gebhart/patrepeval huggingface dataset:
Mouse CD94/NKG2A Is a Natural Killer Cell Receptor for the Nonclassical Major Histocompatibility Complex (MHC) Class I Molecule Qa-1b (1998)

Natural killer (NK) cells preferentially lyse targets that express reduced levels of major histocompatibility complex (MHC) class I proteins. To date, the only known mouse NK receptors for MHC class I belong to the Ly49 family of C-type lectin homodimers. Here, we report the cloning of mouse NKG2A, and demonstrate it forms an additional and distinct class I receptor, a CD94/NKG2A heterodimer. Using soluble tetramers of the nonclassical class I molecule Qa-1(b), we provide direct evidence that CD94/NKG2A recognizes Qa-1(b). We further demonstrate that NK recognition of Qa-1(b) results in the inhibition of target cell lysis. Inhibition appears to depend on the presence of Qdm, a Qa-1(b)-binding peptide derived from the signal sequences of some classical class I molecules. Mouse NKG2A maps adjacent to CD94 in the heart of the NK complex on mouse chromosome six, one of a small cluster of NKG2-like genes. Our findings suggest that mouse NK cells, like their human counterparts, use multiple mechanisms to survey class I expression on target cells.
Parkinson's Disease and Low Frequency Alleles Found Together Throughout LRRK2 (2009)

Mutations within LRRK2, most notably p.G2019S, cause Parkinson's disease (PD) in rare monogenic families, and sporadic occurrences in diverse populations. We investigated variation throughout LRRK2 (84 SNPs; genotype or diplotype found for 49 LD blocks) for 275 cases (European ancestry, onset at age 60 or older) and 275 neurologically healthy control subjects (NINDS Neurogenetics Repository). Three grade-of-membership groups, i.e. genetic risk sets, were identified that exactly matched many subjects (cases: 46, 4, 137; controls: 0, 178, 0), and distinguished 94% of the subjects (i.e. >50% likeness to one set). Set I, affected, carried certain low frequency alleles located in multiple functional domains. Set II was unaffected. Set III, also affected, resembled set II except for slightly elevated frequencies of minor alleles not defining set I. We conclude that certain low frequency alleles distributed throughout LRRK2 are a genetic background to a third of cases, defining a distinct subset.
Determination of Specific Antibody Responses to the Six Species of Ebola and Marburg Viruses by Multiplexed Protein Microarrays (2014)

Infectious hemorrhagic fevers caused by the Marburg and Ebola filoviruses result in human mortality rates of up to 90%, and there are no effective vaccines or therapeutics available for clinical use. The highly infectious and lethal nature of these viruses highlights the need for reliable and sensitive diagnostic methods. We assembled a protein microarray displaying nucleoprotein (NP), virion protein 40 (VP40), and glycoprotein (GP) antigens from isolates representing the six species of filoviruses for use as a surveillance and diagnostic platform. Using the microarrays, we examined serum antibody responses of rhesus macaques vaccinated with trivalent (GP, NP, and VP40) virus-like particles (VLP) prior to infection with the Marburg virus (MARV) (i.e., Marburg marburgvirus) or the Zaire virus (ZEBOV) (i.e., Zaire ebolavirus). The microarray-based assay detected a significant increase in antigen-specific IgG resulting from immunization, while a greater level of antibody responses resulted from challenge of the vaccinated animals with ZEBOV or MARV. Further, while antibody cross-reactivities were observed among NPs and VP40s of Ebola viruses, antibody recognition of GPs was very specific. The performance of mucin-like domain fragments of GP (GP mucin) expressed in Escherichia coli was compared to that of GP ectodomains produced in eukaryotic cells. Based on results with ZEBOV and MARV proteins, antibody recognition of GP mucins that were deficient in posttranslational modifications was comparable to that of the eukaryotic cell-expressed GP ectodomains in assay performance. We conclude that the described protein microarray may translate into a sensitive assay for diagnosis and serological surveillance of infections caused by multiple species of filoviruses.
Chronic Exposure to Beta-Blockers Attenuates Inflammation and Mucin Content in a Murine Asthma Model (2007)

