only in those portions of the eye rudiment where invagination is either retarded or completely absent. In part, these observations suggest that cell death serves (1) to retard or inhibit invagination within death centers, (2) to integrate the series of invaginations which mould the dorsal optic cup and optic fissure, (3) to assist formation of the pigment epithelium monolayer, and (4) to orient the lens vesicle within the eye cup. The spatio‐temporal relationship between necrotic loci suggests that pycnotic cells in the retina may influence their production in the lens and pigment epithelium. Preliminary observations on the mouse, pig, and human substantiate those on the rat.
A Dipole Array Sonic Tool for Vertical and Deviated Wells (1999)

Abstract Dipole array sonic tools are particularly suited for estimating acoustic shear wave velocities in soft, unconsolidated, slow formations. Dipole sources induce flexural waves which are sustained in such formations. By contrast, monopole sources create pseudo-Rayleigh waves, related to shear wave velocity, which, in slow formations, refract away from the borehole and vanish before reaching the receivers. One of the main challenges of dipole sonic logging has been to descend into deviated wells. Operating in deviated wells requires a tool body competent enough to withstand compressive forces. But for a dipole tool, a rigid tool body is impractical because it conveys a strong direct arrival that interferes with the flexural mode. Therefore, in most traditional dipole tools, the sonde body is replaced by an acoustic isolator made of steel cables, which suspends the receiver array from the transmitter array. While such designs eliminate nearly all body arrivals, they restrict the range of application to wells with little or no deviation. A new tool design overcomes these problems, allowing comfortable logging of both dipole and monopole in deviated wells. The main feature of the design is a semi-rigid tool body, which consists of a series of interlocking steel rings configured in a special pattern and individually isolated by an elastomer. The dipole acoustic source has a broad frequency bandwidth extending down to the 600 Hz range, low enough to excite large boreholes and very slow formations. A comparison log in a vertical well between a cable-type isolator and the new semi-rigid isolator yields nearly identical data. Furthermore, a series of example logs run in deviated wells with the semi-rigid acoustic isolator validates this new approach for both the dipole and the monopole arrays. Random road noise, which is observed in deviated wells, is filtered using frequency and depth domain processing. Logging in free and bonded cased wells is also possible with this device. Comparison of travel time and porosity calculations in previously run open-hole logs with cased-hole dipole and monopole logs provided accurate results in both bonded and free casings.
FUNCTIONAL PROPRETIES OF RAPESEED FLOURS, CONCENTRATES AND ISOLATE (1976)

ABSTRACT The functional properties of rapeseed meal, flours, protein concentrates and isolate were evaluated in comparison with those of soybean. Generally, rapeseed products were lower in protein but higher in crude fiber and ash contents than the corresponding soybean flour, concentrate or isolate, Rapeseed flours were comparable to soybean flour in water absorption but showed much higher nitrogen solubility, fat absorption, oil emulsification, whippability and foam stability. The viscoamylograph curves for rapeseed flours were characterized by intermediate peak and high cold viscosities, but their gelation properties were poor. Unfortunately, flour from the low glucosinolate cultivar, Tower, contained 1.2 mg/g of glucosinolates, primarily oxazolidinethione, and only the detoxified concentrates and isolate would be safe for human consumption. Rapeseed concentrates and isolate showed excellent water‐and fat‐holding capacity and the isolate was high in oil emulsification and whipping characteristics. While superior to soybean products in most functional tests, the utilization of rapeseed products may be limited by green or brown colors in the aqueous slurries.
Characterization and vaccine potential of a novel recombinant coccidial antigen (1989)

A cDNA clone derived from sporulated oocysts of Eimeria tenella and encoding the expression product GX3262 was identified using a monoclonal antibody raised against Eimeria acervulina sporozoites. The cDNA fragment containing the coccidial antigen gene was cloned in bacteriophage lambda gt11, transferred to a plasmid, and introduced into Escherichia coli for analysis of the gene products. The strain carrying the plasmid produced GX3262 as part of a fusion protein consisting of the first 1,006 amino acids of E. coli beta-galactosidase and 112 amino acids of the E. tenella protein of approximately 12 kilodaltons. Partially purified antigen, heat-killed recombinant bacterin, and live E. coli containing the recombinant coccidial antigen were used to immunize 1-week-old or newly hatched broiler chicks. Several immunization protocols were utilized, including boosts with partially purified beta-galactosidase-GX3262, bacterin, or small numbers of live E. tenella oocysts. After challenge with an experimental E. tenella infection, the birds were evaluated by scoring cecal lesions to determine the level of protection. The greatest degree of protection was seen after only a single immunization of 2-day-old birds with a live recombinant E. coli preparation. The results presented here identify GX3262 as a potential candidate coccidial vaccine antigen and provide evidence for the first time that newly hatched chickens can be successfully vaccinated with a recombinant antigen.
Synthesis of WDM grating-based optical microwave filter with arbitrary impulse response (2003)

