gebhart/patrepeval huggingface dataset:
Antibodies from Phage Display Libraries as Immunochemical Reagents (1998)

The display of a repertoire of recombinant antibodies on the surface of filamentous phage by fusion to a minor coat protein has provided a powerful methodology for isolating the desired binding specificities (see Chapter 45 and ref. 1). Antibodies have typically been displayed on phage as single-chain Fv fragments (scFv [2]), in which the heavy chain variable region (VH) and the light chain variable region (VL) domains are linked together by a flexible polypeptide (3,4), or as Fab fragments (5) In general, antibodies have been displayed either at the N-terminus of the minor coat protein pill of filamentous phage (2), or at the C-terminal domain of pill (6). For Fab fragments, one chain is fused to pill, and the other assembles with the pill-fused chain after leader peptide-mediated secretion in the bacterial supernatant.
Contribution of Immunological Memory to Protective Immunity Conferred by a Bacillus anthracis Protective Antigen-Based Vaccine (2004)

Protective antigen (PA)-based vaccination is an effective countermeasure to anthrax infection. While neutralizing anti-PA antibody titers elicited by this vaccine serve as good correlates for protection against anthrax (S. Reuveny, M. D. White, Y. Y. Adar, Y. Kafri, Z. Altboum, Y. Gozes, D. Kobiler, A. Shafferman, and B. Velan, Infect. Immun. 69:2888-2893, 2001), no data are available on the contribution of the immunological memory for PA itself to protection. We therefore developed a guinea pig model in which a primary immunization with threshold levels of PA can induce a long-term T-cell immunological memory response without inducing detectable anti-PA antibodies. A revaccination of primed animals with the same threshold PA levels was effective for memory activation, yielding a robust and rapid secondary response. A challenge with a lethal dose (40 50% lethal doses; 2,000 spores) of spores after the booster vaccinations indicated that animals were not protected at days 2, 4, and 6 postboosting. Protection was achieved only from the 8th day postboosting, concomitant with the detection of protective levels of neutralizing antibody titers in the circulation. The practical implications from the studies reported herein are that, as expected, the protective capacity of memory depends on the PA dose used for the primary immunization and that the effectiveness of booster immunizations for the postexposure treatment of anthrax may be very limited when no detectable antibodies are present in primed animals prior to Bacillus anthracis spore exposure. Therefore, to allow for the establishment of memory-dependent protection prior to the expected onset of disease, booster immunizations should not be used without concomitant antimicrobial treatment in postexposure scenarios.
The Impact of Continuous Positive Airway Pressure on Blood Pressure in Patients With Obstructive Sleep Apnea Syndrome (2007)

Among patients with OSAS, CPAP reduces 24-hour ambulatory MBP, with greater treatment-related reductions in ambulatory MBP among patients with a more severe degree of OSAS and a better effective nightly use of the CPAP device. These reductions in blood pressure are likely to contribute to a better prognosis in terms of adverse cardiovascular events.
Psychophysical bases of perceived exertion (1982)

There is a great demand for perceptual effort ratings in order to better understand man at work. Such ratings are important complements to behavioral and physiological measurements of physical performance and work capacity. This is true for both theoretical analysis and application in medicine, human factors, and sports. Perceptual estimates, obtained by psychophysical ratio-scaling methods, are valid when describing general perceptual variation, but category methods are more useful in several applied situations when differences between individuals are described. A presentation is made of ratio-scaling methods, category methods, especially the Borg Scale for ratings of perceived exertion, and a new method that combines the category method with ratio properties. Some of the advantages and disadvantages of the different methods are discussed in both theoretical-psychophysical and psychophysiological frames of reference.
Block Co-PolyMOCs by Stepwise Self-Assembly (2016)