Single-dose administration of beta-adrenoceptor agonists produces bronchodilation and inhibits airway hyperresponsiveness (AHR), and is the standard treatment for the acute relief of asthma. However, chronic repetitive administration of beta-adrenoceptor agonists may increase AHR, airway inflammation, and risk of death. Based upon the paradigm shift that occurred with the use of beta-blockers in congestive heart failure, we previously determined that chronic administration of beta-blockers decreased AHR in a murine model of asthma. To elucidate the mechanisms for the beneficial effects of beta-blockers, we examined the effects of chronic administration of several beta-adrenoceptor ligands in a murine model of allergic asthma. Administration of beta-blockers resulted in a reduction in total cell counts, eosinophils, and the cytokines IL-13, IL-10, IL-5, and TGF-beta1 in bronchoalveolar lavage, and attenuated epithelial mucin content and morphologic changes. The differences in mucin content also occurred if the beta-blockers were administered only during the ovalbumin challenge phase, but administration of beta-blockers for 7 days was not as effective as administration for 28 days. These results indicate that in a murine model of asthma, chronic administration of beta-blockers reduces inflammation and mucous metaplasia, cardinal features of asthma that may contribute to airflow obstruction and AHR. Similar to heart failure, our results provide a second disease model in which beta-blockers producing an acutely detrimental effect may provide a therapeutically beneficial effect with chronic administration.
Simulation of Quantum Walks via Hamiltonian Reduction (2018)

We utilize dimensionality reduction to model and simulate continuous time quantum walks on a multi-partite graph, verifying that they produce a quadratic speedup over classical walks. We also discuss the applicability of dimensionality reduction as a modelling tool to experiments run on quantum hardware.
Dynamic Recommendations in Internet Retailing. (2001)

With current projections regarding the growth of Internet sales, online retailing raises many questions about how to market on the Net. While convenience impels consumers to purchase items on the web, quality remains a significant factor in deciding where to shop online. The competition is increasing and personalization is considered to be the competitive advantage that will determine the winners in the market of online shopping in the following years. Recommender systems are a means of personalizing a site and a solution to the customerâs information overload problem. As such, many e-commerce sites already use them to facilitate the buying process. In this paper we study the application of recommender systems for electronic retail sites, focusing on the peculiar characteristics and requirements of this environment. We also introduce a hybrid model supporting dynamic recommendations, which eliminates the problems the underlying techniques have when applied solely. We then discuss the application of the proposed solution in the case of an innovative research project on electronic retailing funded by the European Commission and conclude with some ideas for further development and research in this area.
Hosting Fullerenes by Dynamic Bond Formation with an Iridium Porphyrin Cyclic Dimer:  A “Chemical Friction” for Rotary Guest Motions (2007)

A cyclic dimer of methyliridium porphyrin 1Ir shows an extraordinary affinity toward fullerenes via a dynamic bond-forming interaction. The crystal structure of inclusion complex 1Ir⊃C60 demonstrates the bond formation between the iridium centers of 1Ir and guest C60, leading to an ellipsoidal deformation of C60. According to variable-temperature 13C NMR spectroscopy, included C70 adopts, over a wide temperature range, an end-on orientation relative to the metalloporphyrin units, as a consequence of the site-specific bond formation onto the CC bonds located at the pole positions of C70. Such a bond formation is dynamic but prevails over van der Waals interactions and gives rise to a “chemical friction” for the rotary motions of the included fullerenes. Noteworthy is a restricted rotation of included C70 along its longer axis as a consequence of thermal slipping of the iridium centers from one CC bond to the neighboring ones at the pole positions of C70. In sharp contrast, rhodium complex 1Rh as a reference does not show any of the above features under identical conditions.
Sequence-specific pausing during in vitro DNA replication on double-stranded DNA templates (1989)