A new grating-based wavelength multiplexed photonic signal processor is presented. This uses a wavelength mapping and partitioning concept, forming a highly parallel delay-processing function. A significant increase in number of taps realised with minimum interconnects, and the ability of generating arbitrary discrete impulse response is demonstrated.
Contact dermatitis due to nitroglycerin ointment (1979)

Topical nitroglycerin ointment is among the most effective long-acting vasodilators currently available. We report two cases of contact dermatitis in which patch testing showed allergy to nitroglycerin-containing compounds. The severity of this dermatitis necessitated the discontinuation of topical nitroglycerin therapy in both patients. A potent corticosteroid cream applied once to previous nitroglycerin application sites prevented or minimized this dermatitis and enabled continuation of topical nitroglycerin therapy. Contact dermatitis due to topical nitroglycerin preparations may be more common than is presently realized. (<i>Arch Dermatol</i>115:853-855, 1979)
Oxaliplatin, an anticancer agent that affects both Na+ and K+ channels in frog peripheral myelinated axons. (2006)

The use of oxaliplatin, a relatively new chemotherapeutic agent, is somewhat limited since it produces a specific peripheral neuropathy regarding other neurotoxic anticancer platinum analogues. In order to investigate the mechanism of such a peripheral neuropathy, the effects of 1-100 micromol/l oxaliplatin were assessed on the nodal ionic currents of single frog myelinated axons as a model of peripheral excitable membranes. Oxaliplatin decreased both Na(+) and K(+) currents in a dose-dependent manner and within 5-10 min, without producing any marked changes in the current kinetics. It was about three to eight times more effective in reducing the Na(+) than the K(+) current. In addition, it shifted the voltage-dependence of both Na(+) and K(+) conductances towards negative membrane potentials. A negative shift in the steady-state inactivation-voltage curve of the peak Na(+) current was also observed in the presence of oxaliplatin. These effects were not reversed by washing the myelinated axons with an oxaliplatin-free solution for at least 30 min. It is concluded that oxaliplatin modifies the voltage-dependent ionic channels mainly by altering the external surface membrane potential. The knowledge of such a mechanism may help to counteract the neurotoxic action of this anticancer agent.
Solvent-Induced Chiroptical Changes in Supramolecular Assemblies of an Optically Active, Regioregular Polythiophene (2002)

The solvent-induced chiroptical properties of an optically active, regioregular (head-to-tail) polythiophene bearing chiral oxazoline residues, poly[3-{4-((R)-4-ethyl-2-oxazolin-2-yl)phenyl}thiophene] (poly-1a), were investigated in mixtures of a good solvent, chloroform, and a variety of poor solvents by means of UV−visible and CD spectroscopies. Poly-1a exhibited an induced circular dichroism (ICD) in chloroform upon the addition of poor solvents such as methanol and acetone with similar Cotton effect patterns, while some poor solvents such as acetonitrile and nitromethane dramatically changed the Cotton effect patterns of poly-1a. The changes in the conformation, morphology, and the size of the poly-1a aggregates induced by different solvents were also investigated with 1H NMR titrations, X-ray diffraction, filtration experiments using membrane filters, and atomic force microscopy (AFM) measurements. On the basis of these results, possible models for the chiral supramolecular aggregates are proposed.
Freeze-Dried Somatic Cells Direct Embryonic Development after Nuclear Transfer (2008)

The natural capacity of simple organisms to survive in a dehydrated state has long been exploited by man, with lyophylization the method of choice for the long term storage of bacterial and yeast cells. More recently, attempts have been made to apply this procedure to the long term storage of blood cells. However, despite significant progress, practical application in a clinical setting is still some way off. Conversely, to date there are no reports of attempts to lyophilize nucleated somatic cells for possible downstream applications. Here we demonstrate that lyophilised somatic cells stored for 3 years at room temperature are able to direct embryonic development following injection into enucleated oocytes. These remarkable results demonstrate that alternative systems for the long-term storage of cell lines are now possible, and open unprecedented opportunities in the fields of biomedicine and for conservation strategies.
Ultrafast Ligand Exchange: Detection of a Pentacoordinate Ru(II) Intermediate and Product Formation (2008)

The ultrafast kinetics of ligand exchange of cis-[Ru(bpy)(2)(CH(3)CN)(2)](2+) were measured in H(2)O and CH(3)CN. The formation of the (3)MLCT excited-state and a five-coordinate intermediate are observed in both solvents within 2 ps after excitation (310 nm, fwhm approximately 300 fs). The (3)MLCT excited-state undergoes vibrational cooling (5-6 ps), then decays to regenerate the ground-state with a lifetime of approximately 50 ps. In CH(3)CN, ligand recombination takes place in 28 ps, while the formation of cis-[Ru(bpy)(2)(CH(3)CN)(H(2)O)](2+) in H(2)O takes place with tau = 77 ps.