We report a stepwise assembly strategy for the integration of metal-organic cages (MOCs) into block copolymers (BCPs). This approach creates "block co-polyMOC" (BCPMOC) materials whose microscopic structures and mechanical properties are readily tunable by adjusting the size and geometry of the MOCs and the composition of the BCPs. In the first assembly step, BCPs functionalized with a pyridyl ligand on the chain end form star-shaped polymers triggered by metal-coordination-induced MOC assembly. The type of MOC junction employed precisely determines the number of arms for the star polymer. In the second step, microphase separation of the BCP is induced, physically cross-linking the star polymers and producing the desired BCPMOC networks in the bulk or gel state. We demonstrate that large spherical M12L24 MOCs, small paddlewheel M2L4 MOCs, or a mixture of both can be incorporated into BCPMOCs to provide materials with tailored branch functionality, phase separation, microdomain spacing, and mechanical properties. Given the synthetic and functional diversity of MOCs and BCPs, our method should enable access to BCPMOCs for a wide range of applications.
Diastereoselective synthesis of the carbacephem framework (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiastereoselective synthesis of the carbacephem frameworkBruce T. Lotz and Marvin J. MillerCite this: J. Org. Chem. 1993, 58, 3, 618–625Publication Date (Print):January 1, 1993Publication History Published online1 May 2002Published inissue 1 January 1993https://pubs.acs.org/doi/10.1021/jo00055a013https://doi.org/10.1021/jo00055a013research-articleACS PublicationsRequest reuse permissionsArticle Views497Altmetric-Citations51LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Properties of Antisera to Ganglioside GM1 and Asialo GM1 (1974)

Abstract The object of this study is to prepare antisera to purified glycosphingolipids for immunocytochemical studies. Rabbits were immunized with ganglioside GM1 complexed either to methylated BSA or to a glycoprotein isolated from human erythrocytes, and to asialo GM1 complexed to the erythrocyte glycoprotein. IgG and IgM antibody fractions were separated by chromatography on Sephadex G-200 and their properties were determined by complement fixation. IgG antibodies to asialo GM1 were highly specific and exhibited little cross-reactivity with GM1 or other glycolipids, but IgM antibodies cross-reacted extensively with gangliosides GM1 and GD1b. Complement fixation of IgG anti-asialo GM1 with asialo GM1 was completely inhibited by about 15 nmoles of ganglio-N-tetraose, the carbohydrate moiety of this glycolipid. Both IgG and IgM antibodies to GM1 cross-reacted extensively with asialo GM1 and GD1b, but specific IgG antibodies to GM1 were revealed by absorption with asialo GM1. The specific and cross-reacting IgG antibodies to GM1 were inhibited by the pentaose moiety of this glycoplipid, but these antibodies were much harder to inhibit than IgG anti-asialo GM1. These results demonstrate that it is possible to prepare specific antisera to purified glycolipids with a single administration of antigen, in contrast to previous studies in which repeated injections of ganglioside mixtures were employed.
Genetic characterization and molecular cloning of the tripeptide permease (tpp) genes of Salmonella typhimurium (1984)

Of the three bacterial peptide transport systems only one, the oligopeptide permease, has been characterized in any detail. We have now isolated Salmonella typhimurium mutants deficient in a second transport system, the tripeptide permease (Tpp), using the toxic peptide alafosfalin. Alafosfalin resistance mutations map at three loci, the gene encoding peptidase A (pepA) and two transport-defective loci, tppA and tppB. Locus tppA has been mapped to 74 min on the S. typhimurium chromosome, cotransducible with aroB, and is a positive regulator of tppB. Locus tppB maps at 27 min in the cotransduction gap between purB and pyrF. We cloned tppB, the structural locus for the tripeptide permease. Two simple methods are described for mapping the location of cloned DNA fragments on the chromosome of S. typhimurium.
Laser triangulation: fundamental uncertainty in distance measurement (1994)