Sequence-specific pausing occurs during DNA synthesis catalyzed by the bacteriophage T4 DNA polymerase holoenzyme in the presence of the T4 helix destabilizing protein (gene 32 protein). Two of the six strongest pause sites on a double-stranded bacteriophage fd DNA template are in regions where hairpin helices are predicted to form when the DNA is single stranded. However, the other pause sites are in regions that are not obviously involved in secondary structure. The positions of the DNA chain ends produced at one pause site of each type were determined to within +/- 2 nucleotides. At this resolution, a clustering of sites is observed, suggesting that the polymerase holoenzyme may become destabilized when moving along selected regions of the DNA and then pause at one or more of several closely spaced positions. The addition of the T4 gene 41 protein (a DNA helicase that forms part of the T4 primosome) to the above replication system greatly increases the rate of fork movement and eliminates detectable pausing. In contrast, the addition of the T4 dda protein (a second DNA helicase that increases the rate of fork movement to a similar extent) has no affect on replication fork pausing. This difference could either be due to specific protein-protein interactions formed between the polymerase holoenzyme and the 41 protein or to the highly processive movement of the 41 protein along the displaced DNA strand.
Control algorithms for ankle robots: A reflection on the state-of-the-art and presentation of two novel algorithms (2008)

With computer speeds greatly increasing, hardware is no longer a hurdle in the development of controllers for wearable lower limb robots. The challenge remains in developing smart algorithms that are able to detect which task a person is about to perform and then supply the robot with the correct desired movements. This paper reflects on some existing control algorithms and then presents theory and test results of two novel concepts. The goal of this paper is to show that the two new concepts are capable of producing the correct motor profile.
A national census of medicines use: a 24‐hour snapshot of Australians aged 50 years and older (2012)

The use of multiple medicines is common and higher than reported in the 1995 National Health Survey. Today, much medicines use is to prevent future disease by influencing risk factors. High levels of polypharmacy highlight the need to support the safe and effective use of medicines in the community. Although doctors recommend or prescribe most medicines, self-directed medication use is common. This highlights the need for consumer access to accurate information and strategies to improve health literacy about medicines.
Long Tethers Binding Redox Centers to Polymer Backbones Enhance Electron Transport in Enzyme “Wiring” Hydrogels (2003)

A redox hydrogel with an apparent electron diffusion coefficient (D(app)) of (5.8 +/- 0.5) x 10(-)(6) cm(2) s(-)(1) is described. The order of magnitude increase in D(app) relative to previously studied redox hydrogels results from the tethering of redox centers to the backbone of the cross-linked redox polymer backbone through 13 atom spacer arms. The long and flexible tethers allow the redox centers to sweep electrons from large-volume elements and to collect electrons of glucose oxidase efficiently. The spacer arms make the collection of electrons from glucose oxidase so efficient that glucose is electrooxidized already at -0.36 V versus Ag/AgCl, the reversible potential of the redox potential of the FAD/FADH(2) centers of the enzyme at pH 7.2. The limiting current density of 1.15 mA cm(-)(2) is reached at a potential as low as -0.1 V versus Ag/AgCl. The novel redox center of the polymer is a tris-dialkylated N,N'-biimidazole Os(2+/3+) complex. Its redox potential, -0.195 V versus Ag/AgCl, is 0.8 V reducing relative to that of Os(bpy)(2+/3+), its 2,2'-bipyridine analogue.
Comparison of the fine specificity of anti-dinitrophenyl-combining site composed of either VL dimer or VL and VH of protein 315 (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComparison of the fine specificity of anti-dinitrophenyl-combining site composed of either VL dimer or VL and VH of protein 315Moshe Gavish, Raymond A. Dwek, and David GivolCite this: Biochemistry 1977, 16, 14, 3154–3159Publication Date (Print):July 12, 1977Publication History Published online1 May 2002Published inissue 12 July 1977https://pubs.acs.org/doi/10.1021/bi00633a018https://doi.org/10.1021/bi00633a018research-articleACS PublicationsRequest reuse permissionsArticle Views37Altmetric-Citations15LEARN 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
Production of DogiK: an Improved Ogi (Nigerian Fermented Weaning Food) with Potentials for Use in Diarrhoea Control (1994)