We discuss the uncertainty limit in distance sensing by laser triangulation. The uncertainty in distance measurement of laser triangulation sensors and other coherent sensors is limited by speckle noise. Speckle arises because of the coherent illumination in combination with rough surfaces. A minimum limit on the distance uncertainty is derived through speckle statistics. This uncertainty is a function of wavelength, observation aperture, and speckle contrast in the spot image. Surprisingly, it is the same distance uncertainty that we obtained from a single-photon experiment and from Heisenberg's uncertainty principle. Experiments confirm the theory. An uncertainty principle connecting lateral resolution and distance uncertainty is introduced. Design criteria for a sensor with minimum distanc uncertainty are determined: small temporal coherence, small spatial coherence, a large observation aperture.
Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19 (2010)

Our approach to protein-protein docking includes three main steps. First, we run PIPER, a rigid body docking program based on the Fast Fourier Transform (FFT) correlation approach, extended to use pairwise interactions potentials. Second, the 1000 best energy conformations are clustered, and the 30 largest clusters are retained for refinement. Third, the stability of the clusters is analyzed by short Monte Carlo simulations, and the structures are refined by the medium-range optimization method SDU. The first two steps of this approach are implemented in the ClusPro 2.0 protein-protein docking server. Despite being fully automated, the last step is computationally too expensive to be included in the server. When comparing the models obtained in CAPRI rounds 13-19 by ClusPro, by the refinement of the ClusPro predictions and by all predictor groups, we arrived at three conclusions. First, for the first time in the CAPRI history, our automated ClusPro server was able to compete with the best human predictor groups. Second, selecting the top ranked models, our current protocol reliably generates high-quality structures of protein-protein complexes from the structures of separately crystallized proteins, even in the absence of biological information, provided that there is limited backbone conformational change. Third, despite occasional successes, homology modeling requires further improvement to achieve reliable docking results.
Inactivation of Lipid-Enveloped Viruses in Labile BloodDerivatives by Unsaturated Fatty Acids (1988)

Virus sterilization of blood plasma derivatives by addition of several naturally occurring fatty acids was evaluated using vesicular stomatitis virus and Sindbis virus as markers for lipid-enveloped virus inactivation and human immunodeficiency virus (HIV). Inactivation of ≥10^4 tissue culture infectious doses (TCID(50)) of marker viruses added to antihemophilic factor (AHF) concentrates, with 60-100% retention of AHF activity, was achieved with oleic, 1l-eicosenoic, linoleic, linolenic, palmitoleic and arachidonic acids. Elaidic, gamma-linolenic, palmitic, and arachidic acids and another fat-soluble compound previously reported to inactivate virus, butylated hydroxytoluene. were less effective. A long chain mono- but not a di- or triglyceride also displayed virucidal properties. Evaluation of the inactivation of HIV added to an immune globulin solution on exposure to 0.033% sodium oleate for 20 min indicated inactivation of ≥10^3,4 TCID(50). The degree of virus inactivation depended on the sample composition. A favorable balance was achieved between degree of virus inactivation and retention of protein function for AHF concentrate, prothrombin complex concentrate, antithrombin III concentrate, and immune globulin solution on incubation with 0.033% (w/v) sodium oleate at 24 °C for 4-6 h. Virus inactivation in whole plasma and plasma cryoprecipitate was not complete despite use of higher concentrations of sodium oleate and/or incubation at 37 °C. Reduced virus kill in these less purified derivatives probably is a consequence of their endogenous lipid and/or albumin.
Arc-modulated radiation therapy (AMRT): a single-arc form of intensity-modulated arc therapy (2008)

Arc-modulated radiation therapy (AMRT) is a novel rotational intensity-modulated radiation therapy (IMRT) technique developed for a clinical linear accelerator that aims to deliver highly conformal radiation treatment using just one arc of gantry rotation. Compared to fixed-gantry IMRT and the multiple-arc intensity-modulated arc therapy (IMAT) techniques, AMRT promises the same treatment quality with a single-arc delivery. In this paper, we present a treatment planning scheme for AMRT, which addresses the challenges in inverse planning, leaf sequencing and dose calculation. The feasibility and performance of this AMRT treatment planning scheme have been verified with multiple clinical cases of various sites on Varian linear accelerators.
Unconventional organization of the division and cell wall gene cluster of Streptococcus pneumoniae (1998)

The genes responsible for cell wall biosynthesis and cell division (dcw genes) were identified and sequenced in Streptococcus pneumoniae. The genetic organization of the dcw cluster in Streptococcus pneumoniae differed significantly from the clusters of other bacteria reported to date. In particular, the genes corresponding to the 2 min region of the Escherichia coli chromosome were found distributed in three genetically separate regions of the Streptococcus pneumoniae chromosome. The first region contained the expected ftsA and ftsZ cell division genes at one end and pbp2b, ddl and murF at the other end. The murD, murG and divIB genes, always found located upstream of ftsA, were found in a second region separated from the first. A third region contained the yllC, yllD, pbp2x and mraY genes. The chromosomal region downstream of ftsZ was also sequenced and characterized. In Streptococcus pneumoniae this region contains four ORFs, all of unknown function, and an ORF encoding the Bacillus subtilis DivIVA homologue. The gene order and the organization of this region was found to be conserved in Staphylococcus aureus, Streptococcus pyogenes and Bacillus subtilis, raising the possibility that previously unidentified loci may also be involved in division.
Data Center Congestion Management requirements (2019)

On IP-routed datacenter networks, RDMA is deployed using RoCEv2
protocol or iWARP. RoCEv2 specification does not define a strong
congestion management mechanisms and load balancing methods. RoCEv2
relies on the existing Link-Layer Flow-Control IEEE 802.1Qbb(Priority-
based Flow Control, PFC) to provide a lossless fabric. RoCEv2
Congestion Management(RCM) use ECN(Explicit Congestion Notification,
defined in RFC3168) to signal the congestion to the destination and
use the congestion notification to reduce the rate of injection and
increase the injection rate when the extent of congestion decreases.
iWRAP depends on TCP congestion handling. This document describes the
current state of flow control and congestion handling in the DC and
provides requirements for new directions for better congestion
control.
Galectin-3C Inhibits Tumor Growth and Increases the Anticancer Activity of Bortezomib in a Murine Model of Human Multiple Myeloma (2011)

Galectin-3 is a human lectin involved in many cellular processes including differentiation, apoptosis, angiogenesis, neoplastic transformation, and metastasis. We evaluated galectin-3C, an N-terminally truncated form of galectin-3 that is thought to act as a dominant negative inhibitor, as a potential treatment for multiple myeloma (MM). Galectin-3 was expressed at varying levels by all 9 human MM cell lines tested. In vitro galectin-3C exhibited modest anti-proliferative effects on MM cells and inhibited chemotaxis and invasion of U266 MM cells induced by stromal cell-derived factor (SDF)-1α. Galectin-3C facilitated the anticancer activity of bortezomib, a proteasome inhibitor approved by the FDA for MM treatment. Galectin-3C and bortezomib also synergistically inhibited MM-induced angiogenesis activity in vitro. Delivery of galectin-3C intravenously via an osmotic pump in a subcutaneous U266 cell NOD/SCID mouse model of MM significantly inhibited tumor growth. The average tumor volume of bortezomib-treated animals was 19.6% and of galectin-3C treated animals was 13.5% of the average volume of the untreated controls at day 35. The maximal effect was obtained with the combination of galectin-3C with bortezomib that afforded a reduction of 94% in the mean tumor volume compared to the untreated controls at day 35. In conclusion, this is the first study to show that inhibition of galectin-3 is efficacious in a murine model of human MM. Our results demonstrated that galectin-3C alone was efficacious in a xenograft mouse model of human MM, and that it enhanced the anti-tumor activity of bortezomib in vitro and in vivo. These data provide the rationale for continued testing of galectin-3C towards initiation of clinical trials for treatment of MM.
Cloning and genetic characterization of Helicobacter pylori catalase and construction of a catalase-deficient mutant strain (1996)