As part of a programme to formulate foods to aid the control of diarrhoeal diseases, an improved ogi (the commonest weaning food in Nigeria) named DogiK has been developed. DogiK was produced by using Lactobacillus starter cultures with antimicrobial activity against diarrhoeagenic bacteria and also possessing amylolytic activity. The survival of diarrhoeagenic bacteria was investigated in locally-fermented ogi and in DogiK. The foods were inoculated with cell suspensions of Salmonella, Shigella, Campylobacter, Aeromonas, Pleisiomonas, Enteropathogenic and Enterotoxigenic Escherichia coli, Yersinia enterocolitica, and Vibrio cholerae. None of the diarrhoeagenic bacteria were detected in DogiK after 6 h whereas in the local ogi Salmonella, E. coli, and Shigella survived for 24 h or more, but showed a sharp decrease in numbers, while V. cholerae survived for 12 h. DogiK is active whether cooked or uncooked and exhibited inhibition of pathogens at neutral pH. It gives consistent quality. Preliminary investigation indicates possession of a better shelf life. Thus, DogiK may have a potential use in the prevention and treatment of diarrhoea.
Anti–Intercellular Adhesion Molecule–1 Antibody Reduces Ischemic Cell Damage After Transient But Not Permanent Middle Cerebral Artery Occlusion in the Wistar Rat (1995)

Ischemic cell damage is promoted by postischemic inflammatory response after 2 hours of transient MCA occlusion, and ischemic cell damage is reduced by administration of an anti-ICAM-1 antibody during reperfusion.
A reliable multicast framework for light-weight sessions and application level framing (1997)

This paper describes scalable reliable multicast (SRM), a reliable multicast framework for light-weight sessions and application level framing. The algorithms of this framework are efficient, robust, and scale well to both very large networks and very large sessions. The SRM framework has been prototyped in wb, a distributed whiteboard application, which has been used on a global scale with sessions ranging from a few to a few hundred participants. The paper describes the principles that have guided the SRM design, including the IP multicast group delivery model, an end-to-end, receiver-based model of reliability, and the application level framing protocol model. As with unicast communications, the performance of a reliable multicast delivery algorithm depends on the underlying topology and operational environment. We investigate that dependence via analysis and simulation, and demonstrate an adaptive algorithm that uses the results of previous loss recovery events to adapt the control parameters used for future loss recovery. With the adaptive algorithm, our reliable multicast delivery algorithm provides good performance over a wide range of underlying topologies.
Position‐specific incorporation of dansylated non‐natural amino acids into streptavidin by using a four‐base codon (2004)

Novel non-natural amino acids carrying a dansyl fluorescent group were designed, synthesized, and incorporated into various positions of streptavidin by using a CGGG four-base codon in an Escherichia coli in vitro translation system. 2,6-Dansyl-aminophenylalanine (2,6-dnsAF) was found to be incorporated into the protein more efficiently than 1,5-dansyl-lysine, 2,6-dansyl-lysine, and 1,5-dansyl-aminophenylalanine. Fluorescence measurements indicate that the position-specific incorporation of the 2,6-dnsAF is a useful technique to probe protein structures. These results also indicate that well-designed non-natural amino acids carrying relatively large side chains can be accepted as substrates of the translation system.
Nanotubes (2001)

Carbon nanotubes were discovered soon after the successful laboratory synthesis of fullerenes. Since their discovery in 1991, there has been intensive research activity in the area of carbon nanotubes, not only because of their fascinating structural features and properties, but also because of their potential technological applications. There is increasing experimental evidence to show that carbon nanotubes may find use in nanoelectronic devices, displays, and in hydrogen storage. In this article, we discuss various important aspects related to the synthesis, structure, characterization, and mechanism of formation of multi-walled and single-walled carbon nanotubes, followed by a presentation of the important electronic, mechanical, hydrogen storage, and other properties of the nanotubes. Doping, as well as other chemical manipulations with boron and nitrogen, bring about significant changes in the properties of the nanotubes. Carbon nanotubes also serve as useful templates to make other nanostructures. Layered metal chalcogenides, boron nitride, and other materials form nanotubes and provide considerable scope for study.
The potential of PET to increase understanding of the biological basis of tumour and normal tissue response to radiotherapy (2005)