The N-terminal sequence of a protein, originally described as an adhesin of Helicobacter pylori, was used in an oligonucleotide-based screening procedure of an H. pylori plasmid library in Escherichia coli. Five independent plasmid clones were isolated, all mapping to the same chromosomal region and encoding the H. pylori catalase. The gene, designated katA, comprises 1,518 nucleotides and encodes a putative protein of 505 amino acids with a predicted Mr of 58,599. A second open reading frame, orf2, encoding a putative 32,715-Da protein of unknown function, follows katA. The transcriptional start site of katA mRNA was determined, but no typical consensus promoter sequence was present. A potential binding site for the Fur protein is located upstream of katA. When introduced into the catalase-deficient E. coli double-mutant UM255, the cloned gene readily complemented E. coli for catalase activity. H. pylori KatA is highly homologous to catalases in both prokaryotes and eukaryotes, with the highest homology being shown to Bordetella pertussis (64.9%), Bacteroides fragilis (59.8%), and Haemophilus influenzae (57.9%) catalases. Transposon insertion mutants were generated in three independent H. pylori strains by TnMax5-mediated transposon shuttle mutagenesis. In contrast to the wild-type strains, no significant catalase-specific enzymatic activity could be detected in the mutant strains, consistent with the fact that no additional katA-homologous gene copies were found in the H. pylori chromosome. No significant difference between wild-type and mutant strains for binding to epithelial cells was apparent, suggesting that KatA is not involved in H. pylori adhesion. The cloning and genetic characterization of katA are essential steps for further investigation of the role of catalase in the defense of H. pylori against oxygen-dependent killing mechanisms by polymorphonuclear granulocytes, a process not well understood for this chronically persisting pathogen.
The cryptic ospC gene of Borrelia burgdorferi B31 is located on a circular plasmid (1993)

Borrelia burgdorferi B31 cells lacking all linear plasmids or all but the 49-kb linear plasmid expressed the otherwise silent gene for the outer membrane protein OspC. In the first demonstration of a function for a circular plasmid of Borrelia spp., ospC was located on a 27-kb circular plasmid of B31.
Immunobiology of liver xenotransplantation (2012)

Pigs are currently the preferred species for future organ xenotransplantation. With advances in the development of genetically modified pigs, clinical xenotransplantation is becoming closer to reality. In preclinical studies (pig-to-nonhuman primate), the xenotransplantation of livers from pigs transgenic for human CD55 or from α1,3-galactosyltransferase gene-knockout pigs+/- transgenic for human CD46, is associated with survival of approximately 7-9 days. Although hepatic function, including coagulation, has proved to be satisfactory, the immediate development of thrombocytopenia is very limiting for pig liver xenotransplantation even as a 'bridge' to allotransplantation. Current studies are directed to understand the immunobiology of platelet activation, aggregation and phagocytosis, in particular the interaction between platelets and liver sinusoidal endothelial cells, hepatocytes and Kupffer cells, toward identifying interventions that may enable clinical application.
The Epidemiology of Transfusion-related Acute Lung Injury Varies According to the Applied Definition of Lung Injury Onset Time (2015)

The epidemiology of TRALI varies when applying two plausible definitions of acute respiratory distress syndrome onset time to severely injured trauma patients. A TRALI definition that standardizes acute respiratory distress syndrome onset time might improve reliability and align efforts to understand epidemiology, biology, and prevention.
A Variational Approach for Bayesian Blind Image Deconvolution (2004)

In this paper, the blind image deconvolution (BID) problem is addressed using the Bayesian framework. In order to solve for the proposed Bayesian model, we present a new methodology based on a variational approximation, which has been recently introduced for several machine learning problems, and can be viewed as a generalization of the expectation maximization (EM) algorithm. This methodology reaps all the benefits of a "full Bayesian model" while bypassing some of its difficulties. We present three algorithms that solve the proposed Bayesian problem in closed form and can be implemented in the discrete Fourier domain. This makes them very cost effective even for very large images. We demonstrate with numerical experiments that these algorithms yield promising improvements as compared to previous BID algorithms. Furthermore, the proposed methodology is quite general with potential application to other Bayesian models for this and other imaging problems.