Imaging is playing an increasing role in the management of radiotherapy patients in terms of diagnosis and treatment planning, thus providing a stimulus for an expansion in its parallel development as a tool for imaging tumour biology in man. Positron emission tomography can be used to image not only glucose metabolism but also different biological processes involved in radiotherapy resistance such as hypoxia, blood flow and proliferation. It has potential for increasing our understanding of the biological mechanisms underlying the heterogeneity of tumour and normal tissue response to radiotherapy. It also has potential for the future definition of biological target volumes in tumours for dose escalation, and in normal tissues for dose reduction. © The British Institute of Radiology.
Insulin Degludec Versus Insulin Glargine in Insulin-Naive Patients With Type 2 Diabetes (2012)

Insulins degludec and glargine administered once daily in combination with OADs provided similar long-term glycemic control in insulin-naive patients with type 2 diabetes, with lower rates of nocturnal hypoglycemia with degludec.
Public Use, Substantive Due Process, and Takings—An Integration (1995)

The results confirm previous findings showing a strong study effect on gut microbial composition and raise concerns about the impact of analysis strategies on the membership and composition of the gut microbiota. This study may be helpful to guide future research aiming to investigate the relationship between diet, health, and the gut microbiota.
Pharmacokinetics and Brain Uptake of Biotinylated Basic Fibroblast Growth Factor Conjugated to a Blood-Brain Barrier Drug Delivery System (2002)

Human basic fibroblast growth factor (bFGF) is a potent neuroprotective agent. The clinical efficacy of this neurotrophin, however, is restricted by poor permeability across the blood-brain barrier (BBB). This study was designed to test the hypotheses that bFGF will retain its biological activity and have an enhanced BBB transport after re-formulation and conjugation to a BBB peptide drug delivery vector. The BBB delivery vector is comprised of a conjugate of streptavidin (SA) and the murine OX26 monoclonal antibody against the rat transferrin receptor, and the conjugate of biotinylated bFGF (bio-bFGF) bound to a vector is designated bio-bFGF/OX26-SA. A radioreceptor binding assay shows that the native bFGF, bio-bFGF, and bio-bFGF/OX26-SA conjugate have IC50 values of 0.12, 0.40, and 0.56 nM, respectively. After an IV bolus injection to the rat, [125I]-bio-bFGF is avidly taken up by peripheral organs, with low brain uptake at 60 min, 0.010+/-0.004% of injected dose (ID)/g brain. By contrast, the brain uptake of the [125I]-bio-bFGF/OX26-SA is increased 5-fold to 0.050+/-0.011%ID/g, although the uptake of the conjugate by peripheral tissues was decreased relative to the unconjugated bio-bFGF. In conclusion, conjugation of bio-bFGF to a BBB drug delivery vector (a) causes only a minor decrease in affinity for the bFGF receptor, (b) decreases the peripheral organ uptake of the bFGF, and (c) increases the brain uptake of the neurotrophin. The re-formulation of bFGF to enable receptor-mediated transcytosis across the BBB may improve the therapeutic index of this neurotrophin as a neuroprotective agent.
Modeling sequencing errors by combining Hidden Markov models (2003)

Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts but for technical reasons they often contain sequencing errors. Therefore, when analyzing EST sequences computationally, such errors must be taken into account. Earlier attempts to model error prone coding regions have shown good performance in detecting and predicting these while correcting sequencing errors using codon usage frequencies. In the research presented here, we improve the detection of translation start and stop sites by integrating a more complex mRNA model with codon usage bias based error correction into one hidden Markov model (HMM), thus generalizing this error correction approach to more complex HMMs. We show that our method maintains the performance in detecting coding sequences.